From f524a56e1b78e9db83a42510edb78fa19853693c Mon Sep 17 00:00:00 2001 From: David Doty Date: Mon, 23 Nov 2020 12:27:12 -0800 Subject: [PATCH 01/18] closes #147: allow row-major and column/major order of export of strands --- scadnano/scadnano.py | 304 +++++++++++++++----- tests/scadnano_tests.py | 610 ++++++++++++++++++++++++---------------- 2 files changed, 607 insertions(+), 307 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 703b0125..e568bb6c 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -47,7 +47,7 @@ __version__ = "0.13.0" # version line; WARNING: do not remove or change this line or comment import dataclasses -from abc import abstractmethod, ABC +from abc import abstractmethod, ABC, ABCMeta import json import enum import itertools @@ -55,7 +55,7 @@ from builtins import ValueError from dataclasses import dataclass, field, InitVar, replace from typing import Tuple, List, Sequence, Iterable, Set, Dict, Union, Optional, FrozenSet, Type, cast, Any, \ - TypeVar, Generic + TypeVar, Generic, Callable from collections import defaultdict, OrderedDict, Counter import sys import os.path @@ -790,7 +790,6 @@ def m13(rotation: int = 5587, variant: M13Variant = M13Variant.p7249) -> str: idt_plate_key = 'plate' idt_well_key = 'well' - # end keys ################## @@ -2196,7 +2195,7 @@ def update_to(self, offset: int) -> 'StrandBuilder[StrandLabel, DomainLabel]': # remove quotes when Py3.6 support dropped def as_scaffold(self) -> 'StrandBuilder[StrandLabel, DomainLabel]': """ - Makes Strand being built a scaffold. + Makes :any:`Strand` being built a scaffold. :return: self """ @@ -2205,6 +2204,31 @@ def as_scaffold(self) -> 'StrandBuilder[StrandLabel, DomainLabel]': self._strand.set_scaffold(True) return self + def with_idt(self, name: str, scale: str = default_idt_scale, + purification: str = default_idt_purification, + plate: Optional[str] = None, well: Optional[str] = None): + """ + Gives :any:`IDTFields` value to :any:`Strand` being built. + Only a name is required; other field have reasonable default values. + + :param name: + name of strand; required field + :param scale: + see :py:data:`IDTFields.scale` + :param purification: + see :py:data:`IDTFields.purification` + :param plate: + see :py:data:`IDTFields.plate` + :param well: + see :py:data:`IDTFields.well` + :return: self + """ + if self._strand is None: + raise ValueError('no Strand created yet; make at least one domain first') + self._strand.idt = IDTFields(name=name, scale=scale, purification=purification, + plate=plate, well=well) + return self + # remove quotes when Py3.6 support dropped def with_modification_5p(self, mod: Modification5Prime) -> 'StrandBuilder[StrandLabel, DomainLabel]': """ @@ -3078,6 +3102,94 @@ def no_modifications_version(self) -> 'Strand': return strand_nomods +# for defining comparables for strongly typed sorting +class Comparable(metaclass=ABCMeta): + @abstractmethod + def __lt__(self, other: Any) -> bool: ... + + +T = TypeVar('T') +# CT = TypeVar('CT', bound=Comparable) + +# KeyFunction = Callable[[T], CT] +KeyFunction = Callable[[T], Any] + + +class StrandOrder(enum.Enum): + """ + Which part of a :any:`Strand` to use for sorting in the + `key function `_ + returned by :py:meth:`strand_order_key_function`. + """ + five_prime = 0 + """5' end of the strand""" + + three_prime = 1 + """3' end of the strand""" + + five_or_three_prime = 2 + """Either 5' end or 3' end is used, whichever is first according to the sort order.""" + + top_left_domain = 3 + """The start offset of the "top-left" :any:`Domain` of the :any:`Strand`: the :any:`Domain` whose + :py:data:`Domain.helix` is minimal, and, among all such :any:`Domain`'s, the one with + minimal :py:data:`Domain.start`.""" + + +def strand_order_key_function(*, column_major: bool = True, strand_order: StrandOrder) -> KeyFunction[Strand]: + """ + Returns a `key function `_ + indicating a sorted order for :any:`Strand`'s. Useful as a parameter for + :py:meth:`Design.`. + + :param column_major: + If true, column major order is used: ordered by base offset first, then by helix. + Otherwise row-major order is used: ordered by helix first, then by base offset. + :param strand_order: + Which part of the strand to use as a key for the sorted order. + See :any:`StrandOrder` for definitions. + :return: + A `key function `_ that can be + passed to :py:meth:`Design.` to specify a sorted order for the :any:`Strand`'s. + """ + + def key(strand: Strand) -> Tuple[int, int]: + # we'll return a tuple (helix_idx, offset) for row-major or (offset, helix_idx) for col-major. + helix_idx: int + offset: int + + if strand_order == StrandOrder.five_prime: + helix_idx = strand.first_bound_domain().helix + offset = strand.first_bound_domain().offset_5p() + elif strand_order == StrandOrder.three_prime: + helix_idx = strand.last_bound_domain().helix + offset = strand.last_bound_domain().offset_3p() + elif strand_order == StrandOrder.five_or_three_prime: + helix_idx_5p = strand.first_bound_domain().helix + offset_5p = strand.first_bound_domain().offset_5p() + helix_idx_3p = strand.last_bound_domain().helix + offset_3p = strand.last_bound_domain().offset_3p() + if column_major: + offset, helix_idx = min((offset_5p, helix_idx_5p), (offset_3p, helix_idx_3p)) + else: + helix_idx, offset = min((helix_idx_5p, offset_5p), (helix_idx_3p, offset_3p)) + elif strand_order == StrandOrder.top_left_domain: + helix_idx = strand.first_bound_domain().helix + offset = strand.first_bound_domain().start + for domain in strand.bound_domains(): + if (helix_idx, offset) > (domain.helix, domain.start): + helix_idx, offset = domain.helix, domain.start + else: + raise ValueError(f'{strand_order} is not a valid StrandOrder') + + if column_major: + return offset, helix_idx + else: + return helix_idx, offset + + return key + + def _pad_and_remove_whitespace_and_uppercase(sequence: str, strand: Strand, start: int = 0) -> str: sequence = _remove_whitespace_and_uppercase(sequence) padded_sequence = _pad_dna(sequence, strand.dna_length(), start) @@ -4223,7 +4335,7 @@ def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) - helix_dct['stap_colors'] = [] helix_dct['scafLoop'] = [] - helix_dct['stapLoop'] = [] + helix_dct['stap_loop'] = [] helices_ids_reverse[helix_dct['num']] = i dct['vstrands'].append(helix_dct) @@ -4789,43 +4901,58 @@ def assign_dna(self, strand: Strand, sequence: str, assign_complement: bool = Tr # because we get complementarity checks this way other_strand.assign_dna_complement_from(strand) - def to_idt_bulk_input_format(self, delimiter: str = ',', warn_duplicate_name: bool = False, + def to_idt_bulk_input_format(self, + delimiter: str = ',', + key: Optional[KeyFunction[Strand]] = None, + warn_duplicate_name: bool = False, warn_on_non_idt_strands: bool = False, export_non_modified_strand_version: bool = False) -> str: - """Return string that is written to the file in the method - :py:meth:`Design.write_idt_bulk_input_file`. - - `delimiter` is the symbol to delimit the four IDT fields name,sequence,scale,purification. - - `warn_duplicate_name` if ``True`` prints a warning when two different :any:`Strand`'s have the same - :py:attr:`IDTField.name` and the same :any:`Strand.dna_sequence`. An :any:`IllegalDesignError` is - raised (regardless of the value of this parameter) - if two different :any:`Strand`'s have the same name but different sequences, IDT scales, or IDT - purifications. - - `warn_on_non_idt_strands` specifies whether to print a warning for strands that lack the field - :any:`Strand.idt`. Such strands will not be part of the output. No warning is ever issued for the - scaffold (regardless of the value of the parameter `warn_on_non_idt_strands`). - - `export_non_modified_strand_version` specifies whether, for each strand that has modifications, - to also output a version of the strand with no modifications, but otherwise having the same data. + """Called by :py:meth:`Design.write_idt_bulk_input_file` to determine what string to write to + the file. This function can be used to get the string directly without creating a file. + + :param delimiter: + the symbol to delimit the four IDT fields name,sequence,scale,purification. + :param key: + `key function `_ used to determine + order in which to output strand sequences. Some useful defaults are provided by + :py:meth:`strand_order_key_function` + :param warn_duplicate_name: + if ``True`` prints a warning when two different :any:`Strand`'s have the same + :py:attr:`IDTField.name` and the same :any:`Strand.dna_sequence`. An :any:`IllegalDesignError` is + raised (regardless of the value of this parameter) + if two different :any:`Strand`'s have the same name but different sequences, IDT scales, or IDT + purifications. + :param warn_on_non_idt_strands: + specifies whether to print a warning for strands that lack the field + :any:`Strand.idt`. Such strands will not be part of the output. No warning is ever issued for the + scaffold (regardless of the value of the parameter `warn_on_non_idt_strands`). + :param export_non_modified_strand_version: + specifies whether, for each strand that has modifications, + to also output a version of the strand with no modifications, but otherwise having the same data. + :return: + string that is written to the file in the method :py:meth:`Design.write_idt_bulk_input_file`. """ - added_strands = self._idt_strands(warn_duplicate_name, warn_on_non_idt_strands, - export_non_modified_strand_version) + added_strands = self._idt_strands(key=key, warn_duplicate_name=warn_duplicate_name, + warn_on_non_idt_strands=warn_on_non_idt_strands, + export_non_modified_strand_version=export_non_modified_strand_version) idt_lines: List[str] = [] - for strand in added_strands.values(): + for strand in added_strands: if strand.idt is None: raise ValueError(f'cannot export strand {strand} to IDT because it has no IDT field') idt_lines.append(delimiter.join( - [strand.idt.name, strand.idt_dna_sequence(), strand.idt.scale, strand.idt.purification] + [strand.idt.name if strand.idt.name is not None else strand.name, strand.idt_dna_sequence(), + strand.idt.scale, strand.idt.purification] )) idt_string = '\n'.join(idt_lines) return idt_string - def _idt_strands(self, warn_duplicate_name: bool, warn_on_non_idt_strands: bool, - export_non_modified_strand_version: bool = False) -> Dict[str, Strand]: + def _idt_strands(self, *, + key: Optional[KeyFunction[Strand]] = None, + warn_duplicate_name: bool, + warn_on_non_idt_strands: bool, + export_non_modified_strand_version: bool = False) -> List[Strand]: added_strands: Dict[str, Strand] = {} # dict: name -> strand for strand in self.strands: if strand.idt is not None: @@ -4875,9 +5002,15 @@ def _idt_strands(self, warn_duplicate_name: bool, warn_on_non_idt_strands: bool, print(f"WARNING: strand with 5' end at (helix, offset) " f"({strand.first_domain().helix}, {strand.first_domain().offset_5p()}) " f"does not have a field idt, so will not be part of IDT output.") - return added_strands - def write_idt_bulk_input_file(self, directory: str = '.', filename: str = None, extension: str = None, + strands = list(added_strands.values()) + if key is not None: + strands.sort(key=key) + return strands + + def write_idt_bulk_input_file(self, *, directory: str = '.', filename: str = None, + key: Optional[KeyFunction[Strand]] = None, + extension: Optional[str] = None, delimiter: str = ',', warn_duplicate_name: bool = True, warn_on_non_idt_strands: bool = True, export_non_modified_strand_version: bool = False) -> None: @@ -4891,29 +5024,46 @@ def write_idt_bulk_input_file(self, directory: str = '.', filename: str = None, If `filename` is not specified but `extension` is, then that extension is used instead of ``idt``. At least one of `filename` or `extension` must be ``None``. - `directory` specifies a directory in which to place the file, either absolute or relative to - the current working directory. Default is the current working directory. - - `delimiter` is the symbol to delimit the four IDT fields name,sequence,scale,purification. - - `warn_duplicate_name` if ``True`` prints a warning when two different :any:`Strand`'s have the same - :py:attr:`IDTField.name` and the same :any:`Strand.dna_sequence`. An :any:`IllegalDesignError` is - raised (regardless of the value of this parameter) - if two different :any:`Strand`'s have the same name but different sequences, IDT scales, or IDT - purifications. - - `warn_on_non_idt_strands` specifies whether to print a warning for strands that lack the field - :any:`Strand.idt`. Such strands will not be output into the file. - The string written is that returned by :meth:`Design.to_idt_bulk_input_format`. + + :param directory: + specifies a directory in which to place the file, either absolute or relative to + the current working directory. Default is the current working directory. + :param filename: + optinoal custom filename to use (instead of currently running script) + :param key: + `key function `_ used to determine + order in which to output strand sequences. Some useful defaults are provided by + :py:meth:`strand_order_key_function` + :param extension: + alternate filename extension to use (instead of idt) + :param delimiter: + is the symbol to delimit the four IDT fields name,sequence,scale,purification. + :param warn_duplicate_name: + if ``True`` prints a warning when two different :any:`Strand`'s have the same + :py:attr:`IDTField.name` and the same :any:`Strand.dna_sequence`. An :any:`IllegalDesignError` is + raised (regardless of the value of this parameter) + if two different :any:`Strand`'s have the same name but different sequences, IDT scales, or IDT + purifications. + :param warn_on_non_idt_strands: + specifies whether to print a warning for strands that lack the field + :any:`Strand.idt`. Such strands will not be output into the file. + :param export_non_modified_strand_version: + For any :any:`Strand` with a :any:`Modification`, also export a version of the :any:`Strand` + without any modifications. The name for this :any:`Strand` is the original name with + '_nomods' appended to it. """ - contents = self.to_idt_bulk_input_format(delimiter, warn_duplicate_name, warn_on_non_idt_strands, - export_non_modified_strand_version) + contents = self.to_idt_bulk_input_format(delimiter=delimiter, + key=key, + warn_duplicate_name=warn_duplicate_name, + warn_on_non_idt_strands=warn_on_non_idt_strands, + export_non_modified_strand_version=export_non_modified_strand_version) if extension is None: extension = 'idt' _write_file_same_name_as_running_python_script(contents, extension, directory, filename) - def write_idt_plate_excel_file(self, directory: str = '.', filename: str = None, + def write_idt_plate_excel_file(self, *, directory: str = '.', filename: str = None, + key: Optional[KeyFunction[Strand]] = None, warn_duplicate_name: bool = False, warn_on_non_idt_strands: bool = False, use_default_plates: bool = False, warn_using_default_plates: bool = True, plate_type: PlateType = PlateType.wells96, @@ -4928,30 +5078,44 @@ def write_idt_plate_excel_file(self, directory: str = '.', filename: str = None, For instance, if the script is named ``my_origami.py``, then the sequences will be written to ``my_origami.xls``. - `directory` specifies a directory in which to place the file, either absolute or relative to - the current working directory. Default is the current working directory. - - `warn_duplicate_name` if ``True`` prints a warning when two different :any:`Strand`'s have the same - :py:attr:`IDTField.name` and the same :any:`Strand.dna_sequence`. An :any:`IllegalDesignError` is - raised (regardless of the value of this parameter) - if two different :any:`Strand`'s have the same name but different sequences, IDT scales, or IDT - purifications. - - `warn_on_non_idt_strands` specifies whether to print a warning for strands that lack the field - :py:data:`Strand.idt`. Such strands will not be output into the file. No warning is ever issued - for the scaffold (regardless of the value of the parameter `warn_on_non_idt_strands`). - - `warn_using_default_plates` specifies whether to print a warning for strands whose - :py:data:`Strand.idt` have the fields - - `plate_type` is a :any:`PlateType` specifying whether to use a 96-well plate or a 384-well plate - if the `use_default_plates` parameter is ``True``. - Ignored if `use_default_plates` is ``False``, because in that case the wells are explicitly set - by the user, who is free to use coordinates for either plate type. + :param directory: + specifies a directory in which to place the file, either absolute or relative to + the current working directory. Default is the current working directory. + :param filename: + custom filename if default (explained above) is not desired + :param key: + `key function `_ used to determine + order in which to output strand sequences. Some useful defaults are provided by + :py:meth:`strand_order_key_function` + :param warn_duplicate_name: + if ``True`` prints a warning when two different :any:`Strand`'s have the same + :py:attr:`IDTField.name` and the same :any:`Strand.dna_sequence`. An :any:`IllegalDesignError` is + raised (regardless of the value of this parameter) + if two different :any:`Strand`'s have the same name but different sequences, IDT scales, or IDT + purifications. + :param warn_on_non_idt_strands: + specifies whether to print a warning for strands that lack the field + :py:data:`Strand.idt`. Such strands will not be output into the file. No warning is ever issued + for the scaffold (regardless of the value of the parameter `warn_on_non_idt_strands`). + :param use_default_plates: + Use default values for plate and well (ignoring those in idt fields, which may be None). + :param warn_using_default_plates: + specifies whether to print a warning for strands whose + :py:data:`Strand.idt` have the fields + :param plate_type: + a :any:`PlateType` specifying whether to use a 96-well plate or a 384-well plate + if the `use_default_plates` parameter is ``True``. + Ignored if `use_default_plates` is ``False``, because in that case the wells are explicitly set + by the user, who is free to use coordinates for either plate type. + :param export_non_modified_strand_version: + For any :any:`Strand` with a :any:`Modification`, also export a version of the :any:`Strand` + without any modifications. The name for this :any:`Strand` is the original name with + '_nomods' appended to it. """ - idt_strands = list(self._idt_strands(warn_duplicate_name, warn_on_non_idt_strands, - export_non_modified_strand_version).values()) + idt_strands = self._idt_strands(key=key, warn_duplicate_name=warn_duplicate_name, + warn_on_non_idt_strands=warn_on_non_idt_strands, + export_non_modified_strand_version=export_non_modified_strand_version) if not use_default_plates: self._write_plates_assuming_explicit_in_each_strand(directory, filename, idt_strands) diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index fac5e1d2..5d55e51d 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -1,20 +1,18 @@ import os # import sys # sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) -import math import unittest import re import json -from typing import Iterable - -from docutils.nodes import label +from typing import Iterable, Union, Dict, Any import scadnano as sc import scadnano.origami_rectangle as rect import scadnano.modifications as mod -def strand_matching(strands: Iterable[sc.Strand], helix: int, forward: bool, start: int, end: int): +def strand_matching(strands: Iterable[sc.Strand], helix: int, forward: bool, start: int, + end: int) -> sc.Strand: """ Finds strand whose first bound domain matches the given parameters. """ @@ -25,7 +23,7 @@ def strand_matching(strands: Iterable[sc.Strand], helix: int, forward: bool, sta s.first_bound_domain().end == end) -def remove_whitespace(sequence): +def remove_whitespace(sequence: str) -> str: sequence = re.sub(r'\s*', '', sequence) return sequence @@ -36,7 +34,7 @@ class TestCreateStrandChainedMethods(unittest.TestCase): def setUp(self) -> None: helices = [sc.Helix(max_offset=100) for _ in range(6)] - self.design_6helix = sc.Design(helices=helices, strands=[], grid=sc.square) + self.design_6helix: sc.Design = sc.Design(helices=helices, strands=[], grid=sc.square) def test_strand__loopouts_with_labels(self) -> None: design = self.design_6helix @@ -349,7 +347,7 @@ class TestCreateHelix(unittest.TestCase): def test_helix_constructor_no_max_offset_with_major_ticks(self) -> None: # tests bug where an exception is raised if major ticks is defined but not max_offset - helix = sc.Helix(major_ticks=[0, 5, 10]) + sc.Helix(major_ticks=[0, 5, 10]) class TestM13(unittest.TestCase): @@ -387,28 +385,28 @@ def test_mod_illegal_exceptions_raised(self) -> None: # strand = sc.Strand(domains=[sc.Substrand(0, True, 0, 5)], dna_sequence='AATGC', # modifications=[biotin3_1, biotin3_2]) # - # biotinI_1 = mod.Biotin(location=sc.ModLocation.internal, offset=2) - # biotinI_2 = mod.Biotin(location=sc.ModLocation.internal, offset=2) + # biotin_i_1 = mod.Biotin(location=sc.ModLocation.internal, offset=2) + # biotin_i_2 = mod.Biotin(location=sc.ModLocation.internal, offset=2) # with self.assertRaises(sc.IllegalDesignError): # strand = sc.Strand(domains=[sc.Substrand(0, True, 0, 5)], dna_sequence='AATGC', - # modifications=[biotinI_1, biotinI_2]) + # modifications=[biotin_i_1, biotin_i_2]) # - # biotinI_small = mod.Biotin(location=sc.ModLocation.internal, offset=-1) + # biotin_i_small = mod.Biotin(location=sc.ModLocation.internal, offset=-1) # with self.assertRaises(sc.IllegalDesignError): # strand = sc.Strand(domains=[sc.Substrand(0, True, 0, 5)], dna_sequence='AATGC', - # modifications=[biotinI_small]) + # modifications=[biotin_i_small]) # seq = strand.idt_dna_sequence() # - # biotinI_large = mod.Biotin(location=sc.ModLocation.internal, offset=10) + # biotin_i_large = mod.Biotin(location=sc.ModLocation.internal, offset=10) # with self.assertRaises(sc.IllegalDesignError): # strand = sc.Strand(domains=[sc.Substrand(0, True, 0, 5)], dna_sequence='AATGC', - # modifications=[biotinI_small]) + # modifications=[biotin_i_small]) # seq = strand.idt_dna_sequence() # - # biotinI_offset_not_T = mod.Biotin(location=sc.ModLocation.internal, offset=0) + # biotin_i_offset_not_T = mod.Biotin(location=sc.ModLocation.internal, offset=0) # with self.assertRaises(sc.IllegalDesignError): # strand = sc.Strand(domains=[sc.Substrand(0, True, 0, 5)], dna_sequence='AATGC', - # modifications=[biotinI_offset_not_T]) + # modifications=[biotin_i_offset_not_T]) # seq = strand.idt_dna_sequence() # # cy3I_offset_off_end = mod.Cy3(location=sc.ModLocation.internal, offset=4) @@ -441,19 +439,19 @@ def test_Cy3(self) -> None: modification_5p=cy3_5) strand3 = sc.Strand(domains=[sc.Domain(1, True, 0, 5)], dna_sequence='ATTGC', modification_3p=cy3_3) - strandI = sc.Strand(domains=[sc.Domain(2, True, 0, 5)], dna_sequence='ATTGC', - modifications_int={1: cy3_i1, 3: cy3_i2}) + strand_i = sc.Strand(domains=[sc.Domain(2, True, 0, 5)], dna_sequence='ATTGC', + modifications_int={1: cy3_i1, 3: cy3_i2}) strand53 = sc.Strand(domains=[sc.Domain(3, True, 0, 5)], dna_sequence='ATTGC', modification_5p=cy3_5, modification_3p=cy3_3) - strand53I = sc.Strand(domains=[sc.Domain(4, True, 0, 5)], dna_sequence='ATTGC', - modification_5p=cy3_5, modification_3p=cy3_3, - modifications_int={1: cy3_i1, 3: cy3_i2}) + strand53_i = sc.Strand(domains=[sc.Domain(4, True, 0, 5)], dna_sequence='ATTGC', + modification_5p=cy3_5, modification_3p=cy3_3, + modifications_int={1: cy3_i1, 3: cy3_i2}) self.assertEqual(r'/5Cy3/ATTGC', strand5.idt_dna_sequence()) self.assertEqual(r'ATTGC/3Cy3Sp/', strand3.idt_dna_sequence()) self.assertEqual(r'/5Cy3/ATTGC/3Cy3Sp/', strand53.idt_dna_sequence()) - self.assertEqual(r'AT/iCy3/TG/iCy3/C', strandI.idt_dna_sequence()) - self.assertEqual(r'/5Cy3/AT/iCy3/TG/iCy3/C/3Cy3Sp/', strand53I.idt_dna_sequence()) + self.assertEqual(r'AT/iCy3/TG/iCy3/C', strand_i.idt_dna_sequence()) + self.assertEqual(r'/5Cy3/AT/iCy3/TG/iCy3/C/3Cy3Sp/', strand53_i.idt_dna_sequence()) def test_biotin(self) -> None: biotin5 = mod.biotin_5p @@ -464,33 +462,33 @@ def test_biotin(self) -> None: self.assertEqual(r'/3Bio/', biotin3.idt_text) self.assertEqual(r'/3Bio/', biotin3.id) self.assertEqual('B', biotin3.display_text) - # biotinI_1 = mod.Biotin(location=sc.ModLocation.internal, offset=1) - biotinI_1 = mod.biotin_int - self.assertEqual(r'/iBiodT/', biotinI_1.idt_text) - self.assertEqual(r'/iBiodT/', biotinI_1.id) - self.assertEqual('B', biotinI_1.display_text) - # biotinI_2 = mod.Biotin(location=sc.ModLocation.internal, offset=2) - biotinI_2 = mod.biotin_int - self.assertEqual(r'/iBiodT/', biotinI_2.idt_text) - self.assertEqual(r'/iBiodT/', biotinI_2.id) - self.assertEqual('B', biotinI_2.display_text) + # biotin_i_1 = mod.Biotin(location=sc.ModLocation.internal, offset=1) + biotin_i_1 = mod.biotin_int + self.assertEqual(r'/iBiodT/', biotin_i_1.idt_text) + self.assertEqual(r'/iBiodT/', biotin_i_1.id) + self.assertEqual('B', biotin_i_1.display_text) + # biotin_i_2 = mod.Biotin(location=sc.ModLocation.internal, offset=2) + biotin_i_2 = mod.biotin_int + self.assertEqual(r'/iBiodT/', biotin_i_2.idt_text) + self.assertEqual(r'/iBiodT/', biotin_i_2.id) + self.assertEqual('B', biotin_i_2.display_text) strand5 = sc.Strand(domains=[sc.Domain(0, True, 0, 5)], dna_sequence='ATTGC', modification_5p=biotin5) strand3 = sc.Strand(domains=[sc.Domain(1, True, 0, 5)], dna_sequence='ATTGC', modification_3p=biotin3) - strandI = sc.Strand(domains=[sc.Domain(2, True, 0, 5)], dna_sequence='ATTGC', - modifications_int={1: biotinI_1, 2: biotinI_2}) + strand_i = sc.Strand(domains=[sc.Domain(2, True, 0, 5)], dna_sequence='ATTGC', + modifications_int={1: biotin_i_1, 2: biotin_i_2}) strand53 = sc.Strand(domains=[sc.Domain(3, True, 0, 5)], dna_sequence='ATTGC', modification_5p=biotin5, modification_3p=biotin3) - strand53I = sc.Strand(domains=[sc.Domain(4, True, 0, 5)], dna_sequence='ATTGC', + strand53i = sc.Strand(domains=[sc.Domain(4, True, 0, 5)], dna_sequence='ATTGC', modification_5p=biotin5, modification_3p=biotin3, - modifications_int={1: biotinI_1, 2: biotinI_2}) + modifications_int={1: biotin_i_1, 2: biotin_i_2}) self.assertEqual(r'/5Biosg/ATTGC', strand5.idt_dna_sequence()) self.assertEqual(r'ATTGC/3Bio/', strand3.idt_dna_sequence()) - self.assertEqual(r'A/iBiodT//iBiodT/GC', strandI.idt_dna_sequence()) + self.assertEqual(r'A/iBiodT//iBiodT/GC', strand_i.idt_dna_sequence()) self.assertEqual(r'/5Biosg/ATTGC/3Bio/', strand53.idt_dna_sequence()) - self.assertEqual(r'/5Biosg/A/iBiodT//iBiodT/GC/3Bio/', strand53I.idt_dna_sequence()) + self.assertEqual(r'/5Biosg/A/iBiodT//iBiodT/GC/3Bio/', strand53i.idt_dna_sequence()) def test_to_json_serializable(self) -> None: biotin5 = mod.biotin_5p @@ -501,30 +499,30 @@ def test_to_json_serializable(self) -> None: self.assertEqual(r'/3Bio/', biotin3.idt_text) self.assertEqual(r'/3Bio/', biotin3.id) self.assertEqual('B', biotin3.display_text) - # biotinI_1 = mod.Biotin(location=sc.ModLocation.internal, offset=1) - biotinI_1 = mod.biotin_int - self.assertEqual(r'/iBiodT/', biotinI_1.idt_text) - self.assertEqual(r'/iBiodT/', biotinI_1.id) - self.assertEqual('B', biotinI_1.display_text) - # biotinI_2 = mod.Biotin(location=sc.ModLocation.internal, offset=2) - biotinI_2 = mod.biotin_int - self.assertEqual(r'/iBiodT/', biotinI_2.idt_text) - self.assertEqual(r'/iBiodT/', biotinI_2.id) - self.assertEqual('B', biotinI_2.display_text) + # biotin_i_1 = mod.Biotin(location=sc.ModLocation.internal, offset=1) + biotin_i_1 = mod.biotin_int + self.assertEqual(r'/iBiodT/', biotin_i_1.idt_text) + self.assertEqual(r'/iBiodT/', biotin_i_1.id) + self.assertEqual('B', biotin_i_1.display_text) + # biotin_i_2 = mod.Biotin(location=sc.ModLocation.internal, offset=2) + biotin_i_2 = mod.biotin_int + self.assertEqual(r'/iBiodT/', biotin_i_2.idt_text) + self.assertEqual(r'/iBiodT/', biotin_i_2.id) + self.assertEqual('B', biotin_i_2.display_text) strand5 = sc.Strand(domains=[sc.Domain(0, True, 0, 5)], dna_sequence='ATTGC', modification_5p=biotin5) strand3 = sc.Strand(domains=[sc.Domain(1, True, 0, 5)], dna_sequence='ATTGC', modification_3p=biotin3) - strandI = sc.Strand(domains=[sc.Domain(2, True, 0, 5)], dna_sequence='ATTGC', - modifications_int={1: biotinI_1, 2: biotinI_2}) + strand_i = sc.Strand(domains=[sc.Domain(2, True, 0, 5)], dna_sequence='ATTGC', + modifications_int={1: biotin_i_1, 2: biotin_i_2}) strand53 = sc.Strand(domains=[sc.Domain(3, True, 0, 5)], dna_sequence='ATTGC', modification_5p=biotin5, modification_3p=biotin3) - strand53I = sc.Strand(domains=[sc.Domain(4, True, 0, 5)], dna_sequence='ATTGC', - modification_5p=biotin5, modification_3p=biotin3, - modifications_int={1: biotinI_1, 2: biotinI_2}) + strand53_i = sc.Strand(domains=[sc.Domain(4, True, 0, 5)], dna_sequence='ATTGC', + modification_5p=biotin5, modification_3p=biotin3, + modifications_int={1: biotin_i_1, 2: biotin_i_2}) - strands = [strand5, strand3, strandI, strand53, strand53I] + strands = [strand5, strand3, strand_i, strand53, strand53_i] design = sc.Design(strands=strands, grid=sc.square) # print(design.to_json()) @@ -541,20 +539,20 @@ def test_to_json_serializable(self) -> None: self.assertEqual("/5Biosg/", strand5_mod5_json) self.assertEqual("/3Bio/", strand3_mod3_json) - strandI_mods_int_json = json_dict[sc.strands_key][2][sc.modifications_int_key] - self.assertDictEqual({"1": "/iBiodT/", "2": "/iBiodT/"}, strandI_mods_int_json) + strand_i_mods_int_json = json_dict[sc.strands_key][2][sc.modifications_int_key] + self.assertDictEqual({"1": "/iBiodT/", "2": "/iBiodT/"}, strand_i_mods_int_json) strand53_mod5_json = json_dict[sc.strands_key][3][sc.modification_5p_key] strand53_mod3_json = json_dict[sc.strands_key][3][sc.modification_3p_key] self.assertEqual("/5Biosg/", strand53_mod5_json) self.assertEqual("/3Bio/", strand53_mod3_json) - strand53I_mod5_json = json_dict[sc.strands_key][4][sc.modification_5p_key] - strand53I_mod3_json = json_dict[sc.strands_key][4][sc.modification_3p_key] - strand53I_mods_int_json = json_dict[sc.strands_key][4][sc.modifications_int_key] - self.assertEqual("/5Biosg/", strand53I_mod5_json) - self.assertEqual("/3Bio/", strand53I_mod3_json) - self.assertDictEqual({"1": "/iBiodT/", "2": "/iBiodT/"}, strand53I_mods_int_json) + strand53_i_mod5_json = json_dict[sc.strands_key][4][sc.modification_5p_key] + strand53_i_mod3_json = json_dict[sc.strands_key][4][sc.modification_3p_key] + strand53_i_mods_int_json = json_dict[sc.strands_key][4][sc.modifications_int_key] + self.assertEqual("/5Biosg/", strand53_i_mod5_json) + self.assertEqual("/3Bio/", strand53_i_mod3_json) + self.assertDictEqual({"1": "/iBiodT/", "2": "/iBiodT/"}, strand53_i_mods_int_json) class TestImportCadnanoV2(unittest.TestCase): @@ -598,6 +596,222 @@ def test_Nature09_monolith(self) -> None: filename=f'{file_name}.{sc.default_scadnano_file_extension}') +class TestExportDNASequences(unittest.TestCase): + + def setUp(self) -> None: + r""" Removing scaffold from this design: + 0 8 16 24 32 40 48 56 64 72 80 88 96 +0 +------- -------- -------- -------- -------- -------- -------- -------- -------- -------- -------- -------+ + /<------- -------+ +------- -------- -------] <------- -------- -------- -------] <------+ +------- -------]\ + ( | | | | ) +1 \[------- -------+ +------> [------+ +------- -------- -------> [------+ +------- -------+ +------- ------->/ + +------- -------- -------- -------- -------- -------+ +------- -------- -------- -------- -------- -------+ + | | | | | | +2 +------- -------- -------- -------- -------- -------+ +------- -------- -------- -------- -------- -------+ + /<------- -------+ +------- -------+ +------] <------- -------- -------+ +------] <------+ +------- -------]\ + ( | | | | ) +3 \[------- -------+ +------> [------+ +------- -------- -------> [------+ +------- -------+ +------- ------->/ + +------- -------- -------- -------- -------- -------+ +------- -------- -------- -------- -------- -------+ + | | | | | | +4 +------- -------- -------- -------- -------- -------+ +------- -------- -------- -------- -------- -------+ + /<------- -------+ +------- -------+ +------] <------- -------- -------+ +------] <------+ +------- -------]\ + ( | | | | ) +5 \[------- -------+ +------> [------- -------- -------- -------> [------- -------- -------+ +------- ------->/ + +------- -------- -------- -------- -------- -------] <------- -------- -------- -------- -------- -------+ + +gives this (removed scaffold to make it easier for me to visually track the strands) + + 0 8 16 24 32 40 48 56 64 72 80 88 96 +0 <-------A-------+ +-------D--------D-------] <-------G--------G--------G-------] <------+ +-------P-------] + | | | | +1 [-------A-------+ +------> [------+ +-------H--------H-------> [------+ +-------M-------+ +-------P-------> + | | | | +2 <-------B-------+ +-------E-------+ +------] <-------I--------I-------+ +------] <------+ +-------Q-------] + | | | | +3 [-------B-------+ +------> [------+ +-------J--------J-------> [------+ +-------N-------+ +-------Q-------> + | | | | +4 <-------C-------+ +-------F-------+ +------] <-------K--------K-------+ +------] <------+ +-------R-------] + | | | | +5 [-------C-------+ +------> [-------L--------L--------L-------> [-------O--------O-------+ +-------R-------> + +We give the strands simple single-letter names to help test they appear in the correct order in the output. + +row major 5': DGPAEIHMQBFKJNRCLO +col major 5': ABCEFLDHJIKOGMNPQR +row major 3': AGMDHPBINEJQCKOFLR +col major 3': ABCDEFGIKHJLMNOPQR +row major 5' or 3': ADGMPEHIBNQFJKCORL +col major 5' or 3': ABCDEFLHJGIKOMNPQR +row major top-left domain start: ADGMPEHIBNQFJKCORL +col major top-left domain start: ABCDEFLHJGIKMNOPQR + """ + helices = [sc.Helix(max_offset=100) for _ in range(6)] + self.design_6h: sc.Design = sc.Design(helices=helices, strands=[], grid=sc.square) + d = self.design_6h + + d.strand(1, 0).move(16).cross(0).move(-16).with_idt('A') # A + d.strand(3, 0).move(16).cross(2).move(-16).with_idt('B') # B + d.strand(5, 0).move(16).cross(4).move(-16).with_idt('C') # C + + d.strand(0, 40).move(-24).cross(1).move(8).with_idt('D') # D + + d.strand(1, 24).move(8).cross(2).move(-16).cross(3).move(8).with_idt('E') # E + d.strand(3, 24).move(8).cross(4).move(-16).cross(5).move(8).with_idt('F') # F + + d.strand(0, 72).move(-32).with_idt('G') # G + + d.strand(2, 40).move(-8).cross(1).move(24).with_idt('H') # H + d.strand(1, 56).move(8).cross(2).move(-24).with_idt('I') # I + + d.strand(4, 40).move(-8).cross(3).move(24).with_idt('J') # J + d.strand(3, 56).move(8).cross(4).move(-24).with_idt('K') # K + + d.strand(5, 24).move(32).with_idt('L') # L + + d.strand(2, 72).move(-8).cross(1).move(16).cross(0).move(-8).with_idt('M') # M + d.strand(4, 72).move(-8).cross(3).move(16).cross(2).move(-8).with_idt('N') # N + + d.strand(5, 56).move(24).cross(4).move(-8).with_idt('O') # O + + d.strand(0, 96).move(-16).cross(1).move(16).with_idt('P') # P + d.strand(2, 96).move(-16).cross(3).move(16).with_idt('Q') # Q + d.strand(4, 96).move(-16).cross(5).move(16).with_idt('R') # R + + for strand in d.strands: + d.assign_dna(strand, 'A' * 32, assign_complement=False) + + def _get_names_idt(self, design: sc.Design, key: sc.KeyFunction[sc.Strand]) -> str: + # call design.to_idt_bulk_input_format with given key functions, + # get IDT names of strands exported, and return them joined into a single string + idt_str = design.to_idt_bulk_input_format(key=key) + idt_lines = idt_str.split('\n') + names = [] + for line in idt_lines: + name = line.split(',')[0] + names.append(name) + names_joined = ''.join(names) + return names_joined + + def test_to_idt_bulk_input_format__row_major_5p(self) -> None: + key = sc.strand_order_key_function(column_major=False, strand_order=sc.StrandOrder.five_prime) + names_joined = self._get_names_idt(self.design_6h, key) + self.assertEqual('DGPAEIHMQBFKJNRCLO', names_joined) + + def test_to_idt_bulk_input_format__col_major_5p(self) -> None: + key = sc.strand_order_key_function(column_major=True, strand_order=sc.StrandOrder.five_prime) + names_joined = self._get_names_idt(self.design_6h, key) + self.assertEqual('ABCEFLDHJIKOGMNPQR', names_joined) + + def test_to_idt_bulk_input_format__row_major_3p(self) -> None: + key = sc.strand_order_key_function(column_major=False, strand_order=sc.StrandOrder.three_prime) + names_joined = self._get_names_idt(self.design_6h, key) + self.assertEqual('AGMDHPBINEJQCKOFLR', names_joined) + + def test_to_idt_bulk_input_format__col_major_3p(self) -> None: + key = sc.strand_order_key_function(column_major=True, strand_order=sc.StrandOrder.three_prime) + names_joined = self._get_names_idt(self.design_6h, key) + self.assertEqual('ABCDEFGIKHJLMNOPQR', names_joined) + + def test_to_idt_bulk_input_format__row_major_5p_or_3p(self) -> None: + key = sc.strand_order_key_function(column_major=False, + strand_order=sc.StrandOrder.five_or_three_prime) + names_joined = self._get_names_idt(self.design_6h, key) + self.assertEqual('ADGMPEHIBNQFJKCORL', names_joined) + + def test_to_idt_bulk_input_format__col_major_5p_or_3p(self) -> None: + key = sc.strand_order_key_function(column_major=True, strand_order=sc.StrandOrder.five_or_three_prime) + names_joined = self._get_names_idt(self.design_6h, key) + self.assertEqual('ABCDEFLHJGIKOMNPQR', names_joined) + + def test_to_idt_bulk_input_format__row_major_top_left_domain_start(self) -> None: + key = sc.strand_order_key_function(column_major=False, strand_order=sc.StrandOrder.top_left_domain) + names_joined = self._get_names_idt(self.design_6h, key) + self.assertEqual('ADGMPEHIBNQFJKCORL', names_joined) + + def test_to_idt_bulk_input_format__col_major_top_left_domain_start(self) -> None: + key = sc.strand_order_key_function(column_major=True, strand_order=sc.StrandOrder.top_left_domain) + names_joined = self._get_names_idt(self.design_6h, key) + self.assertEqual('ABCDEFLHJGIKMNOPQR', names_joined) + + def test_to_idt_bulk_input_format__duplicate_names_same_sequence(self) -> None: + length = 8 + helices = [sc.Helix(max_offset=length)] + ss1_r = sc.Domain(0, True, 0, 4) + ss2_r = sc.Domain(0, True, 4, 8) + ss_l = sc.Domain(0, False, 0, 4) + + s1_r = sc.Strand([ss1_r], idt=sc.IDTFields('s1_r')) + s2_r = sc.Strand([ss2_r], idt=sc.IDTFields('s1_r')) + s_l = sc.Strand([ss_l], idt=sc.IDTFields('s_l')) + + strands = [s1_r, s2_r, s_l] + + design = sc.Design(helices=helices, strands=strands, grid=sc.square) + + design.assign_dna(s_l, 'AGTT') + design.assign_dna(s2_r, 'AACT') + + # should not raise exception + design.to_idt_bulk_input_format() + + def test_to_idt_bulk_input_format__duplicate_names_different_sequences(self) -> None: + ss1_r = sc.Domain(0, True, 0, 4) + ss2_r = sc.Domain(0, True, 4, 8) + ss_l = sc.Domain(0, False, 0, 4) + + s1_r = sc.Strand([ss1_r], idt=sc.IDTFields('s1_r')) + s2_r = sc.Strand([ss2_r], idt=sc.IDTFields('s1_r')) + s_l = sc.Strand([ss_l], idt=sc.IDTFields('s_l')) + + strands = [s1_r, s2_r, s_l] + + design = sc.Design(strands=strands, grid=sc.square) + + design.assign_dna(s_l, 'AGTT') + design.assign_dna(s2_r, 'GGGG') + + with self.assertRaises(sc.IllegalDesignError): + design.to_idt_bulk_input_format() + + def test_to_idt_bulk_input_format__duplicate_names_different_scales(self) -> None: + ss1_r = sc.Domain(0, True, 0, 4) + ss2_r = sc.Domain(0, True, 4, 8) + ss_l = sc.Domain(0, False, 0, 4) + + s1_r = sc.Strand([ss1_r], idt=sc.IDTFields('s1_r', scale='25nm')) + s2_r = sc.Strand([ss2_r], idt=sc.IDTFields('s1_r', scale='100nm')) + s_l = sc.Strand([ss_l], idt=sc.IDTFields('s_l')) + + strands = [s1_r, s2_r, s_l] + + design = sc.Design(strands=strands, grid=sc.square) + + design.assign_dna(s_l, 'AGTT') + design.assign_dna(s2_r, 'AACT') + + with self.assertRaises(sc.IllegalDesignError): + design.to_idt_bulk_input_format() + + def test_to_idt_bulk_input_format__duplicate_names_different_purifications(self) -> None: + ss1_r = sc.Domain(0, True, 0, 4) + ss2_r = sc.Domain(0, True, 4, 8) + ss_l = sc.Domain(0, False, 0, 4) + + s1_r = sc.Strand([ss1_r], idt=sc.IDTFields('s1_r', purification='STD')) + s2_r = sc.Strand([ss2_r], idt=sc.IDTFields('s1_r', purification='HPLC')) + s_l = sc.Strand([ss_l], idt=sc.IDTFields('s_l')) + + strands = [s1_r, s2_r, s_l] + + design = sc.Design(strands=strands, grid=sc.square) + + design.assign_dna(s_l, 'AGTT') + design.assign_dna(s2_r, 'AACT') + + with self.assertRaises(sc.IllegalDesignError): + design.to_idt_bulk_input_format() + + class TestExportCadnanoV2(unittest.TestCase): """ Tests the export feature to cadnano v2 (see misc/cadnano-format-specs/v2.txt). @@ -611,11 +825,11 @@ def test_export_design_with_helix_group(self): e = 'east' s = 'south' helices = [ - sc.Helix(max_offset=24, group=s), - sc.Helix(max_offset=25, group=s), + sc.Helix(max_offset=24, group=s), + sc.Helix(max_offset=25, group=s), ] helices.extend([ - sc.Helix(max_offset=22, group=e), + sc.Helix(max_offset=22, group=e), sc.Helix(max_offset=23, group=e), ]) @@ -630,19 +844,19 @@ def test_export_design_with_helix_group(self): design = sc.Design(helices=helices, groups=groups, strands=[]) design.write_scadnano_file(directory=self.input_path, - filename=f'test_export_design_with_helix_group.{self.ext}') + filename=f'test_export_design_with_helix_group.{self.ext}') design.export_cadnano_v2(directory=self.output_path, - filename='test_export_design_with_helix_group.json') + filename='test_export_design_with_helix_group.json') def test_export_design_with_helix_group_not_same_grid(self): e = 'east' s = 'south' helices = [ - sc.Helix(max_offset=24, group=s), - sc.Helix(max_offset=25, group=s), + sc.Helix(max_offset=24, group=s), + sc.Helix(max_offset=25, group=s), ] helices.extend([ - sc.Helix(max_offset=22, group=e), + sc.Helix(max_offset=22, group=e), sc.Helix(max_offset=23, group=e), ]) @@ -657,14 +871,13 @@ def test_export_design_with_helix_group_not_same_grid(self): design = sc.Design(helices=helices, groups=groups, strands=[]) design.write_scadnano_file(directory=self.input_path, - filename=f'test_export_design_with_helix_group_not_same_grid.{self.ext}') - + filename=f'test_export_design_with_helix_group_not_same_grid.{self.ext}') + with self.assertRaises(ValueError) as context: design.export_cadnano_v2(directory=self.output_path, - filename='test_export_design_with_helix_group_not_same_grid.json') + filename='test_export_design_with_helix_group_not_same_grid.json') self.assertTrue('helix groups' in context.exception.args[0]) - def test_2_staple_2_helix_origami_extremely_simple(self): helices = [sc.Helix(max_offset=32), sc.Helix(max_offset=32)] scaf_part = sc.Domain(helix=0, forward=True, start=0, end=32) @@ -804,7 +1017,7 @@ class TestDesignFromJson(unittest.TestCase): """ def setUp(self) -> None: - """ + r""" 0 8 16 | | | 0 +--X-----------+ @@ -1043,7 +1256,7 @@ def test_reverse_all__one_strand(self) -> None: self.assertEqual(8, ss.end) def test_reverse_all__three_strands(self) -> None: - """ + r""" before 0 8 16 | | | @@ -1081,52 +1294,52 @@ def test_reverse_all__three_strands(self) -> None: design.reverse_all() self.assertEqual(3, len(design.strands)) - stapL = design.strands[0] - stapR = design.strands[1] + stap_l = design.strands[0] + stap_r = design.strands[1] scaf = design.strands[2] - self.assertEqual(0, stapL.offset_5p()) - self.assertEqual(0, stapL.offset_3p()) - self.assertEqual(15, stapR.offset_5p()) - self.assertEqual(15, stapR.offset_3p()) + self.assertEqual(0, stap_l.offset_5p()) + self.assertEqual(0, stap_l.offset_3p()) + self.assertEqual(15, stap_r.offset_5p()) + self.assertEqual(15, stap_r.offset_3p()) self.assertEqual(8, scaf.offset_5p()) self.assertEqual(7, scaf.offset_3p()) - self.assertEqual(2, len(stapL.domains)) - stapL_ss0 = stapL.domains[0] - stapL_ss1 = stapL.domains[1] - - self.assertEqual(0, stapL_ss0.helix) - self.assertEqual(True, stapL_ss0.forward) - self.assertEqual(0, stapL_ss0.start) - self.assertEqual(8, stapL_ss0.end) - self.assertEqual([3], stapL_ss0.deletions) - self.assertEqual([], stapL_ss0.insertions) - - self.assertEqual(1, stapL_ss1.helix) - self.assertEqual(False, stapL_ss1.forward) - self.assertEqual(0, stapL_ss1.start) - self.assertEqual(8, stapL_ss1.end) - self.assertEqual([], stapL_ss1.deletions) - self.assertEqual([(4, 2)], stapL_ss1.insertions) - - self.assertEqual(2, len(stapR.domains)) - stapR_ss0 = stapR.domains[0] - stapR_ss1 = stapR.domains[1] - - self.assertEqual(1, stapR_ss0.helix) - self.assertEqual(False, stapR_ss0.forward) - self.assertEqual(8, stapR_ss0.start) - self.assertEqual(16, stapR_ss0.end) - self.assertEqual([], stapR_ss0.deletions) - self.assertEqual([], stapR_ss0.insertions) - - self.assertEqual(0, stapR_ss1.helix) - self.assertEqual(True, stapR_ss1.forward) - self.assertEqual(8, stapR_ss1.start) - self.assertEqual(16, stapR_ss1.end) - self.assertEqual([], stapR_ss1.deletions) - self.assertEqual([], stapR_ss1.insertions) + self.assertEqual(2, len(stap_l.domains)) + stap_l_ss0 = stap_l.domains[0] + stap_l_ss1 = stap_l.domains[1] + + self.assertEqual(0, stap_l_ss0.helix) + self.assertEqual(True, stap_l_ss0.forward) + self.assertEqual(0, stap_l_ss0.start) + self.assertEqual(8, stap_l_ss0.end) + self.assertEqual([3], stap_l_ss0.deletions) + self.assertEqual([], stap_l_ss0.insertions) + + self.assertEqual(1, stap_l_ss1.helix) + self.assertEqual(False, stap_l_ss1.forward) + self.assertEqual(0, stap_l_ss1.start) + self.assertEqual(8, stap_l_ss1.end) + self.assertEqual([], stap_l_ss1.deletions) + self.assertEqual([(4, 2)], stap_l_ss1.insertions) + + self.assertEqual(2, len(stap_r.domains)) + stap_r_ss0 = stap_r.domains[0] + stap_r_ss1 = stap_r.domains[1] + + self.assertEqual(1, stap_r_ss0.helix) + self.assertEqual(False, stap_r_ss0.forward) + self.assertEqual(8, stap_r_ss0.start) + self.assertEqual(16, stap_r_ss0.end) + self.assertEqual([], stap_r_ss0.deletions) + self.assertEqual([], stap_r_ss0.insertions) + + self.assertEqual(0, stap_r_ss1.helix) + self.assertEqual(True, stap_r_ss1.forward) + self.assertEqual(8, stap_r_ss1.start) + self.assertEqual(16, stap_r_ss1.end) + self.assertEqual([], stap_r_ss1.deletions) + self.assertEqual([], stap_r_ss1.insertions) self.assertEqual(3, len(scaf.domains)) scaf_ss0 = scaf.domains[0] @@ -1928,7 +2141,8 @@ def test_add_full_crossover__small_design_illegal_only_one_helix_has_domain(self <------- -------- -------- -------- -------- -------] <------- -------- -------- -------- -------- -------] """ - def add_nicks(self, design: sc.Design): + @staticmethod + def add_nicks(design: sc.Design): design.add_nick(helix=5, offset=48, forward=False) design.add_nick(helix=0, offset=40, forward=False) design.add_nick(helix=0, offset=72, forward=False) @@ -1987,7 +2201,8 @@ def test_add_nick__6_helix_rectangle(self) -> None: """ - def add_crossovers_after_nicks(self, design: sc.Design): + @staticmethod + def add_crossovers_after_nicks(design: sc.Design): # scaffold seam crossovers design.add_full_crossover(helix=1, helix2=2, offset=48, forward=False) design.add_full_crossover(helix=3, helix2=4, offset=48, forward=False) @@ -2042,7 +2257,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: # {"helix": 5, "forward": true, "start": 0, "end": 16}, # {"helix": 4, "forward": false, "start": 0, "end": 16} - stap3 = sc.Strand([ + stap = sc.Strand([ sc.Domain(5, True, 0, 16), sc.Domain(4, False, 0, 16), ]) @@ -2203,14 +2418,14 @@ class TestAutocalculatedData(unittest.TestCase): def test_helix_min_max_offsets_illegal_explicitly_specified(self) -> None: helices = [sc.Helix(min_offset=5, max_offset=5)] with self.assertRaises(sc.IllegalDesignError): - design = sc.Design(helices=helices, strands=[], grid=sc.square) + sc.Design(helices=helices, strands=[], grid=sc.square) def test_helix_min_max_offsets_illegal_autocalculated(self) -> None: helices = [sc.Helix(min_offset=5)] ss = sc.Domain(0, True, 0, 4) strand = sc.Strand([ss]) with self.assertRaises(sc.IllegalDesignError): - design = sc.Design(helices=helices, strands=[strand], grid=sc.square) + sc.Design(helices=helices, strands=[strand], grid=sc.square) def test_helix_min_max_offsets(self) -> None: helices = [sc.Helix(), sc.Helix(min_offset=-5), sc.Helix(max_offset=5), @@ -2401,8 +2616,8 @@ def test_helix_groups_fail_nonexistent(self) -> None: ] group_north = sc.HelixGroup(position=sc.Position3D(x=0, y=-200, z=0), grid=sc.honeycomb) groups = {self.n: group_north} - with self.assertRaises(sc.IllegalDesignError) as ex: - design = sc.Design(helices=helices, groups=groups, strands=[]) + with self.assertRaises(sc.IllegalDesignError): + sc.Design(helices=helices, groups=groups, strands=[]) def _asserts_for_fixture(self, design: sc.Design): n = self.n @@ -2475,8 +2690,8 @@ def test_JSON_bad_uses_groups_and_top_level_grid(self) -> None: ] } ''' - with self.assertRaises(sc.IllegalDesignError) as ex: - design = sc.Design.from_scadnano_json_str(json_str) + with self.assertRaises(sc.IllegalDesignError): + sc.Design.from_scadnano_json_str(json_str) def test_JSON_bad_uses_groups_and_top_level_helices_view_order(self) -> None: json_str = ''' @@ -2517,8 +2732,8 @@ def test_JSON_bad_uses_groups_and_top_level_helices_view_order(self) -> None: ] } ''' - with self.assertRaises(sc.IllegalDesignError) as ex: - design = sc.Design.from_scadnano_json_str(json_str) + with self.assertRaises(sc.IllegalDesignError): + sc.Design.from_scadnano_json_str(json_str) def test_JSON_bad_no_groups_but_helices_reference_groups(self) -> None: json_str = ''' @@ -2549,8 +2764,8 @@ def test_JSON_bad_no_groups_but_helices_reference_groups(self) -> None: } ''' - with self.assertRaises(sc.IllegalDesignError) as ex: - design = sc.Design.from_scadnano_json_str(json_str) + with self.assertRaises(sc.IllegalDesignError): + sc.Design.from_scadnano_json_str(json_str) class TestNames(unittest.TestCase): @@ -2605,11 +2820,11 @@ def test_strand_domain_names_json(self) -> None: self.assertEqual('domain_forward0', design_from_json.strands[0].domains[0].name) self.assertEqual('domain_forward1', design_from_json.strands[0].domains[1].name) - + self.assertEqual('domain_reverse0', design_from_json.strands[1].domains[0].name) self.assertEqual('loopout', design_from_json.strands[1].domains[1].name) self.assertEqual('domain_forward2', design_from_json.strands[1].domains[2].name) - + self.assertEqual(None, design_from_json.strands[2].domains[0].name) self.assertEqual('domain_forward0', design_from_json.strands[2].domains[1].name) @@ -2624,7 +2839,7 @@ def test_strand_names_can_be_nonunique(self) -> None: sc.Domain(0, False, 8, 16, name='domain_reverse1'), ]) strands = [strand0, strand1] - d = sc.Design(helices=helices, strands=strands, grid=sc.square) + sc.Design(helices=helices, strands=strands, grid=sc.square) class TestJSON(unittest.TestCase): @@ -2844,7 +3059,7 @@ def test_error_when_grid_missing(self) -> None: } """ with self.assertRaises(sc.IllegalDesignError) as ex: - d = sc.Design.from_scadnano_json_str(json_str) + sc.Design.from_scadnano_json_str(json_str) msg = ex.exception.args[0] self.assertTrue('grid' in msg) @@ -2862,7 +3077,7 @@ def test_error_when_domain_helix_missing(self) -> None: } """ with self.assertRaises(sc.IllegalDesignError) as ex: - d = sc.Design.from_scadnano_json_str(json_str) + sc.Design.from_scadnano_json_str(json_str) msg = ex.exception.args[0] self.assertTrue('helix' in msg) @@ -2880,7 +3095,7 @@ def test_error_when_domain_forward_and_right_missing(self) -> None: } """ with self.assertRaises(sc.IllegalDesignError) as ex: - d = sc.Design.from_scadnano_json_str(json_str) + sc.Design.from_scadnano_json_str(json_str) msg = ex.exception.args[0] self.assertTrue('forward' in msg) self.assertTrue('right' in msg) @@ -2899,7 +3114,7 @@ def test_error_when_domain_start_missing(self) -> None: } """ with self.assertRaises(sc.IllegalDesignError) as ex: - d = sc.Design.from_scadnano_json_str(json_str) + sc.Design.from_scadnano_json_str(json_str) msg = ex.exception.args[0] self.assertTrue('start' in msg) @@ -2917,7 +3132,7 @@ def test_error_when_domain_end_missing(self) -> None: } """ with self.assertRaises(sc.IllegalDesignError) as ex: - d = sc.Design.from_scadnano_json_str(json_str) + sc.Design.from_scadnano_json_str(json_str) msg = ex.exception.args[0] self.assertTrue('end' in msg) @@ -2929,7 +3144,7 @@ def test_error_when_strands_missing(self) -> None: } """ with self.assertRaises(sc.IllegalDesignError) as ex: - d = sc.Design.from_scadnano_json_str(json_str) + sc.Design.from_scadnano_json_str(json_str) msg = ex.exception.args[0] self.assertTrue('strands' in msg) @@ -3056,7 +3271,7 @@ def test_json_tristan_example_issue_32(self) -> None: ] } """ - d = sc.Design.from_scadnano_json_str(json_str) + sc.Design.from_scadnano_json_str(json_str) def test_to_json__hairpin(self) -> None: """ @@ -3077,7 +3292,7 @@ def test_to_json__hairpin(self) -> None: strand_forward = sc.Strand([ss_f, loop, ss_r]) design = sc.Design(strands=[strand_forward], grid=sc.square) design.assign_dna(strand_forward, 'AAACC TGCAC') - json = design.to_json() + design.to_json() # should be no error getting here def test_to_json__roll(self) -> None: @@ -3087,7 +3302,7 @@ def test_to_json__roll(self) -> None: strand_f = sc.Strand([ss_f]) strand_r = sc.Strand([ss_r]) design = sc.Design(helices=[helix], strands=[strand_f, strand_r], grid=sc.square) - json = design.to_json() + design.to_json() # should be no error getting here @@ -3136,109 +3351,30 @@ def test_consecutive_domains_loopout(self) -> None: ss2 = sc.Loopout(4) ss3 = sc.Loopout(4) with self.assertRaises(sc.IllegalDesignError): - strand = sc.Strand([ss1, ss2, ss3]) + sc.Strand([ss1, ss2, ss3]) strand = sc.Strand([ss1, ss2]) strand.domains.append(ss3) with self.assertRaises(sc.IllegalDesignError): - design = sc.Design(helices=helices, strands=[strand], grid=sc.square) + sc.Design(helices=helices, strands=[strand], grid=sc.square) def test_singleton_loopout(self) -> None: helices = [sc.Helix(max_offset=10)] loopout = sc.Loopout(4) with self.assertRaises(sc.StrandError): - strand = sc.Strand([loopout]) + sc.Strand([loopout]) strand = sc.Strand([]) strand.domains.append(loopout) with self.assertRaises(sc.StrandError): - design = sc.Design(helices=helices, strands=[strand], grid=sc.square) + sc.Design(helices=helices, strands=[strand], grid=sc.square) def test_strand_offset_beyond_maxbases(self) -> None: helices = [sc.Helix(max_offset=10)] ss1 = sc.Domain(0, True, 0, 20) strands = [sc.Strand([ss1])] with self.assertRaises(sc.StrandError): - design = sc.Design(helices=helices, strands=strands) - - def test_to_idt_bulk_input_format__duplicate_names_same_sequence(self) -> None: - length = 8 - helices = [sc.Helix(max_offset=length)] - ss1_r = sc.Domain(0, True, 0, 4) - ss2_r = sc.Domain(0, True, 4, 8) - ss_l = sc.Domain(0, False, 0, 4) - - s1_r = sc.Strand([ss1_r], idt=sc.IDTFields('s1_r')) - s2_r = sc.Strand([ss2_r], idt=sc.IDTFields('s1_r')) - s_l = sc.Strand([ss_l], idt=sc.IDTFields('s_l')) - - strands = [s1_r, s2_r, s_l] - - design = sc.Design(helices=helices, strands=strands, grid=sc.square) - - design.assign_dna(s_l, 'AGTT') - design.assign_dna(s2_r, 'AACT') - - # should not raise exception - idt_str = design.to_idt_bulk_input_format() - - def test_to_idt_bulk_input_format__duplicate_names_different_sequences(self) -> None: - ss1_r = sc.Domain(0, True, 0, 4) - ss2_r = sc.Domain(0, True, 4, 8) - ss_l = sc.Domain(0, False, 0, 4) - - s1_r = sc.Strand([ss1_r], idt=sc.IDTFields('s1_r')) - s2_r = sc.Strand([ss2_r], idt=sc.IDTFields('s1_r')) - s_l = sc.Strand([ss_l], idt=sc.IDTFields('s_l')) - - strands = [s1_r, s2_r, s_l] - - design = sc.Design(strands=strands, grid=sc.square) - - design.assign_dna(s_l, 'AGTT') - design.assign_dna(s2_r, 'GGGG') - - with self.assertRaises(sc.IllegalDesignError): - idt_str = design.to_idt_bulk_input_format() - - def test_to_idt_bulk_input_format__duplicate_names_different_scales(self) -> None: - ss1_r = sc.Domain(0, True, 0, 4) - ss2_r = sc.Domain(0, True, 4, 8) - ss_l = sc.Domain(0, False, 0, 4) - - s1_r = sc.Strand([ss1_r], idt=sc.IDTFields('s1_r', scale='25nm')) - s2_r = sc.Strand([ss2_r], idt=sc.IDTFields('s1_r', scale='100nm')) - s_l = sc.Strand([ss_l], idt=sc.IDTFields('s_l')) - - strands = [s1_r, s2_r, s_l] - - design = sc.Design(strands=strands, grid=sc.square) - - design.assign_dna(s_l, 'AGTT') - design.assign_dna(s2_r, 'AACT') - - with self.assertRaises(sc.IllegalDesignError): - idt_str = design.to_idt_bulk_input_format() - - def test_to_idt_bulk_input_format__duplicate_names_different_purifications(self) -> None: - length = 8 - ss1_r = sc.Domain(0, True, 0, 4) - ss2_r = sc.Domain(0, True, 4, 8) - ss_l = sc.Domain(0, False, 0, 4) - - s1_r = sc.Strand([ss1_r], idt=sc.IDTFields('s1_r', purification='STD')) - s2_r = sc.Strand([ss2_r], idt=sc.IDTFields('s1_r', purification='HPLC')) - s_l = sc.Strand([ss_l], idt=sc.IDTFields('s_l')) - - strands = [s1_r, s2_r, s_l] - - design = sc.Design(strands=strands, grid=sc.square) - - design.assign_dna(s_l, 'AGTT') - design.assign_dna(s2_r, 'AACT') - - with self.assertRaises(sc.IllegalDesignError): - idt_str = design.to_idt_bulk_input_format() + sc.Design(helices=helices, strands=strands) def test_assign_dna__conflicting_sequences_directly_assigned(self) -> None: ss_right = sc.Domain(0, True, 0, 5) @@ -3274,14 +3410,14 @@ def test_overlapping_caught_in_strange_counterexample(self) -> None: strands = [s1, s2] with self.assertRaises(sc.IllegalDesignError): - design = sc.Design(strands=strands, grid=sc.square) + sc.Design(strands=strands, grid=sc.square) def test_major_tick_outside_range(self) -> None: with self.assertRaises(sc.IllegalDesignError): - helix = sc.Helix(max_offset=9, major_ticks=[2, 5, 10]) + sc.Helix(max_offset=9, major_ticks=[2, 5, 10]) def test_major_tick_just_inside_range(self) -> None: - helix = sc.Helix(max_offset=9, major_ticks=[0, 5, 9]) + sc.Helix(max_offset=9, major_ticks=[0, 5, 9]) def test_two_illegally_overlapping_strands(self) -> None: ss_bot = sc.Domain(helix=0, forward=False, start=0, end=9) @@ -3431,8 +3567,8 @@ def test_with_label__dict(self) -> None: self.assertDictEqual(expected_strand.label, actual_strand.label) def test_with_domain_label(self) -> None: - label0 = 'abc' - label1 = {'name': 'abc', 'type': 3} + label0: Union[str, Dict[str, Any]] = 'abc' + label1: Union[str, Dict[str, Any]] = {'name': 'abc', 'type': 3} self.design.strand(0, 0).to(5).with_domain_label(label0).cross(1).to(0).with_domain_label(label1) actual_strand = self.design.strands[0] expected_strand = sc.Strand(domains=[ @@ -3445,8 +3581,8 @@ def test_with_domain_label(self) -> None: def test_with_domain_label__and__with_label(self) -> None: strand_label = 'xyz' - label0 = 'abc' - label1 = {'name': 'abc', 'type': 3} + label0: Union[str, Dict[str, Any]] = 'abc' + label1: Union[str, Dict[str, Any]] = {'name': 'abc', 'type': 3} self.design.strand(0, 0).to(5).with_domain_label(label0).cross(1).to(0).with_domain_label(label1) \ .with_label(strand_label) actual_strand = self.design.strands[0] @@ -3460,7 +3596,7 @@ def test_with_domain_label__and__with_label(self) -> None: self.assertDictEqual(expected_strand.domains[1].label, actual_strand.domains[1].label) -def set_colors_black(*strands): +def set_colors_black(*strands) -> None: for strand in strands: strand.set_color(sc.Color(r=0, g=0, b=0)) @@ -4006,7 +4142,7 @@ def test_assign_dna__upper_left_edge_staple_of_16H_origami_rectangle(self) -> No self.assertEqual(expected_seq_stap_upperleft, stap.dna_sequence) def test_assign_dna__2helix_with_deletions(self) -> None: - """ + r""" scaf index: 2 3 4 5 offset: 0 D1 2 3 D4 5 + - - + From 481d9669211506cb4f966d6995689cbc2b63f35a Mon Sep 17 00:00:00 2001 From: David Doty Date: Mon, 23 Nov 2020 18:36:59 -0800 Subject: [PATCH 02/18] updated unit tests --- tests/scadnano_tests.py | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 5d55e51d..fc584bd0 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -649,33 +649,33 @@ def setUp(self) -> None: self.design_6h: sc.Design = sc.Design(helices=helices, strands=[], grid=sc.square) d = self.design_6h - d.strand(1, 0).move(16).cross(0).move(-16).with_idt('A') # A - d.strand(3, 0).move(16).cross(2).move(-16).with_idt('B') # B - d.strand(5, 0).move(16).cross(4).move(-16).with_idt('C') # C + d.strand(1, 0).move(16).cross(0).move(-16).with_idt('A') + d.strand(3, 0).move(16).cross(2).move(-16).with_idt('B') + d.strand(5, 0).move(16).cross(4).move(-16).with_idt('C') - d.strand(0, 40).move(-24).cross(1).move(8).with_idt('D') # D + d.strand(0, 40).move(-24).cross(1).move(8).with_idt('D') - d.strand(1, 24).move(8).cross(2).move(-16).cross(3).move(8).with_idt('E') # E - d.strand(3, 24).move(8).cross(4).move(-16).cross(5).move(8).with_idt('F') # F + d.strand(1, 24).move(8).cross(2).move(-16).cross(3).move(8).with_idt('E') + d.strand(3, 24).move(8).cross(4).move(-16).cross(5).move(8).with_idt('F') - d.strand(0, 72).move(-32).with_idt('G') # G + d.strand(0, 72).move(-32).with_idt('G') - d.strand(2, 40).move(-8).cross(1).move(24).with_idt('H') # H - d.strand(1, 56).move(8).cross(2).move(-24).with_idt('I') # I + d.strand(2, 40).move(-8).cross(1).move(24).with_idt('H') + d.strand(1, 56).move(8).cross(2).move(-24).with_idt('I') - d.strand(4, 40).move(-8).cross(3).move(24).with_idt('J') # J - d.strand(3, 56).move(8).cross(4).move(-24).with_idt('K') # K + d.strand(4, 40).move(-8).cross(3).move(24).with_idt('J') + d.strand(3, 56).move(8).cross(4).move(-24).with_idt('K') - d.strand(5, 24).move(32).with_idt('L') # L + d.strand(5, 24).move(32).with_idt('L') - d.strand(2, 72).move(-8).cross(1).move(16).cross(0).move(-8).with_idt('M') # M - d.strand(4, 72).move(-8).cross(3).move(16).cross(2).move(-8).with_idt('N') # N + d.strand(2, 72).move(-8).cross(1).move(16).cross(0).move(-8).with_idt('M') + d.strand(4, 72).move(-8).cross(3).move(16).cross(2).move(-8).with_idt('N') - d.strand(5, 56).move(24).cross(4).move(-8).with_idt('O') # O + d.strand(5, 56).move(24).cross(4).move(-8).with_idt('O') - d.strand(0, 96).move(-16).cross(1).move(16).with_idt('P') # P - d.strand(2, 96).move(-16).cross(3).move(16).with_idt('Q') # Q - d.strand(4, 96).move(-16).cross(5).move(16).with_idt('R') # R + d.strand(0, 96).move(-16).cross(1).move(16).with_idt('P') + d.strand(2, 96).move(-16).cross(3).move(16).with_idt('Q') + d.strand(4, 96).move(-16).cross(5).move(16).with_idt('R') for strand in d.strands: d.assign_dna(strand, 'A' * 32, assign_complement=False) From 76b4b64fb9ad4c345501c732c7cd14247671882c Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 1 Dec 2020 11:55:20 -0800 Subject: [PATCH 03/18] fixed documentation of hex coordinate system --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index e568bb6c..cdb96da1 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1167,7 +1167,7 @@ class Helix(_JSONSerializable): In the case of the hexagonal lattice, The convention is that incrementing `v` moves down and to the right if h is even, and moves down and to the left if `h` is odd. - This is the "odd-r horizontal layout" coordinate system here: + This is the "odd-q" coordinate system here: https://www.redblobgames.com/grids/hexagons/) However, the default y position in the main view for helices does not otherwise depend on grid_position. The default is to list the y-coordinates in order by helix idx. From a1e74674b7bdcc61208a06ac4e420938cbf9868d Mon Sep 17 00:00:00 2001 From: David Doty Date: Sat, 12 Dec 2020 15:46:09 -0800 Subject: [PATCH 04/18] fixed documentation of hex coordinate system --- scadnano/scadnano.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index cdb96da1..0d984ff4 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -309,10 +309,11 @@ class Grid(str, enum.Enum): hex = "hex" """ - Hexagonal lattice. Uses the *"odd-r horizontal layout"* coordinate system described here: + Hexagonal lattice. Uses the *"odd-q horizontal layout"* coordinate system described here: https://www.redblobgames.com/grids/hexagons/. - Incrementing `v` moves down and to the right if `h` is even, - and moves down and to the left if `h` is odd. + Incrementing `v` moves down. + Incrementing `h` moves down and to the right if `h` is even, + and moves up and to the right if `h` is odd. """ honeycomb = "honeycomb" From 9d1ac962405a73bb314fcb9d3ee161d04a0c0fce Mon Sep 17 00:00:00 2001 From: David Doty Date: Sat, 12 Dec 2020 16:57:03 -0800 Subject: [PATCH 05/18] fixed documentation of Loopout to say they are not allowed on ends of Strand, and added example of creating one with chained method calls. --- scadnano/scadnano.py | 25 +++++++++++++++++-------- 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 0d984ff4..a0b0459c 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1779,12 +1779,11 @@ class Loopout(_JSONSerializable): One could think of a :any:`Loopout` as a type of :any:`Domain`, but none of the fields of :any:`Domain` make sense for :any:`Loopout`, so they are not related to each other in the type hierarchy. It is interpreted that a :any:`Loopout` is a single-stranded region bridging two - :any:`Domain`'s that are connected to :any:`Helix`'s, or if it occurs on the end of a :any:`Strand`, - then it is a single-stranded extension. It is illegal for two consecutive :any:`Domain`'s to both - be :any:`Loopout`'s, and for a :any:`Strand` to have only one element of :any:`Strand.domains` - that is a :any:`Loopout`. - - Loopout has only a single field :py:data:`Loopout.length` that specifies the length of the loopout. + :any:`Domain`'s that are connected to :any:`Helix`'s. + It is illegal for two consecutive :any:`Domain`'s to both + be :any:`Loopout`'s, + or for a :any:`Loopout` to occur on either end of the :any:`Strand` + (i.e., each :any:`Strand` must begin and end with a :any:`Domain`). For example, one use of a loopout is to describe a hairpin (a.k.a., `stem-loop `_). @@ -1799,6 +1798,15 @@ class Loopout(_JSONSerializable): loop = sc.Loopout(length=5) domain_r = sc.Domain(helix=0, forward=False, start=0, end=10) hairpin = sc.Strand([domain_f, loop, domain_r]) + + It can also be created with chained method calls + + .. code-block:: Python + + import scadnano as sc + + design = sc.Design(helices=[sc.Helix(max_offset=10)]) + design.strand(0,0).move(10).loopout(0,5).move(-10) """ length: int @@ -5069,7 +5077,8 @@ def write_idt_plate_excel_file(self, *, directory: str = '.', filename: str = No use_default_plates: bool = False, warn_using_default_plates: bool = True, plate_type: PlateType = PlateType.wells96, export_non_modified_strand_version: bool = False) -> None: - """Write ``.xls`` (Microsoft Excel) file encoding the strands of this :any:`Design` with the field + """ + Write ``.xls`` (Microsoft Excel) file encoding the strands of this :any:`Design` with the field :py:data:`Strand.idt`, suitable for uploading to IDT (Integrated DNA Technologies, Coralville, IA, https://www.idtdna.com/) to describe a 96-well or 384-well plate @@ -5089,7 +5098,7 @@ def write_idt_plate_excel_file(self, *, directory: str = '.', filename: str = No order in which to output strand sequences. Some useful defaults are provided by :py:meth:`strand_order_key_function` :param warn_duplicate_name: - if ``True`` prints a warning when two different :any:`Strand`'s have the same + if ``True`` prints a warning when two different :any:`Strand`'s have the same :py:attr:`IDTField.name` and the same :any:`Strand.dna_sequence`. An :any:`IllegalDesignError` is raised (regardless of the value of this parameter) if two different :any:`Strand`'s have the same name but different sequences, IDT scales, or IDT From 4b13ef26ccf1fee51e0f63e4571b7861fe608f3e Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 13 Dec 2020 09:08:59 -0800 Subject: [PATCH 06/18] closes #14; add support for circular Strands --- examples/circular.py | 18 +++++++++ examples/output_designs/circular.sc | 34 ++++++++++++++++ scadnano/scadnano.py | 61 +++++++++++++++++++++++++++-- tests/scadnano_tests.py | 40 +++++++++++++++++++ 4 files changed, 149 insertions(+), 4 deletions(-) create mode 100644 examples/circular.py create mode 100644 examples/output_designs/circular.sc diff --git a/examples/circular.py b/examples/circular.py new file mode 100644 index 00000000..21168368 --- /dev/null +++ b/examples/circular.py @@ -0,0 +1,18 @@ +import scadnano as sc +import modifications as mod +import dataclasses + +def create_design(): + helices = [sc.Helix(max_offset=30) for _ in range(2)] + design = sc.Design(helices=helices, grid=sc.square) + + design.strand(0,0).move(10).cross(1).move(-10).as_circular() + design.strand(0,10).move(10).loopout(1, 5).move(-10).as_circular() + design.strand(0,20).move(10).cross(1).move(-10) + + return design + + +if __name__ == '__main__': + design = create_design() + design.write_scadnano_file(directory='output_designs') diff --git a/examples/output_designs/circular.sc b/examples/output_designs/circular.sc new file mode 100644 index 00000000..82f0bd44 --- /dev/null +++ b/examples/output_designs/circular.sc @@ -0,0 +1,34 @@ +{ + "version": "0.13.0", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]} + ], + "strands": [ + { + "circular": true, + "color": "#f74308", + "domains": [ + {"helix": 0, "forward": true, "start": 0, "end": 10}, + {"helix": 1, "forward": false, "start": 0, "end": 10} + ] + }, + { + "circular": true, + "color": "#57bb00", + "domains": [ + {"helix": 0, "forward": true, "start": 10, "end": 20}, + {"loopout": 5}, + {"helix": 1, "forward": false, "start": 10, "end": 20} + ] + }, + { + "color": "#888888", + "domains": [ + {"helix": 0, "forward": true, "start": 20, "end": 30}, + {"helix": 1, "forward": false, "start": 20, "end": 30} + ] + } + ] +} \ No newline at end of file diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index a0b0459c..79fa077d 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -749,6 +749,7 @@ def m13(rotation: int = 5587, variant: M13Variant = M13Variant.p7249) -> str: # Strand keys strand_name_key = 'name' +circular_key = 'circular' color_key = 'color' dna_sequence_key = 'sequence' legacy_dna_sequence_keys = ['dna_sequence'] # support legacy names for these ideas @@ -2201,6 +2202,17 @@ def update_to(self, offset: int) -> 'StrandBuilder[StrandLabel, DomainLabel]': return self + def as_circular(self) -> 'StrandBuilder[StrandLabel, DomainLabel]': + """ + Makes :any:`Strand` being built circular. + + :return: self + """ + if self._strand is None: + raise ValueError('no Strand created yet; make at least one domain first') + self._strand.set_circular() + return self + # remove quotes when Py3.6 support dropped def as_scaffold(self) -> 'StrandBuilder[StrandLabel, DomainLabel]': """ @@ -2477,6 +2489,13 @@ class Strand(_JSONSerializable, Generic[StrandLabel, DomainLabel]): and could be either single-stranded or double-stranded, whereas each :any:`Loopout` is single-stranded and has no associated :any:`Helix`.""" + circular: bool = False + """If True, this :any:`Strand` is circular and has no 5' or 3' end. Although there is still a + first and last :any:`Domain`, we interpret there to be a crossover from the 3' end of the last domain + to the 5' end of the first domain, and any circular permutation of :py:data:`Strand.domains` + should result in a functionally equivalent :any:`Strand`. It is illegal to have a + :any:`Modification5Prime` or :any:`Modification3Prime` on a circular :any:`Strand`.""" + dna_sequence: Optional[str] = None """Do not assign directly to this field. Always use :any:`Design.assign_dna` (for complementarity checking) or :any:`Strand.set_dna_sequence` @@ -2509,10 +2528,14 @@ class Strand(_JSONSerializable, Generic[StrandLabel, DomainLabel]): :any:`Design` is a scaffold, then the design is considered a DNA origami design.""" modification_5p: Optional[Modification5Prime] = None - """5' modification; None if there is no 5' modification.""" + """ + 5' modification; None if there is no 5' modification. Illegal to have if :py:`Strand.circular` is True. + """ modification_3p: Optional[Modification3Prime] = None - """3' modification; None if there is no 5' modification.""" + """ + 3' modification; None if there is no 3' modification. Illegal to have if :py:`Strand.circular` is True. + """ modifications_int: Dict[int, ModificationInternal] = field(default_factory=dict) """:any:`Modification`'s to the DNA sequence (e.g., biotin, Cy3/Cy5 fluorphores). Maps offset to @@ -2574,6 +2597,8 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D dct: Dict[str, Any] = OrderedDict() if self.name is not None: dct[strand_name_key] = self.name + if self.circular: + dct[circular_key] = self.circular if self.color is not None: dct[color_key] = self.color.to_json_serializable(suppress_indent) if self.dna_sequence is not None: @@ -2617,6 +2642,7 @@ def from_json(json_map: dict) -> 'Strand': # remove quotes when Py3.6 support d raise IllegalDesignError('Loopout at end of Strand not supported') is_scaffold = json_map.get(is_scaffold_key, False) + circular = json_map.get(circular_key, False) dna_sequence = optional_field(None, json_map, dna_sequence_key, *legacy_dna_sequence_keys) @@ -2638,6 +2664,7 @@ def decimal_int_to_hex(d: int) -> str: return Strand( domains=domains, dna_sequence=dna_sequence, + circular=circular, color=color, idt=idt, is_scaffold=is_scaffold, @@ -2699,6 +2726,28 @@ def set_color(self, color: Color) -> None: """Sets color of this :any:`Strand`.""" self.color = color + def set_circular(self, circular: bool = True) -> None: + """ + Sets this to be a circular :any:`Strand` (or non-circular if optional parameter is False. + + :param circular: + whether to make this :any:`Strand` circular (True) or linear (False) + :raises StrandError: + if this :any:`Strand` has a 5' or 3' modification + """ + if circular and self.modification_5p is not None: + raise StrandError(self, "cannot have a 5' modification on a circular strand") + if circular and self.modification_3p is not None: + raise StrandError(self, "cannot have a 3' modification on a circular strand") + self.circular = circular + + def set_linear(self) -> None: + """ + Makes this a linear (non-circular) :any:`Strand`. Equivalent to calling + `self.set_circular(False)`. + """ + self.set_circular(False) + def set_default_idt(self, use_default_idt: bool = True, skip_scaffold: bool = True, unique_names: bool = False) -> None: """ @@ -2744,11 +2793,15 @@ def set_default_idt(self, use_default_idt: bool = True, skip_scaffold: bool = Tr self.idt = None def set_modification_5p(self, mod: Modification5Prime = None) -> None: - """Sets 5' modification to be `mod`.""" + """Sets 5' modification to be `mod`. `mod` cannot be non-None if :any:`Strand.circular` is True.""" + if self.circular and mod is not None: + raise StrandError(self, "cannot have a 5' modification on a circular strand") self.modification_5p = mod def set_modification_3p(self, mod: Modification3Prime = None) -> None: - """Sets 3' modification to be `mod`.""" + """Sets 3' modification to be `mod`. `mod` cannot be non-None if :any:`Strand.circular` is True.""" + if self.circular and mod is not None: + raise StrandError(self, "cannot have a 3' modification on a circular strand") self.modification_3p = mod def remove_modification_5p(self) -> None: diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index fc584bd0..bf58fc15 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -3601,6 +3601,46 @@ def set_colors_black(*strands) -> None: strand.set_color(sc.Color(r=0, g=0, b=0)) +class TestCircularStrands(unittest.TestCase): + + def setUp(self) -> None: + helices = [sc.Helix(max_offset=10) for _ in range(2)] + self.design = sc.Design(helices=helices, strands=[]) + self.design.strand(0, 0).move(10).cross(1).move(-10) + self.strand = self.design.strands[0] + r''' + 0 [--------\ + | + 1 <--------/ + ''' + + def test_can_add_internal_mod_to_circular_strand(self) -> None: + self.strand.set_circular() + self.assertEqual(True, self.strand.circular) + self.strand.set_modification_internal(2, mod.biotin_int) + self.assertEqual(1, len(self.strand.modifications_int)) + + def test_cannot_make_strand_circular_if_5p_mod(self) -> None: + self.strand.set_modification_5p(mod.biotin_5p) + with self.assertRaises(sc.StrandError): + self.strand.set_circular(True) + + def test_cannot_make_strand_circular_if_3p_mod(self) -> None: + self.strand.set_modification_3p(mod.biotin_3p) + with self.assertRaises(sc.StrandError): + self.strand.set_circular(True) + + def test_add_5p_mod_to_circular_strand(self) -> None: + self.strand.set_circular(True) + with self.assertRaises(sc.StrandError): + self.strand.set_modification_5p(mod.biotin_5p) + + def test_add_3p_mod_to_circular_strand(self) -> None: + self.strand.set_circular(True) + with self.assertRaises(sc.StrandError): + self.strand.set_modification_3p(mod.biotin_3p) + + class TestAddStrand(unittest.TestCase): def test_add_strand__with_loopout(self) -> None: From 893075f37846b2c153a725f975afb3c76da68765 Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 13 Dec 2020 09:17:16 -0800 Subject: [PATCH 07/18] fixed docstring errors and bumped version --- scadnano/scadnano.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 79fa077d..185c4197 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -44,7 +44,7 @@ # commented out for now to support Py3.6, which does not support this feature # from __future__ import annotations -__version__ = "0.13.0" # version line; WARNING: do not remove or change this line or comment +__version__ = "0.13.1" # version line; WARNING: do not remove or change this line or comment import dataclasses from abc import abstractmethod, ABC, ABCMeta @@ -2529,12 +2529,14 @@ class Strand(_JSONSerializable, Generic[StrandLabel, DomainLabel]): modification_5p: Optional[Modification5Prime] = None """ - 5' modification; None if there is no 5' modification. Illegal to have if :py:`Strand.circular` is True. + 5' modification; None if there is no 5' modification. + Illegal to have if :py:data:`Strand.circular` is True. """ modification_3p: Optional[Modification3Prime] = None """ - 3' modification; None if there is no 3' modification. Illegal to have if :py:`Strand.circular` is True. + 3' modification; None if there is no 3' modification. + Illegal to have if :py:data:`Strand.circular` is True. """ modifications_int: Dict[int, ModificationInternal] = field(default_factory=dict) From 7f5d3c96556721d825dd4ae8f94042369a627214 Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 13 Dec 2020 10:03:42 -0800 Subject: [PATCH 08/18] updated add_half_crossover and add_nick to handle circular strands --- scadnano/scadnano.py | 92 +++++++++++++++++++++++++++++------------ tests/scadnano_tests.py | 63 +++++++++++++++++++++++++++- 2 files changed, 126 insertions(+), 29 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 185c4197..99bdb047 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -5353,6 +5353,10 @@ def add_nick(self, helix: int, offset: int, forward: bool, new_color: bool = Tru :py:data:`Domain.start` = ``5``, :py:data:`Domain.end` = ``10``. + If the :any:`Strand` is circular, then it will be made linear with the 5' and 3' ends at the + nick position, modified in place. Otherwise, this :any:`Strand` will be deleted from the design, + and two new :any:`Strand`'s will be added. + :param helix: index of helix where nick will occur :param offset: offset to nick (nick will be between offset and offset-1) :param forward: forward or reverse :any:`Domain` on `helix` at `offset`? @@ -5376,6 +5380,17 @@ def add_nick(self, helix: int, offset: int, forward: bool, new_color: bool = Tru domain_left: Domain[DomainLabel] = Domain(helix, forward, domain_to_remove.start, offset) domain_right: Domain[DomainLabel] = Domain(helix, forward, offset, domain_to_remove.end) + # "before" and "after" mean in the 5' --> 3' direction, i.e., if a reverse domain: + # <--------] + # nicked like this: + # <---]<---] + # The before domain is on the right and the after domain is on the left. + # + # If nicking a forward domain: + # [--------> + # nicked like this: + # [--->[---> + # The before domain is on the left and the after domain is on the right. if domain_to_remove.forward: domain_to_add_before = domain_left domain_to_add_after = domain_right @@ -5405,28 +5420,45 @@ def add_nick(self, helix: int, offset: int, forward: bool, new_color: bool = Tru seq_before_whole = None seq_after_whole = None - self.strands.remove(strand) + domains_before = domains_before + cast(List[Union[Domain, Loopout]], [domain_to_add_before]) # noqa + domains_after = cast(List[Union[Domain, Loopout]], [domain_to_add_after]) + domains_after # noqa - idt_present = strand.idt is not None - strand_before: Strand[StrandLabel, DomainLabel] = Strand( - domains=domains_before + cast(List[Union[Domain, Loopout]], [domain_to_add_before]), # noqa - dna_sequence=seq_before_whole, - color=strand.color, - idt=strand.idt if idt_present else None, - ) + if strand.circular: + # if strand is circular, we modify its domains in place + domains = domains_after + domains_before + strand.domains = domains - color_after = next(self.color_cycler) if new_color else strand.color - strand_after: Strand[StrandLabel, DomainLabel] = Strand( - domains=cast(List[Union[Domain, Loopout]], [domain_to_add_after]) + domains_after, # noqa - dna_sequence=seq_after_whole, - color=color_after, - use_default_idt=idt_present, - ) + # DNA sequence was rotated, so re-assign it + if seq_before_whole is not None and seq_after_whole is not None: + seq = seq_before_whole + seq_after_whole + strand.set_dna_sequence(seq) - self.helices[helix].domains.remove(domain_to_remove) - self.helices[helix].domains.extend([domain_to_add_before, domain_to_add_after]) + strand.set_circular(False) - self.strands.extend([strand_before, strand_after]) + else: + # if strand is not circular, we delete it and create two new strands + self.strands.remove(strand) + + idt_present = strand.idt is not None + strand_before: Strand[StrandLabel, DomainLabel] = Strand( + domains=domains_before, + dna_sequence=seq_before_whole, + color=strand.color, + idt=strand.idt if idt_present else None, + ) + + color_after = next(self.color_cycler) if new_color else strand.color + strand_after: Strand[StrandLabel, DomainLabel] = Strand( + domains=domains_after, + dna_sequence=seq_after_whole, + color=color_after, + use_default_idt=idt_present, + ) + + self.helices[helix].domains.remove(domain_to_remove) + self.helices[helix].domains.extend([domain_to_add_before, domain_to_add_after]) + + self.strands.extend([strand_before, strand_after]) def add_half_crossover(self, helix: int, helix2: int, offset: int, forward: bool, offset2: int = None, forward2: bool = None) -> None: @@ -5438,6 +5470,10 @@ def add_half_crossover(self, helix: int, helix2: int, offset: int, forward: bool half-crossovers, to call this method, there must *already* be nicks adjacent to the given offsets on the given helices. (either on the left or right side) + If the crossover is within a :any:`Strand`, i.e., between its 5' and ' ends, the :any:`Strand` + will simply be made circular, modifying it in place. Otherwise, the old two :any:`Strand`'s will be + deleted, and a new :any:`Strand` added. + :param helix: index of one helix of half crossover :param helix2: index of other helix of half crossover :param offset: offset on `helix` at which to add half crossover @@ -5465,15 +5501,17 @@ def add_half_crossover(self, helix: int, helix2: int, offset: int, forward: bool strand2 = domain2.strand() if strand1 == strand2: - raise IllegalDesignError(f"Cannot add crossover from " - f"(helix={helix}, offset={offset}) to " - f"(helix={helix2}, offset={offset2}) " - f"because that would join two Domains " - f"already on the same Strand! " - f"Currently circular Strands are not supported. " - f"Instead, try adding nicks first, or rearrange the order of " - f"crossover addition, to ensure that all strands are " - f"non-circular, even in intermediate stages.") + strand1.set_circular() + return + # raise IllegalDesignError(f"Cannot add crossover from " + # f"(helix={helix}, offset={offset}) to " + # f"(helix={helix2}, offset={offset2}) " + # f"because that would join two Domains " + # f"already on the same Strand! " + # f"Currently circular Strands are not supported. " + # f"Instead, try adding nicks first, or rearrange the order of " + # f"crossover addition, to ensure that all strands are " + # f"non-circular, even in intermediate stages.") if domain1.offset_3p() == offset and domain2.offset_5p() == offset2: strand_first = strand1 diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index bf58fc15..841f93e0 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -3601,7 +3601,10 @@ def set_colors_black(*strands) -> None: strand.set_color(sc.Color(r=0, g=0, b=0)) -class TestCircularStrands(unittest.TestCase): +class TestCircularStrandsLegalMods(unittest.TestCase): + ''' + Tests that circular strands cannot have 5' or 3' mods. + ''' def setUp(self) -> None: helices = [sc.Helix(max_offset=10) for _ in range(2)] @@ -3616,7 +3619,7 @@ def setUp(self) -> None: def test_can_add_internal_mod_to_circular_strand(self) -> None: self.strand.set_circular() - self.assertEqual(True, self.strand.circular) + self.assertTrue(self.strand.circular) self.strand.set_modification_internal(2, mod.biotin_int) self.assertEqual(1, len(self.strand.modifications_int)) @@ -3641,6 +3644,62 @@ def test_add_3p_mod_to_circular_strand(self) -> None: self.strand.set_modification_3p(mod.biotin_3p) +class TestCircularStrandEdits(unittest.TestCase): + ''' + Tests that circular strand edits (nicking, ligating, adding crossovers/loopouts) + works properly with circular strands. + ''' + + def setUp(self) -> None: + helices = [sc.Helix(max_offset=10) for _ in range(2)] + self.design = sc.Design(helices=helices, strands=[]) + self.design.strand(0, 0).move(10).cross(1).move(-10) + self.design.strand(0, 15).move(5).cross(1).move(-10).cross(0).move(5) + self.design.strand(0, 20).move(10) + self.design.strand(1, 30).move(-10) + self.design.strand(0, 30).move(10).loopout(1, 5).move(-10) + self.design.strand(0, 40).move(10).cross(1).move(-10).as_circular() + self.num_strands = len(self.design.strands) + r''' + 0 10 20 30 40 + strand 0 strand 1 strand 2 strand 4 strand 5 + 0 [--------\ /--->[---\ [--------> [--------\ /--------\ + | | | ) | | + 1 <--------/ \--------/ <--------] <--------/ \--------/ + strand 3 + ''' + + def test_add_crossover_from_linear_strand_to_itself_makes_it_circular(self) -> None: + self.design.add_half_crossover(0, 1, 0, True) + self.assertTrue(self.design.strands[0].circular) + self.assertEqual(self.num_strands, len(self.design.strands)) + + def test_add_nick_to_circular_strand_makes_it_linear(self) -> None: + self.design.add_nick(0, 45, True) + self.assertFalse(self.design.strands[5].circular) + self.assertEqual(self.num_strands, len(self.design.strands)) + + strand = self.design.strands[5] + self.assertEqual(3, len(strand.domains)) + self.assertEqual(3, len(strand.bound_domains())) + + d0, d1, d2 = strand.bound_domains() + self.assertEqual(0, d0.helix) + self.assertEqual(True, d0.forward) + self.assertEqual(45, d0.start) + self.assertEqual(50, d0.end) + + self.assertEqual(1, d1.helix) + self.assertEqual(False, d1.forward) + self.assertEqual(40, d1.start) + self.assertEqual(50, d1.end) + + self.assertEqual(0, d2.helix) + self.assertEqual(True, d2.forward) + self.assertEqual(40, d2.start) + self.assertEqual(45, d2.end) + + class TestAddStrand(unittest.TestCase): def test_add_strand__with_loopout(self) -> None: From 84db6a8bc93cbdde38daa02d2e640193c721d937 Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 13 Dec 2020 17:31:47 -0800 Subject: [PATCH 09/18] added ligate method to design and associated unit tests --- scadnano/scadnano.py | 136 ++++++++++++- tests/scadnano_tests.py | 430 +++++++++++++++++++++++++++------------- 2 files changed, 424 insertions(+), 142 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 99bdb047..e4055952 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -5433,7 +5433,7 @@ def add_nick(self, helix: int, offset: int, forward: bool, new_color: bool = Tru seq = seq_before_whole + seq_after_whole strand.set_dna_sequence(seq) - strand.set_circular(False) + strand.set_linear() else: # if strand is not circular, we delete it and create two new strands @@ -5455,11 +5455,139 @@ def add_nick(self, helix: int, offset: int, forward: bool, new_color: bool = Tru use_default_idt=idt_present, ) - self.helices[helix].domains.remove(domain_to_remove) - self.helices[helix].domains.extend([domain_to_add_before, domain_to_add_after]) - self.strands.extend([strand_before, strand_after]) + helix_domains = self.helices[helix].domains + idx_domain_to_remove = helix_domains.index(domain_to_remove) + helix_domains[idx_domain_to_remove] = domain_left + helix_domains.insert(idx_domain_to_remove + 1, domain_right) + + def ligate(self, helix: int, offset: int, forward: bool) -> None: + """ + Reverse operation of :py:meth:`Design.add_nick`. + "Ligates" a nick between two adjacent :any:`Domain`'s in the same direction on a :any:`Helix` + with index `helix`, + in direction given by `forward`, at offset `offset`. + + For example, if there are a :any:`Domain`'s with + :py:data:`Domain.helix` = ``0``, + :py:data:`Domain.forward` = ``True``, + :py:data:`Domain.start` = ``0``, + :py:data:`Domain.end` = ``5``, + (recall that :py:data:`Domain.end` is exclusive, meaning that the largest offset on this + :any:`Domain` is 4 = ``offset-1``) + and the other domain having the fields + :py:data:`Domain.helix` = ``0``, + :py:data:`Domain.forward` = ``True``, + :py:data:`Domain.start` = ``5``, + :py:data:`Domain.end` = ``10``. + then calling ``ligate(helix=0, offset=5, forward=True)`` will combine them into one :any:`Domain`, + having the fields + :py:data:`Domain.helix` = ``0``, + :py:data:`Domain.forward` = ``True``, + :py:data:`Domain.start` = ``0``, + :py:data:`Domain.end` = ``10``. + + If the :any:`Domain`'s are on the same :any:`Strand` (i.e., they are the 5' and 3' ends of that + :any:`Strand`, which is necessarily linear), then the :any:`Strand` is made is circular in place, + Otherwise, the two :any:`Strand`'s of each :any:`Domain` will be joined into one, + replacing the previous strand on the 5'-most side of the nick (i.e., the one whose 3' end + terminated at the nick), and deleting the other strand. + + :param helix: index of helix where nick will be ligated + :param offset: offset to ligate (nick to ligate must be between offset and offset-1) + :param forward: forward or reverse :any:`Domain` on `helix` at `offset`? + """ + for dom_right in self.domains_at(helix, offset): + if dom_right.forward == forward: + break + else: + raise IllegalDesignError(f'no domain at helix {helix} in direction ' + f'{"forward" if forward else "reverse"} at offset {offset}') + for dom_left in self.domains_at(helix, offset - 1): + if dom_left.forward == forward: + break + else: + raise IllegalDesignError(f'no domain at helix {helix} in direction ' + f'{"forward" if forward else "reverse"} at offset {offset}') + if dom_right.start != offset: + raise IllegalDesignError(f'to ligate at offset {offset}, it must be the start offset of a domain,' + f'but there is no domain at helix {helix} in direction ' + f'{"forward" if forward else "reverse"} with start offset = {offset}') + if dom_left.end != offset: + raise IllegalDesignError(f'to ligate at offset {offset}, it must be the end offset of a domain,' + f'but there is no domain at helix {helix} in direction ' + f'{"forward" if forward else "reverse"} with end offset = {offset}') + + strand_left = dom_left.strand() + strand_right = dom_right.strand() + + dom_new = Domain(helix=helix, forward=forward, start=dom_left.start, end=dom_right.end, + deletions=dom_left.deletions + dom_right.deletions, + insertions=dom_left.insertions + dom_right.insertions, + name=dom_left.name, label=dom_left.label) + + # normalize 5'/3' distinction; below refers to which Strand has the 5'/3' end that will be ligated + # So strand_5p is the one whose 3' end will be the 3' end of the whole new Strand + # strand_5p and dom_5p are the ones on the 5' side of the nick, + # CAUTION: they are on the 3' side of the nick, + # i.e., the 3' end of strand_5p will be the 3' end of the new strand + # e.g., + # + # strand_3p strand_5p + # [--------->[---------> + # dom_3p dom_5p + # + # or + # + # strand_5p strand_3p + # <---------]<---------] + # dom_5p dom_3p + if not forward: + dom_5p = dom_left + dom_3p = dom_right + strand_5p = strand_left + strand_3p = strand_right + else: + dom_5p = dom_right + dom_3p = dom_left + strand_5p = strand_right + strand_3p = strand_left + + if strand_left is strand_right: + # join domains and make strand circular + strand = strand_left + assert strand.first_bound_domain() is dom_5p + assert strand.last_bound_domain() is dom_3p + strand.domains[0] = dom_new # set first domain equal to new joined domain + strand.domains.pop() # remove last domain + strand.set_circular() + for domain in strand.domains: + domain._parent_strand = strand + + else: + # join strands + strand_3p.domains.pop() + strand_3p.domains.append(dom_new) + strand_3p.domains.extend(strand_5p.domains[1:]) + strand_3p.is_scaffold = strand_left.is_scaffold or strand_right.is_scaffold + strand_3p.set_modification_3p(strand_5p.modification_3p) + for idx, mod in strand_5p.modifications_int.items(): + new_idx = idx + strand_3p.dna_length() + strand_3p.set_modification_internal(new_idx, mod) + if strand_3p.dna_sequence is not None and strand_5p.dna_sequence is not None: + strand_3p.dna_sequence += strand_5p.dna_sequence + if strand_5p.is_scaffold and not strand_3p.is_scaffold and strand_5p.color is not None: + strand_3p.set_color(strand_5p.color) + self.strands.remove(strand_5p) + for domain in strand_3p.domains: + domain._parent_strand = strand_3p + + helix_domains = self.helices[helix].domains + idx_domain_to_remove_left = helix_domains.index(dom_left) + helix_domains[idx_domain_to_remove_left] = dom_new + helix_domains.remove(dom_right) + def add_half_crossover(self, helix: int, helix2: int, offset: int, forward: bool, offset2: int = None, forward2: bool = None) -> None: """ diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 841f93e0..99c6e85e 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -1652,9 +1652,9 @@ def test_inline_deletions_insertions__deletions_insertions_in_multiple_domains_t self.assertListEqual([], strand1.domains[0].insertions) -class TestNickAndCrossover(unittest.TestCase): +class TestNickLigateAndCrossover(unittest.TestCase): """ - Tests add_nick() and add_*_crossover() methods on Design as an easier way of specifying an origami. + Tests add_nick(), ligate(), add_*_crossover(), and remove_*_crossover() methods on Design """ r""" @@ -1669,6 +1669,19 @@ class TestNickAndCrossover(unittest.TestCase): 1 [------- -------> <------- -------] TTTGGGCC AAACCCGG + + + small_nicked_design + 0 8 16 + ACGTACGA AACCGGTA +0 [------> [------> + <------] <------] + TGCATGCT TTGGCCAT + + AAACCCGG TTTGGGCC +1 [------> [------> + <------] <------] + TTTGGGCC AAACCCGG design: @@ -1693,6 +1706,7 @@ class TestNickAndCrossover(unittest.TestCase): """ def setUp(self) -> None: + # small design strands_small_design = [ sc.Strand([sc.Domain(0, True, 0, 16)]), sc.Strand([sc.Domain(0, False, 0, 16)]), @@ -1703,6 +1717,26 @@ def setUp(self) -> None: self.small_design.assign_dna(strands_small_design[0], "ACGTACGA AACCGGTA") self.small_design.assign_dna(strands_small_design[2], "AAACCCGG TTTGGGCC") + # small nicked design + small_nicked_helices = [sc.Helix(max_offset=100) for _ in range(2)] + self.small_nicked_design = sc.Design(helices=small_nicked_helices, grid=sc.square) + # forward strands + self.small_nicked_design.strand(0, 0).move(8) + self.small_nicked_design.strand(0, 8).move(8) + self.small_nicked_design.strand(1, 0).move(8) + self.small_nicked_design.strand(1, 8).move(8) + # reverse strands + self.small_nicked_design.strand(0, 8).move(-8) + self.small_nicked_design.strand(0, 16).move(-8) + self.small_nicked_design.strand(1, 8).move(-8) + self.small_nicked_design.strand(1, 16).move(-8) + + self.small_nicked_design.assign_dna(self.small_nicked_design.strands[0], "ACGTACGA") + self.small_nicked_design.assign_dna(self.small_nicked_design.strands[1], "AACCGGTA") + self.small_nicked_design.assign_dna(self.small_nicked_design.strands[2], "AAACCCGG") + self.small_nicked_design.assign_dna(self.small_nicked_design.strands[3], "TTTGGGCC") + + # origami self.max_offset: int = 8 * 12 scafs = [] staps = [] @@ -1713,7 +1747,7 @@ def setUp(self) -> None: stap = sc.Strand([stap_ss]) scafs.append(scaf) staps.append(stap) - self.design: sc.Design = sc.Design(strands=scafs + staps, grid=sc.square) + self.origami: sc.Design = sc.Design(strands=scafs + staps, grid=sc.square) def test_add_nick__twice_on_same_domain(self) -> None: """ @@ -1735,7 +1769,26 @@ def test_add_nick__twice_on_same_domain(self) -> None: self.assertIn(sc.Strand([sc.Domain(0, True, 8, 16)]), design.strands) self.assertIn(sc.Strand([sc.Domain(0, True, 16, 24)]), design.strands) - def test_add_nick__small_design_no_nicks_added(self) -> None: + def test_ligate__twice_on_same_domain(self) -> None: + """ + before + 0 8 16 24 + 0 [------> [------> [------> + + after + 0 8 16 24 + 0 [------- -------- -------> + """ + design = sc.Design(helices=[sc.Helix(max_offset=24)], grid=sc.square) + design.strand(0, 0).move(8) + design.strand(0, 8).move(8) + design.strand(0, 16).move(8) + design.ligate(helix=0, offset=8, forward=True) + design.ligate(helix=0, offset=16, forward=True) + self.assertEqual(1, len(design.strands)) + self.assertIn(sc.Strand([sc.Domain(0, True, 0, 24)]), design.strands) + + def test_add_nick__small_design_no_nicks_added_yet(self) -> None: """ 0 8 16 ACGTACGA AACCGGTA @@ -1763,6 +1816,51 @@ def test_add_nick__small_design_no_nicks_added(self) -> None: strand = strand_matching(self.small_design.strands, 1, False, 0, 16) self.assertEqual(remove_whitespace('GGCCCAAA CCGGGTTT'), strand.dna_sequence) + def test_ligate__small_nicked_design_no_ligation_yet(self) -> None: + """ + 0 8 16 + ACGTACGA AACCGGTA + 0 [------> [------> + <------] <------] + TGCATGCT TTGGCCAT + + AAACCCGG TTTGGGCC + 1 [------> [------> + <------] <------] + TTTGGGCC AAACCCGG + """ + design = self.small_nicked_design + self.assertEqual(8, len(design.strands)) + self.assertIn(sc.Strand([sc.Domain(0, True, 0, 8)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(0, False, 0, 8)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, True, 0, 8)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, False, 0, 8)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(0, True, 8, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(0, False, 8, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, True, 8, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, False, 8, 16)]), design.strands) + # DNA + strand = strand_matching(design.strands, 0, True, 0, 8) + self.assertEqual(remove_whitespace('ACGTACGA'), strand.dna_sequence) + strand = strand_matching(design.strands, 0, True, 8, 16) + self.assertEqual(remove_whitespace('AACCGGTA'), strand.dna_sequence) + + strand = strand_matching(design.strands, 0, False, 0, 8) + self.assertEqual(remove_whitespace('TCGTACGT'), strand.dna_sequence) + strand = strand_matching(design.strands, 0, False, 8, 16) + self.assertEqual(remove_whitespace('TACCGGTT'), strand.dna_sequence) + + strand = strand_matching(design.strands, 1, True, 0, 8) + self.assertEqual(remove_whitespace('AAACCCGG'), strand.dna_sequence) + strand = strand_matching(design.strands, 1, True, 8, 16) + self.assertEqual(remove_whitespace('TTTGGGCC'), strand.dna_sequence) + + strand = strand_matching(design.strands, 1, False, 0, 8) + self.assertEqual(remove_whitespace('CCGGGTTT'), strand.dna_sequence) + strand = strand_matching(design.strands, 1, False, 8, 16) + self.assertEqual(remove_whitespace('GGCCCAAA'), strand.dna_sequence) + + def test_add_nick__small_design_H0_forward(self) -> None: """ 0 8 16 @@ -1776,27 +1874,64 @@ def test_add_nick__small_design_H0_forward(self) -> None: <------- -------] TTTGGGCC AAACCCGG """ - self.small_design.add_nick(helix=0, offset=8, forward=True) - self.assertEqual(5, len(self.small_design.strands)) + + design = self.small_design + design.add_nick(helix=0, offset=8, forward=True) + self.assertEqual(5, len(design.strands)) # two new Strands - self.assertIn(sc.Strand([sc.Domain(0, True, 0, 8)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(0, True, 8, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(0, True, 0, 8)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(0, True, 8, 16)]), design.strands) # existing Strands - self.assertIn(sc.Strand([sc.Domain(0, False, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(1, True, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(0, False, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, True, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), design.strands) # DNA - strand = strand_matching(self.small_design.strands, 0, True, 0, 8) + strand = strand_matching(design.strands, 0, True, 0, 8) self.assertEqual(remove_whitespace('ACGTACGA'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 0, True, 8, 16) + strand = strand_matching(design.strands, 0, True, 8, 16) self.assertEqual(remove_whitespace('AACCGGTA'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 0, False, 0, 16) + strand = strand_matching(design.strands, 0, False, 0, 16) self.assertEqual(remove_whitespace('TACCGGTT TCGTACGT'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, True, 0, 16) + strand = strand_matching(design.strands, 1, True, 0, 16) self.assertEqual(remove_whitespace('AAACCCGG TTTGGGCC'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, False, 0, 16) + strand = strand_matching(design.strands, 1, False, 0, 16) + self.assertEqual(remove_whitespace('GGCCCAAA CCGGGTTT'), strand.dna_sequence) + + + def test_ligate__small_nicked_design_ligate_all(self) -> None: + """ + 0 8 16 + ACGTACGA AACCGGTA + 0 [------- -------> + <------- -------] + TGCATGCT TTGGCCAT + + AAACCCGG TTTGGGCC + 1 [------- -------> + <------- -------] + TTTGGGCC AAACCCGG + """ + design = self.small_nicked_design + design.ligate(0, 8, True) + design.ligate(0, 8, False) + design.ligate(1, 8, True) + design.ligate(1, 8, False) + self.assertEqual(4, len(design.strands)) + self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(0, False, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, True, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), design.strands) + # DNA + strand = strand_matching(design.strands, 0, True, 0, 16) + self.assertEqual(remove_whitespace('ACGTACGA AACCGGTA'), strand.dna_sequence) + strand = strand_matching(design.strands, 0, False, 0, 16) + self.assertEqual(remove_whitespace('TACCGGTT TCGTACGT'), strand.dna_sequence) + strand = strand_matching(design.strands, 1, True, 0, 16) + self.assertEqual(remove_whitespace('AAACCCGG TTTGGGCC'), strand.dna_sequence) + strand = strand_matching(design.strands, 1, False, 0, 16) self.assertEqual(remove_whitespace('GGCCCAAA CCGGGTTT'), strand.dna_sequence) + def test_add_nick__small_design_H0_reverse(self) -> None: """ 0 8 16 @@ -1810,25 +1945,26 @@ def test_add_nick__small_design_H0_reverse(self) -> None: <------- -------] TTTGGGCC AAACCCGG """ - self.small_design.add_nick(helix=0, offset=8, forward=False) - self.assertEqual(5, len(self.small_design.strands)) + design = self.small_design + design.add_nick(helix=0, offset=8, forward=False) + self.assertEqual(5, len(design.strands)) # two new Strands - self.assertIn(sc.Strand([sc.Domain(0, False, 0, 8)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(0, False, 8, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(0, False, 0, 8)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(0, False, 8, 16)]), design.strands) # existing Strands - self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(1, True, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, True, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), design.strands) # DNA - strand = strand_matching(self.small_design.strands, 0, True, 0, 16) + strand = strand_matching(design.strands, 0, True, 0, 16) self.assertEqual(remove_whitespace('ACGTACGA AACCGGTA'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 0, False, 8, 16) + strand = strand_matching(design.strands, 0, False, 8, 16) self.assertEqual(remove_whitespace('TACCGGTT'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 0, False, 0, 8) + strand = strand_matching(design.strands, 0, False, 0, 8) self.assertEqual(remove_whitespace('TCGTACGT'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, True, 0, 16) + strand = strand_matching(design.strands, 1, True, 0, 16) self.assertEqual(remove_whitespace('AAACCCGG TTTGGGCC'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, False, 0, 16) + strand = strand_matching(design.strands, 1, False, 0, 16) self.assertEqual(remove_whitespace('GGCCCAAA CCGGGTTT'), strand.dna_sequence) def test_add_nick__small_design_H1_forward(self) -> None: @@ -1844,25 +1980,26 @@ def test_add_nick__small_design_H1_forward(self) -> None: <------- -------] TTTGGGCC AAACCCGG """ - self.small_design.add_nick(helix=1, offset=8, forward=True) - self.assertEqual(5, len(self.small_design.strands)) + design = self.small_design + design.add_nick(helix=1, offset=8, forward=True) + self.assertEqual(5, len(design.strands)) # two new Strands - self.assertIn(sc.Strand([sc.Domain(1, True, 0, 8)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(1, True, 8, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(1, True, 0, 8)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, True, 8, 16)]), design.strands) # existing Strands - self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(0, False, 0, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(0, False, 0, 16)]), design.strands) # DNA - strand = strand_matching(self.small_design.strands, 0, True, 0, 16) + strand = strand_matching(design.strands, 0, True, 0, 16) self.assertEqual(remove_whitespace('ACGTACGA AACCGGTA'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 0, False, 0, 16) + strand = strand_matching(design.strands, 0, False, 0, 16) self.assertEqual(remove_whitespace('TACCGGTT TCGTACGT'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, True, 0, 8) + strand = strand_matching(design.strands, 1, True, 0, 8) self.assertEqual(remove_whitespace('AAACCCGG'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, True, 8, 16) + strand = strand_matching(design.strands, 1, True, 8, 16) self.assertEqual(remove_whitespace('TTTGGGCC'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, False, 0, 16) + strand = strand_matching(design.strands, 1, False, 0, 16) self.assertEqual(remove_whitespace('GGCCCAAA CCGGGTTT'), strand.dna_sequence) def test_add_nick__small_design_H1_reverse(self) -> None: @@ -1878,25 +2015,26 @@ def test_add_nick__small_design_H1_reverse(self) -> None: <------] <------] TTTGGGCC AAACCCGG """ - self.small_design.add_nick(helix=1, offset=8, forward=False) - self.assertEqual(5, len(self.small_design.strands)) + design = self.small_design + design.add_nick(helix=1, offset=8, forward=False) + self.assertEqual(5, len(design.strands)) # two new Strands - self.assertIn(sc.Strand([sc.Domain(1, False, 0, 8)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(1, False, 8, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(1, False, 0, 8)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, False, 8, 16)]), design.strands) # existing Strands - self.assertIn(sc.Strand([sc.Domain(1, True, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(0, False, 0, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(1, True, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(0, False, 0, 16)]), design.strands) # DNA - strand = strand_matching(self.small_design.strands, 0, True, 0, 16) + strand = strand_matching(design.strands, 0, True, 0, 16) self.assertEqual(remove_whitespace('ACGTACGA AACCGGTA'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 0, False, 0, 16) + strand = strand_matching(design.strands, 0, False, 0, 16) self.assertEqual(remove_whitespace('TACCGGTT TCGTACGT'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, True, 0, 16) + strand = strand_matching(design.strands, 1, True, 0, 16) self.assertEqual(remove_whitespace('AAACCCGG TTTGGGCC'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, False, 0, 8) + strand = strand_matching(design.strands, 1, False, 0, 8) self.assertEqual(remove_whitespace('CCGGGTTT'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, False, 8, 16) + strand = strand_matching(design.strands, 1, False, 8, 16) self.assertEqual(remove_whitespace('GGCCCAAA'), strand.dna_sequence) def test_add_full_crossover__small_design_H0_forward(self) -> None: @@ -1912,28 +2050,29 @@ def test_add_full_crossover__small_design_H0_forward(self) -> None: <------+ +------] TTTGGGCC AAACCCGG """ - self.small_design.add_full_crossover(helix=0, helix2=1, offset=8, forward=True) - self.assertEqual(4, len(self.small_design.strands)) + design = self.small_design + design.add_full_crossover(helix=0, helix2=1, offset=8, forward=True) + self.assertEqual(4, len(design.strands)) # two new Strands self.assertIn(sc.Strand([ sc.Domain(0, True, 0, 8), sc.Domain(1, False, 0, 8), - ]), self.small_design.strands) + ]), design.strands) self.assertIn(sc.Strand([ sc.Domain(1, False, 8, 16), sc.Domain(0, True, 8, 16), - ]), self.small_design.strands) + ]), design.strands) # existing Strands - self.assertIn(sc.Strand([sc.Domain(0, False, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(1, True, 0, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(0, False, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, True, 0, 16)]), design.strands) # DNA - strand = strand_matching(self.small_design.strands, 0, False, 0, 16) + strand = strand_matching(design.strands, 0, False, 0, 16) self.assertEqual(remove_whitespace('TACCGGTT TCGTACGT'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, True, 0, 16) + strand = strand_matching(design.strands, 1, True, 0, 16) self.assertEqual(remove_whitespace('AAACCCGG TTTGGGCC'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 0, True, 0, 8) + strand = strand_matching(design.strands, 0, True, 0, 8) self.assertEqual(remove_whitespace('ACGTACGA CCGGGTTT'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, False, 8, 16) + strand = strand_matching(design.strands, 1, False, 8, 16) self.assertEqual(remove_whitespace('GGCCCAAA AACCGGTA'), strand.dna_sequence) def test_add_full_crossover__small_design_H0_reverse(self) -> None: @@ -1949,28 +2088,29 @@ def test_add_full_crossover__small_design_H0_reverse(self) -> None: <------- -------] TTTGGGCC AAACCCGG """ - self.small_design.add_full_crossover(helix=0, helix2=1, offset=8, forward=False) - self.assertEqual(4, len(self.small_design.strands)) + design = self.small_design + design.add_full_crossover(helix=0, helix2=1, offset=8, forward=False) + self.assertEqual(4, len(design.strands)) # two new Strands self.assertIn(sc.Strand([ sc.Domain(1, True, 0, 8), sc.Domain(0, False, 0, 8), - ]), self.small_design.strands) + ]), design.strands) self.assertIn(sc.Strand([ sc.Domain(0, False, 8, 16), sc.Domain(1, True, 8, 16), - ]), self.small_design.strands) + ]), design.strands) # existing Strands - self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), design.strands) # DNA - strand = strand_matching(self.small_design.strands, 0, True, 0, 16) + strand = strand_matching(design.strands, 0, True, 0, 16) self.assertEqual(remove_whitespace('ACGTACGA AACCGGTA'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 0, False, 8, 16) + strand = strand_matching(design.strands, 0, False, 8, 16) self.assertEqual(remove_whitespace('TACCGGTT TTTGGGCC'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, True, 0, 8) + strand = strand_matching(design.strands, 1, True, 0, 8) self.assertEqual(remove_whitespace('AAACCCGG TCGTACGT'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, False, 0, 16) + strand = strand_matching(design.strands, 1, False, 0, 16) self.assertEqual(remove_whitespace('GGCCCAAA CCGGGTTT'), strand.dna_sequence) def test_add_half_crossover__small_design_H0_reverse_8(self) -> None: @@ -1986,34 +2126,35 @@ def test_add_half_crossover__small_design_H0_reverse_8(self) -> None: <------- -------] TTTGGGCC AAACCCGG """ - self.small_design.add_nick(helix=0, offset=8, forward=False) - self.small_design.add_nick(helix=1, offset=8, forward=True) - self.small_design.add_half_crossover(helix=0, helix2=1, offset=8, forward=False) - self.assertEqual(5, len(self.small_design.strands)) + design = self.small_design + design.add_nick(helix=0, offset=8, forward=False) + design.add_nick(helix=1, offset=8, forward=True) + design.add_half_crossover(helix=0, helix2=1, offset=8, forward=False) + self.assertEqual(5, len(design.strands)) # three new Strands self.assertIn(sc.Strand([ sc.Domain(1, True, 0, 8), - ]), self.small_design.strands) + ]), design.strands) self.assertIn(sc.Strand([ sc.Domain(0, False, 0, 8), - ]), self.small_design.strands) + ]), design.strands) self.assertIn(sc.Strand([ sc.Domain(0, False, 8, 16), sc.Domain(1, True, 8, 16), - ]), self.small_design.strands) + ]), design.strands) # existing Strands - self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), design.strands) # DNA - strand = strand_matching(self.small_design.strands, 0, True, 0, 16) + strand = strand_matching(design.strands, 0, True, 0, 16) self.assertEqual(remove_whitespace('ACGTACGA AACCGGTA'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 0, False, 8, 16) + strand = strand_matching(design.strands, 0, False, 8, 16) self.assertEqual(remove_whitespace('TACCGGTT TTTGGGCC'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 0, False, 0, 8) + strand = strand_matching(design.strands, 0, False, 0, 8) self.assertEqual(remove_whitespace('TCGTACGT'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, True, 0, 8) + strand = strand_matching(design.strands, 1, True, 0, 8) self.assertEqual(remove_whitespace('AAACCCGG'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, False, 0, 16) + strand = strand_matching(design.strands, 1, False, 0, 16) self.assertEqual(remove_whitespace('GGCCCAAA CCGGGTTT'), strand.dna_sequence) def test_add_half_crossover__small_design_H0_reverse_0(self) -> None: @@ -2029,22 +2170,23 @@ def test_add_half_crossover__small_design_H0_reverse_0(self) -> None: <------- -------] TTTGGGCC AAACCCGG """ - self.small_design.add_half_crossover(helix=0, helix2=1, offset=0, forward=False) - self.assertEqual(3, len(self.small_design.strands)) + design = self.small_design + design.add_half_crossover(helix=0, helix2=1, offset=0, forward=False) + self.assertEqual(3, len(design.strands)) # one new Strand self.assertIn(sc.Strand([ sc.Domain(0, False, 0, 16), sc.Domain(1, True, 0, 16), - ]), self.small_design.strands) + ]), design.strands) # existing Strands - self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), design.strands) # DNA - strand = strand_matching(self.small_design.strands, 0, True, 0, 16) + strand = strand_matching(design.strands, 0, True, 0, 16) self.assertEqual(remove_whitespace('ACGTACGA AACCGGTA'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 0, False, 0, 16) + strand = strand_matching(design.strands, 0, False, 0, 16) self.assertEqual(remove_whitespace('TACCGGTT TCGTACGT AAACCCGG TTTGGGCC'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, False, 0, 16) + strand = strand_matching(design.strands, 1, False, 0, 16) self.assertEqual(remove_whitespace('GGCCCAAA CCGGGTTT'), strand.dna_sequence) def test_add_half_crossover__small_design_H0_reverse_15(self) -> None: @@ -2060,22 +2202,23 @@ def test_add_half_crossover__small_design_H0_reverse_15(self) -> None: <------- -------] TTTGGGCC AAACCCGG """ - self.small_design.add_half_crossover(helix=0, helix2=1, offset=15, forward=False) - self.assertEqual(3, len(self.small_design.strands)) + design = self.small_design + design.add_half_crossover(helix=0, helix2=1, offset=15, forward=False) + self.assertEqual(3, len(design.strands)) # one new Strand self.assertIn(sc.Strand([ sc.Domain(1, True, 0, 16), sc.Domain(0, False, 0, 16), - ]), self.small_design.strands) + ]), design.strands) # existing Strands - self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), self.small_design.strands) - self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), self.small_design.strands) + self.assertIn(sc.Strand([sc.Domain(0, True, 0, 16)]), design.strands) + self.assertIn(sc.Strand([sc.Domain(1, False, 0, 16)]), design.strands) # DNA - strand = strand_matching(self.small_design.strands, 0, True, 0, 16) + strand = strand_matching(design.strands, 0, True, 0, 16) self.assertEqual(remove_whitespace('ACGTACGA AACCGGTA'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, True, 0, 16) + strand = strand_matching(design.strands, 1, True, 0, 16) self.assertEqual(remove_whitespace('AAACCCGG TTTGGGCC TACCGGTT TCGTACGT'), strand.dna_sequence) - strand = strand_matching(self.small_design.strands, 1, False, 0, 16) + strand = strand_matching(design.strands, 1, False, 0, 16) self.assertEqual(remove_whitespace('GGCCCAAA CCGGGTTT'), strand.dna_sequence) def test_add_half_crossover__small_design_illegal(self) -> None: @@ -2158,24 +2301,24 @@ def add_nicks(design: sc.Design): design.add_nick(helix=5, offset=56, forward=True) def test_add_nick__6_helix_rectangle(self) -> None: - self.add_nicks(self.design) - self.assertEqual(25, len(self.design.strands)) - for helix in range(0, len(self.design.helices), 2): + self.add_nicks(self.origami) + self.assertEqual(25, len(self.origami.strands)) + for helix in range(0, len(self.origami.helices), 2): # even helix - self.assertIn(sc.Strand([sc.Domain(helix, True, 0, 96)]), self.design.strands) - self.assertIn(sc.Strand([sc.Domain(helix, False, 0, 40)]), self.design.strands) - self.assertIn(sc.Strand([sc.Domain(helix, False, 40, 72)]), self.design.strands) - self.assertIn(sc.Strand([sc.Domain(helix, False, 72, 96)]), self.design.strands) + self.assertIn(sc.Strand([sc.Domain(helix, True, 0, 96)]), self.origami.strands) + self.assertIn(sc.Strand([sc.Domain(helix, False, 0, 40)]), self.origami.strands) + self.assertIn(sc.Strand([sc.Domain(helix, False, 40, 72)]), self.origami.strands) + self.assertIn(sc.Strand([sc.Domain(helix, False, 72, 96)]), self.origami.strands) # odd helix - if helix + 1 < len(self.design.helices) - 1: - self.assertIn(sc.Strand([sc.Domain(helix + 1, False, 0, 96)]), self.design.strands) + if helix + 1 < len(self.origami.helices) - 1: + self.assertIn(sc.Strand([sc.Domain(helix + 1, False, 0, 96)]), self.origami.strands) else: # nick in scaffold on bottom helix - self.assertIn(sc.Strand([sc.Domain(helix + 1, False, 0, 48)]), self.design.strands) - self.assertIn(sc.Strand([sc.Domain(helix + 1, False, 48, 96)]), self.design.strands) - self.assertIn(sc.Strand([sc.Domain(helix + 1, True, 0, 24)]), self.design.strands) - self.assertIn(sc.Strand([sc.Domain(helix + 1, True, 24, 56)]), self.design.strands) - self.assertIn(sc.Strand([sc.Domain(helix + 1, True, 56, 96)]), self.design.strands) + self.assertIn(sc.Strand([sc.Domain(helix + 1, False, 0, 48)]), self.origami.strands) + self.assertIn(sc.Strand([sc.Domain(helix + 1, False, 48, 96)]), self.origami.strands) + self.assertIn(sc.Strand([sc.Domain(helix + 1, True, 0, 24)]), self.origami.strands) + self.assertIn(sc.Strand([sc.Domain(helix + 1, True, 24, 56)]), self.origami.strands) + self.assertIn(sc.Strand([sc.Domain(helix + 1, True, 56, 96)]), self.origami.strands) # TODO: re-write this test after support for circular Strands is added and test making crossovers first r""" @@ -2233,10 +2376,10 @@ def add_crossovers_after_nicks(design: sc.Design): design.add_half_crossover(helix=4, helix2=5, offset=95, forward=True) def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: - self.add_nicks(self.design) - self.add_crossovers_after_nicks(self.design) + self.add_nicks(self.origami) + self.add_crossovers_after_nicks(self.origami) - self.assertEqual(19, len(self.design.strands)) + self.assertEqual(19, len(self.origami.strands)) # staples left edge # {"helix": 1, "forward": true, "start": 0, "end": 16}, @@ -2245,7 +2388,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(1, True, 0, 16), sc.Domain(0, False, 0, 16), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 3, "forward": true, "start": 0, "end": 16}, # {"helix": 2, "forward": false, "start": 0, "end": 16} @@ -2253,7 +2396,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(3, True, 0, 16), sc.Domain(2, False, 0, 16), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 5, "forward": true, "start": 0, "end": 16}, # {"helix": 4, "forward": false, "start": 0, "end": 16} @@ -2261,7 +2404,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(5, True, 0, 16), sc.Domain(4, False, 0, 16), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # staples right edge # {"helix": 0, "forward": false, "start": 80, "end": 96}, @@ -2270,7 +2413,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(0, False, 80, 96), sc.Domain(1, True, 80, 96), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 2, "forward": false, "start": 80, "end": 96}, # {"helix": 3, "forward": true, "start": 80, "end": 96} @@ -2278,7 +2421,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(2, False, 80, 96), sc.Domain(3, True, 80, 96), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 4, "forward": false, "start": 80, "end": 96}, # {"helix": 5, "forward": true, "start": 80, "end": 96} @@ -2286,12 +2429,12 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(4, False, 80, 96), sc.Domain(5, True, 80, 96), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # staples remainder # {"helix": 0, "forward": false, "start": 40, "end": 72} stap = sc.Strand([sc.Domain(0, False, 40, 72)]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 2, "forward": false, "start": 32, "end": 40}, # {"helix": 1, "forward": true, "start": 32, "end": 56} @@ -2299,7 +2442,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(2, False, 32, 40), sc.Domain(1, True, 32, 56), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 1, "forward": true, "start": 56, "end": 64}, # {"helix": 2, "forward": false, "start": 40, "end": 64} @@ -2307,7 +2450,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(1, True, 56, 64), sc.Domain(2, False, 40, 64), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 4, "forward": false, "start": 32, "end": 40}, # {"helix": 3, "forward": true, "start": 32, "end": 56} @@ -2315,7 +2458,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(4, False, 32, 40), sc.Domain(3, True, 32, 56), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 3, "forward": true, "start": 56, "end": 64}, # {"helix": 4, "forward": false, "start": 40, "end": 64} @@ -2323,11 +2466,11 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(3, True, 56, 64), sc.Domain(4, False, 40, 64), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 5, "forward": true, "start": 24, "end": 56} stap = sc.Strand([sc.Domain(5, True, 24, 56)]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 0, "forward": false, "start": 16, "end": 40}, # {"helix": 1, "forward": true, "start": 16, "end": 24} @@ -2335,7 +2478,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(0, False, 16, 40), sc.Domain(1, True, 16, 24), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 1, "forward": true, "start": 24, "end": 32}, # {"helix": 2, "forward": false, "start": 16, "end": 32}, @@ -2345,7 +2488,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(2, False, 16, 32), sc.Domain(3, True, 16, 24), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 3, "forward": true, "start": 24, "end": 32}, # {"helix": 4, "forward": false, "start": 16, "end": 32}, @@ -2355,7 +2498,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(4, False, 16, 32), sc.Domain(5, True, 16, 24), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 5, "forward": true, "start": 56, "end": 80}, # {"helix": 4, "forward": false, "start": 72, "end": 80} @@ -2363,7 +2506,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(5, True, 56, 80), sc.Domain(4, False, 72, 80), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 2, "forward": false, "start": 64, "end": 72}, # {"helix": 1, "forward": true, "start": 64, "end": 80}, @@ -2373,7 +2516,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(1, True, 64, 80), sc.Domain(0, False, 72, 80), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # {"helix": 4, "forward": false, "start": 64, "end": 72}, # {"helix": 3, "forward": true, "start": 64, "end": 80}, @@ -2383,7 +2526,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(3, True, 64, 80), sc.Domain(2, False, 72, 80), ]) - self.assertIn(stap, self.design.strands) + self.assertIn(stap, self.origami.strands) # scaffold # {"helix": 5, "forward": false, "start": 0, "end": 48}, @@ -2410,7 +2553,7 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None: sc.Domain(4, True, 48, 96), sc.Domain(5, False, 48, 96), ]) - self.assertIn(scaf, self.design.strands) + self.assertIn(scaf, self.origami.strands) class TestAutocalculatedData(unittest.TestCase): @@ -3670,11 +3813,13 @@ def setUp(self) -> None: ''' def test_add_crossover_from_linear_strand_to_itself_makes_it_circular(self) -> None: + # add crossover to strand 0 self.design.add_half_crossover(0, 1, 0, True) self.assertTrue(self.design.strands[0].circular) self.assertEqual(self.num_strands, len(self.design.strands)) def test_add_nick_to_circular_strand_makes_it_linear(self) -> None: + # nick strand 5 self.design.add_nick(0, 45, True) self.assertFalse(self.design.strands[5].circular) self.assertEqual(self.num_strands, len(self.design.strands)) @@ -3699,6 +3844,15 @@ def test_add_nick_to_circular_strand_makes_it_linear(self) -> None: self.assertEqual(40, d2.start) self.assertEqual(45, d2.end) + def test_ligate_linear_strand_to_itself_makes_it_circular(self) -> None: + self.assertEqual(3, len(self.design.strands[1].domains)) + self.design.ligate(0, 15, True) + self.assertEqual(self.num_strands, len(self.design.strands)) + self.assertTrue(self.design.strands[1].circular) + self.assertEqual(2, len(self.design.strands[1].domains)) + + #TODO: add functionality for removing crossovers and loopouts and ligating, and test that here + class TestAddStrand(unittest.TestCase): From 4a7dd1d6235519ed26044ef7585ec34eb881672d Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 13 Dec 2020 19:05:37 -0800 Subject: [PATCH 10/18] added unit tests for nicking on circular strand with 3 domains and a loopout, nicking on all three domains --- tests/scadnano_tests.py | 194 ++++++++++++++++++++++++++++++++++++++-- 1 file changed, 188 insertions(+), 6 deletions(-) diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 99c6e85e..682de1b1 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -3794,13 +3794,13 @@ class TestCircularStrandEdits(unittest.TestCase): ''' def setUp(self) -> None: - helices = [sc.Helix(max_offset=10) for _ in range(2)] + helices = [sc.Helix(max_offset=10) for _ in range(3)] self.design = sc.Design(helices=helices, strands=[]) self.design.strand(0, 0).move(10).cross(1).move(-10) self.design.strand(0, 15).move(5).cross(1).move(-10).cross(0).move(5) self.design.strand(0, 20).move(10) self.design.strand(1, 30).move(-10) - self.design.strand(0, 30).move(10).loopout(1, 5).move(-10) + self.design.strand(0, 30).move(10).loopout(1, 5).move(-10).cross(2).move(10).as_circular() self.design.strand(0, 40).move(10).cross(1).move(-10).as_circular() self.num_strands = len(self.design.strands) r''' @@ -3808,17 +3808,37 @@ def setUp(self) -> None: strand 0 strand 1 strand 2 strand 4 strand 5 0 [--------\ /--->[---\ [--------> [--------\ /--------\ | | | ) | | - 1 <--------/ \--------/ <--------] <--------/ \--------/ - strand 3 + 1 <--------/ \--------/ <--------] /--------/ \--------/ + strand 3 | + 2 \-------->cross to 5' end here ''' def test_add_crossover_from_linear_strand_to_itself_makes_it_circular(self) -> None: # add crossover to strand 0 + r''' + 0 + strand 0 + 0 /--------\ + | | + 1 \--------/ + ''' + self.assertEqual(2, len(self.design.strands[0].domains)) + self.assertFalse(self.design.strands[0].circular) self.design.add_half_crossover(0, 1, 0, True) self.assertTrue(self.design.strands[0].circular) self.assertEqual(self.num_strands, len(self.design.strands)) + self.assertEqual(2, len(self.design.strands[0].domains)) + + def test_add_nick_to_2_domain_circular_strand_makes_it_linear_nick_first_domain(self) -> None: + r''' + 40 + strand 5 + 0 /--->[---\ + | | + 1 \--------/ + ''' + self.assertTrue(self.design.strands[5].circular) - def test_add_nick_to_circular_strand_makes_it_linear(self) -> None: # nick strand 5 self.design.add_nick(0, 45, True) self.assertFalse(self.design.strands[5].circular) @@ -3844,14 +3864,176 @@ def test_add_nick_to_circular_strand_makes_it_linear(self) -> None: self.assertEqual(40, d2.start) self.assertEqual(45, d2.end) + def test_add_nick_to_2_domain_circular_strand_makes_it_linear_nick_second_domain(self) -> None: + # nick strand 5 + r''' + 40 + strand 5 + 0 /--------\ + | | + 1 \---]<---/ + ''' + self.design.add_nick(1, 45, False) + strand = self.design.strands[5] + self.assertFalse(strand.circular) + self.assertEqual(self.num_strands, len(self.design.strands)) + + self.assertEqual(3, len(strand.domains)) + self.assertEqual(3, len(strand.bound_domains())) + + d0, d1, d2 = strand.bound_domains() + self.assertEqual(1, d0.helix) + self.assertEqual(False, d0.forward) + self.assertEqual(40, d0.start) + self.assertEqual(45, d0.end) + + self.assertEqual(0, d1.helix) + self.assertEqual(True, d1.forward) + self.assertEqual(40, d1.start) + self.assertEqual(50, d1.end) + + self.assertEqual(1, d2.helix) + self.assertEqual(False, d2.forward) + self.assertEqual(45, d2.start) + self.assertEqual(50, d2.end) + + def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_first_domain(self) -> None: + # nick strand 4 + r''' + 30 40 + strand 4 + 0 [--->[---\ + ) loopout + 1 /--------/ + | + 2 \-------->cross to 5' end here + ''' + self.design.add_nick(0, 35, True) + strand = self.design.strands[4] + self.assertFalse(strand.circular) + self.assertEqual(self.num_strands, len(self.design.strands)) + + self.assertEqual(5, len(strand.domains)) + self.assertEqual(4, len(strand.bound_domains())) + + d0, loopout, d1, d2, d3 = strand.domains + self.assertIsInstance(loopout, sc.Loopout) + + self.assertEqual(0, d0.helix) + self.assertEqual(True, d0.forward) + self.assertEqual(35, d0.start) + self.assertEqual(40, d0.end) + + self.assertEqual(1, d1.helix) + self.assertEqual(False, d1.forward) + self.assertEqual(30, d1.start) + self.assertEqual(40, d1.end) + + self.assertEqual(2, d2.helix) + self.assertEqual(True, d2.forward) + self.assertEqual(30, d2.start) + self.assertEqual(40, d2.end) + + self.assertEqual(0, d3.helix) + self.assertEqual(True, d3.forward) + self.assertEqual(30, d3.start) + self.assertEqual(35, d3.end) + + def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_middle_domain(self) -> None: + # nick strand 4 + r''' + 30 40 + strand 4 + 0 [--------\ + ) loopout + 1 /---]<---/ + | + 2 \-------->cross to 5' end here + ''' + self.design.add_nick(1, 35, False) + strand = self.design.strands[4] + self.assertFalse(strand.circular) + self.assertEqual(self.num_strands, len(self.design.strands)) + + self.assertEqual(5, len(strand.domains)) + self.assertEqual(4, len(strand.bound_domains())) + + d0, d1, d2, loopout, d3 = strand.domains + self.assertIsInstance(loopout, sc.Loopout) + + self.assertEqual(1, d0.helix) + self.assertEqual(False, d0.forward) + self.assertEqual(30, d0.start) + self.assertEqual(35, d0.end) + + self.assertEqual(2, d1.helix) + self.assertEqual(True, d1.forward) + self.assertEqual(30, d1.start) + self.assertEqual(40, d1.end) + + self.assertEqual(0, d2.helix) + self.assertEqual(True, d2.forward) + self.assertEqual(30, d2.start) + self.assertEqual(40, d2.end) + + self.assertEqual(1, d3.helix) + self.assertEqual(False, d3.forward) + self.assertEqual(35, d3.start) + self.assertEqual(40, d3.end) + + def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_last_domain(self) -> None: + # nick strand 4 + r''' + 30 40 + strand 4 + 0 [--------\ + ) loopout + 1 /--------/ + | + 2 \--->[--->cross to 5' end here + ''' + self.design.add_nick(2, 35, True) + strand = self.design.strands[4] + self.assertFalse(strand.circular) + self.assertEqual(self.num_strands, len(self.design.strands)) + + self.assertEqual(5, len(strand.domains)) + self.assertEqual(4, len(strand.bound_domains())) + + d0, d1, loopout, d2, d3 = strand.domains + self.assertIsInstance(loopout, sc.Loopout) + + self.assertEqual(2, d0.helix) + self.assertEqual(True, d0.forward) + self.assertEqual(35, d0.start) + self.assertEqual(40, d0.end) + + self.assertEqual(0, d1.helix) + self.assertEqual(True, d1.forward) + self.assertEqual(30, d1.start) + self.assertEqual(40, d1.end) + + self.assertEqual(1, d2.helix) + self.assertEqual(False, d2.forward) + self.assertEqual(30, d2.start) + self.assertEqual(40, d2.end) + + self.assertEqual(2, d3.helix) + self.assertEqual(True, d3.forward) + self.assertEqual(30, d3.start) + self.assertEqual(35, d3.end) + def test_ligate_linear_strand_to_itself_makes_it_circular(self) -> None: + self.assertFalse(self.design.strands[1].circular) self.assertEqual(3, len(self.design.strands[1].domains)) + self.design.ligate(0, 15, True) + self.assertEqual(self.num_strands, len(self.design.strands)) self.assertTrue(self.design.strands[1].circular) self.assertEqual(2, len(self.design.strands[1].domains)) - #TODO: add functionality for removing crossovers and loopouts and ligating, and test that here + #TODO: add functionality for removing crossovers and loopouts, and test that here class TestAddStrand(unittest.TestCase): From 8eda390b180f2f27ba924f74d17ef07dab5cf96e Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 13 Dec 2020 19:20:40 -0800 Subject: [PATCH 11/18] Update scadnano_tests.py --- tests/scadnano_tests.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 682de1b1..4fefa46b 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -3903,7 +3903,7 @@ def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_first_domain( 30 40 strand 4 0 [--->[---\ - ) loopout + ) loopout length 5 1 /--------/ | 2 \-------->cross to 5' end here @@ -3945,7 +3945,7 @@ def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_middle_domain 30 40 strand 4 0 [--------\ - ) loopout + ) loopout length 5 1 /---]<---/ | 2 \-------->cross to 5' end here @@ -3987,7 +3987,7 @@ def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_last_domain(s 30 40 strand 4 0 [--------\ - ) loopout + ) loopout length 5 1 /--------/ | 2 \--->[--->cross to 5' end here From c58b8320da8a0607a198c1980e41d846def165c9 Mon Sep 17 00:00:00 2001 From: David Doty Date: Mon, 14 Dec 2020 14:04:44 -0800 Subject: [PATCH 12/18] modified circular strand example script to have length 8 domains --- examples/circular.py | 8 ++++---- examples/output_designs/circular.sc | 14 +++++++------- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/examples/circular.py b/examples/circular.py index 21168368..adabd036 100644 --- a/examples/circular.py +++ b/examples/circular.py @@ -3,12 +3,12 @@ import dataclasses def create_design(): - helices = [sc.Helix(max_offset=30) for _ in range(2)] + helices = [sc.Helix(max_offset=24) for _ in range(2)] design = sc.Design(helices=helices, grid=sc.square) - design.strand(0,0).move(10).cross(1).move(-10).as_circular() - design.strand(0,10).move(10).loopout(1, 5).move(-10).as_circular() - design.strand(0,20).move(10).cross(1).move(-10) + design.strand(0,0).move(8).cross(1).move(-8).as_circular() + design.strand(0,8).move(8).loopout(1, 5).move(-8).as_circular() + design.strand(0,16).move(8).cross(1).move(-8) return design diff --git a/examples/output_designs/circular.sc b/examples/output_designs/circular.sc index 82f0bd44..5c4019cd 100644 --- a/examples/output_designs/circular.sc +++ b/examples/output_designs/circular.sc @@ -1,5 +1,5 @@ { - "version": "0.13.0", + "version": "0.13.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, @@ -10,24 +10,24 @@ "circular": true, "color": "#f74308", "domains": [ - {"helix": 0, "forward": true, "start": 0, "end": 10}, - {"helix": 1, "forward": false, "start": 0, "end": 10} + {"helix": 0, "forward": true, "start": 0, "end": 8}, + {"helix": 1, "forward": false, "start": 0, "end": 8} ] }, { "circular": true, "color": "#57bb00", "domains": [ - {"helix": 0, "forward": true, "start": 10, "end": 20}, + {"helix": 0, "forward": true, "start": 8, "end": 16}, {"loopout": 5}, - {"helix": 1, "forward": false, "start": 10, "end": 20} + {"helix": 1, "forward": false, "start": 8, "end": 16} ] }, { "color": "#888888", "domains": [ - {"helix": 0, "forward": true, "start": 20, "end": 30}, - {"helix": 1, "forward": false, "start": 20, "end": 30} + {"helix": 0, "forward": true, "start": 16, "end": 24}, + {"helix": 1, "forward": false, "start": 16, "end": 24} ] } ] From 5b1d08421fc6aa1c66f209dd393012e023dff9cc Mon Sep 17 00:00:00 2001 From: David Doty Date: Mon, 14 Dec 2020 16:06:58 -0800 Subject: [PATCH 13/18] bumped version to match web interface --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index e4055952..980f2b3f 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -44,7 +44,7 @@ # commented out for now to support Py3.6, which does not support this feature # from __future__ import annotations -__version__ = "0.13.1" # version line; WARNING: do not remove or change this line or comment +__version__ = "0.13.4" # version line; WARNING: do not remove or change this line or comment import dataclasses from abc import abstractmethod, ABC, ABCMeta From 22d446eced1fccae06974ce84342af9421842e9c Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 15 Dec 2020 18:20:20 -0800 Subject: [PATCH 14/18] updated tutorial script (still not completely in line with #154, however, since issue #111 still need to be implemented) --- ...helix_origami_rectangle_twist_corrected.py | 84 - ...helix_origami_rectangle_twist_corrected.sc | 1990 --------------- .../24_helix_rectangle_twist_corrected.sc | 1749 ------------- examples/6_helix_bundle_honeycomb.py | 70 +- .../tutorial-examples/24_helix_rectangle.py | 86 + .../tutorial-examples/24_helix_rectangle.sc | 2182 +++++++++++++++++ .../24_helix_rectangle.xls} | Bin 30208 -> 30208 bytes .../24_helix_rectangle_manual.sc} | 0 scadnano/scadnano.py | 70 +- tests/scadnano_tests.py | 43 +- 10 files changed, 2373 insertions(+), 3901 deletions(-) delete mode 100644 examples/24_helix_origami_rectangle_twist_corrected.py delete mode 100644 examples/24_helix_origami_rectangle_twist_corrected.sc delete mode 100644 examples/24_helix_rectangle_twist_corrected.sc create mode 100644 examples/tutorial-examples/24_helix_rectangle.py create mode 100644 examples/tutorial-examples/24_helix_rectangle.sc rename examples/{24_helix_origami_rectangle_twist_corrected.xls => tutorial-examples/24_helix_rectangle.xls} (57%) rename examples/{24_helix_rectangle.sc => tutorial-examples/24_helix_rectangle_manual.sc} (100%) diff --git a/examples/24_helix_origami_rectangle_twist_corrected.py b/examples/24_helix_origami_rectangle_twist_corrected.py deleted file mode 100644 index 856f0e5b..00000000 --- a/examples/24_helix_origami_rectangle_twist_corrected.py +++ /dev/null @@ -1,84 +0,0 @@ -import scadnano as sc - - -def create_design(): - design = precursor_scaffolds() - add_scaffold_nicks(design) - add_scaffold_crossovers(design) - design.strands[0].set_scaffold() - add_precursor_staples(design) - add_staple_nicks(design) - add_staple_crossovers(design) - add_deletions(design) - design.assign_m13_to_scaffold() - export_idt_plate_file(design) - return design - - -def export_idt_plate_file(design: sc.Design): - for strand in design.strands: - if strand != design.scaffold: - strand.set_default_idt(use_default_idt=True) - design.write_idt_plate_excel_file(use_default_plates=True) - - -def add_deletions(design: sc.Design): - for helix in range(24): - for offset in range(27, 294, 48): - design.add_deletion(helix, offset) - - -def add_staple_crossovers(design: sc.Design): - for helix in range(23): - start_offset = 24 if helix % 2 == 0 else 40 - for offset in range(start_offset, 296, 32): - if offset != 152: # skip crossover near seam - design.add_full_crossover(helix=helix, helix2=helix + 1, offset=offset, - forward=helix % 2 == 1) - - -def add_staple_nicks(design: sc.Design): - for helix in range(24): - start_offset = 32 if helix % 2 == 0 else 48 - for offset in range(start_offset, 280, 32): - design.add_nick(helix, offset, forward=helix % 2 == 1) - - -def add_precursor_staples(design: sc.Design): - staples = [sc.Strand([sc.Domain(helix=helix, forward=helix % 2 == 1, start=8, end=296)]) - for helix in range(24)] - for staple in staples: - design.add_strand(staple) - - -def precursor_scaffolds() -> sc.Design: - helices = [sc.Helix(max_offset=304) for _ in range(24)] - scaffolds = [sc.Strand([sc.Domain(helix=helix, forward=helix % 2 == 0, start=8, end=296)]) - for helix in range(24)] - return sc.Design(helices=helices, strands=scaffolds, grid=sc.square) - - -def add_scaffold_nicks(design: sc.Design): - for helix in range(1, 24): - design.add_nick(helix=helix, offset=152, forward=helix % 2 == 0) - - -def add_scaffold_crossovers(design: sc.Design): - crossovers = [] - - # scaffold interior - for helix in range(1, 23, 2): - crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, offset=152, forward=False)) - - # scaffold edges - for helix in range(0, 23, 2): - crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, offset=8, forward=True, half=True)) - crossovers.append( - sc.Crossover(helix=helix, helix2=helix + 1, offset=295, forward=True, half=True)) - - design.add_crossovers(crossovers) - - -if __name__ == '__main__': - design = create_design() - design.write_scadnano_file() \ No newline at end of file diff --git a/examples/24_helix_origami_rectangle_twist_corrected.sc b/examples/24_helix_origami_rectangle_twist_corrected.sc deleted file mode 100644 index ecb3af72..00000000 --- a/examples/24_helix_origami_rectangle_twist_corrected.sc +++ /dev/null @@ -1,1990 +0,0 @@ -{ - "version": "0.11.0", - "grid": "square", - "helices": [ - {"max_offset": 304, "grid_position": [0, 0]}, - {"max_offset": 304, "grid_position": [0, 1]}, - {"max_offset": 304, "grid_position": [0, 2]}, - {"max_offset": 304, "grid_position": [0, 3]}, - {"max_offset": 304, "grid_position": [0, 4]}, - {"max_offset": 304, "grid_position": [0, 5]}, - {"max_offset": 304, "grid_position": [0, 6]}, - {"max_offset": 304, "grid_position": [0, 7]}, - {"max_offset": 304, "grid_position": [0, 8]}, - {"max_offset": 304, "grid_position": [0, 9]}, - {"max_offset": 304, "grid_position": [0, 10]}, - {"max_offset": 304, "grid_position": [0, 11]}, - {"max_offset": 304, "grid_position": [0, 12]}, - {"max_offset": 304, "grid_position": [0, 13]}, - {"max_offset": 304, "grid_position": [0, 14]}, - {"max_offset": 304, "grid_position": [0, 15]}, - {"max_offset": 304, "grid_position": [0, 16]}, - {"max_offset": 304, "grid_position": [0, 17]}, - {"max_offset": 304, "grid_position": [0, 18]}, - {"max_offset": 304, "grid_position": [0, 19]}, - {"max_offset": 304, "grid_position": [0, 20]}, - {"max_offset": 304, "grid_position": [0, 21]}, - {"max_offset": 304, "grid_position": [0, 22]}, - {"max_offset": 304, "grid_position": [0, 23]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGT", - "domains": [ - {"helix": 23, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 22, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 21, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 20, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 19, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 18, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 17, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 16, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 15, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 14, "forward": true, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 13, "forward": false, "start": 8, "end": 152, "deletions": [27, 75, 123]}, - {"helix": 12, "forward": true, 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index 961970d0..d4cf539f 100644 --- a/examples/6_helix_bundle_honeycomb.py +++ b/examples/6_helix_bundle_honeycomb.py @@ -1,7 +1,7 @@ import scadnano as sc -def create_design(): +def create_design() -> sc.Design: m13_rotation = 6702 m13_variant = sc.M13Variant.p7560 # print(sc.m13(m13_rotation, m13_variant)) @@ -16,10 +16,9 @@ def create_design(): return design -def initial_design(): +def initial_design() -> sc.Design: max_offset = 1295 helices = [ - # below uses cadnano honeycomb coordinates # https://github.com/UC-Davis-molecular-computing/scadnano-python-package/blob/master/misc/cadnano-format-specs/v2.txt sc.Helix(grid_position=(1, 1), max_offset=max_offset), @@ -28,38 +27,6 @@ def initial_design(): sc.Helix(grid_position=(1, 2), max_offset=max_offset), sc.Helix(grid_position=(2, 2), max_offset=max_offset), sc.Helix(grid_position=(2, 1), max_offset=max_offset), - - # below uses original mistaken convention from mistaken cadnano specs - # sc.Helix(grid_position=(1, 0, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 0, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(1, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 0, 0), max_offset=max_offset), - - # # below uses odd-q coordinates: - # sc.Helix(grid_position=(1, -1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 0, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(1, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 0, 0), max_offset=max_offset), - - # below uses even-q coordinates: - # sc.Helix(grid_position=(1, 0, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 0, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(1, 2, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 0, 0), max_offset=max_offset), - - # below uses odd-r coordinates: - # sc.Helix(grid_position=(1, 0, 0), max_offset=max_offset), - # sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(1, 2, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 2, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset), - # sc.Helix(grid_position=(2, 0, 0), max_offset=max_offset), ] scafs = [ sc.Strand([sc.Domain(helix=0, forward=True, start=16, end=1276)]), @@ -81,7 +48,7 @@ def initial_design(): return sc.Design(helices=helices, strands=strands, grid=sc.honeycomb) -def add_nicks(design: sc.Design): +def add_nicks(design: sc.Design) -> None: design.add_nick(helix=5, offset=399, forward=False) # scaffold for offset in range(56, 1246, 42): design.add_nick(helix=0, offset=offset, forward=False) @@ -94,7 +61,7 @@ def add_nicks(design: sc.Design): design.add_nick(helix=5, offset=offset, forward=True) -def add_crossovers(design: sc.Design): +def add_crossovers(design: sc.Design) -> None: # staples interior for offset in range(84, 1246, 42): design.add_full_crossover(helix=0, helix2=1, offset=offset, forward=False) @@ -115,27 +82,28 @@ def add_crossovers(design: sc.Design): design.add_half_crossover(helix=2, helix2=3, offset=1245, forward=False) # scaffold interior - crossovers = [] for offset in range(58, 1250, 42): - crossovers.append(sc.Crossover(helix=0, helix2=1, offset=offset, forward=True)) + design.add_full_crossover(helix=0, helix2=1, offset=offset, forward=True) for offset in range(30, 1250, 42): - crossovers.append(sc.Crossover(helix=1, helix2=2, offset=offset, forward=False)) + design.add_full_crossover(helix=1, helix2=2, offset=offset, forward=False) for offset in range(54, 1250, 42): - crossovers.append(sc.Crossover(helix=2, helix2=3, offset=offset, forward=True)) + design.add_full_crossover(helix=2, helix2=3, offset=offset, forward=True) for offset in range(26, 1250, 42): - crossovers.append(sc.Crossover(helix=3, helix2=4, offset=offset, forward=False)) + design.add_full_crossover(helix=3, helix2=4, offset=offset, forward=False) # scaffold edges - crossovers.append(sc.Crossover(helix=0, helix2=1, offset=16, forward=True, half=True)) - crossovers.append(sc.Crossover(helix=2, helix2=3, offset=12, forward=True, half=True)) - crossovers.append(sc.Crossover(helix=4, helix2=5, offset=19, forward=True, half=True)) - crossovers.append(sc.Crossover(helix=0, helix2=1, offset=1275, forward=True, half=True)) - crossovers.append(sc.Crossover(helix=2, helix2=3, offset=1271, forward=True, half=True)) - crossovers.append(sc.Crossover(helix=4, helix2=5, offset=1278, forward=True, half=True)) + design.add_half_crossover(helix=0, helix2=1, offset=16, forward=True) + design.add_half_crossover(helix=2, helix2=3, offset=12, forward=True) + design.add_half_crossover(helix=4, helix2=5, offset=19, forward=True) + design.add_half_crossover(helix=0, helix2=1, offset=1275, forward=True) + design.add_half_crossover(helix=2, helix2=3, offset=1271, forward=True) + design.add_half_crossover(helix=4, helix2=5, offset=1278, forward=True) - design.add_crossovers(crossovers) - -if __name__ == '__main__': +def main() -> None: design = create_design() design.write_scadnano_file(directory='output_designs') + + +if __name__ == '__main__': + main() diff --git a/examples/tutorial-examples/24_helix_rectangle.py b/examples/tutorial-examples/24_helix_rectangle.py new file mode 100644 index 00000000..82439310 --- /dev/null +++ b/examples/tutorial-examples/24_helix_rectangle.py @@ -0,0 +1,86 @@ +import scadnano as sc + + +def main() -> None: + design = create_design() + export_idt_plate_file(design) + design.write_scadnano_file() + + +def create_design() -> sc.Design: + design = helices_only() + + add_scaffold_precursors(design) + add_scaffold_crossovers(design) + + add_staple_precursors(design) + add_staple_crossovers(design) + add_staple_nicks(design) + + add_twist_correction_deletions(design) + design.assign_m13_to_scaffold() + + return design + + +def helices_only() -> sc.Design: + helices = [sc.Helix(max_offset=288) for _ in range(24)] + return sc.Design(helices=helices, grid=sc.square) + + +def add_scaffold_precursors(design: sc.Design) -> None: + for helix in range(0, 23, 2): # scaffold goes forward on even helices + design.strand(helix, 0).move(288).as_scaffold() + for helix in range(1, 23, 2): # scaffold goes reverse on odd helices + design.strand(helix, 288).move(-288).as_scaffold() + design.strand(23, 288).move(-144).as_scaffold() + design.strand(23, 144).move(-144).as_scaffold() + + +def add_scaffold_crossovers(design: sc.Design) -> None: + for helix in range(1, 23, 2): # scaffold interior crossovers + design.add_full_crossover(helix=helix, helix2=helix + 1, offset=144, forward=False) + + for helix in range(0, 23, 2): # scaffold edges crossovers + design.add_half_crossover(helix=helix, helix2=helix + 1, offset=0, forward=True) + design.add_half_crossover(helix=helix, helix2=helix + 1, offset=287, forward=True) + + +def add_staple_precursors(design: sc.Design) -> None: + staples = [sc.Strand([sc.Domain(helix=helix, forward=helix % 2 == 1, start=0, end=288)]) # noqa + for helix in range(24)] + for staple in staples: + design.add_strand(staple) + + +def add_staple_crossovers(design: sc.Design) -> None: + for helix in range(23): + start_offset = 16 if helix % 2 == 0 else 32 + for offset in range(start_offset, 288, 32): + if offset != 144: # skip crossover near seam + design.add_full_crossover(helix=helix, helix2=helix + 1, offset=offset, + forward=helix % 2 == 1) + + +def add_staple_nicks(design: sc.Design) -> None: + for helix in range(24): + start_offset = 24 if helix % 2 == 0 else 40 + for offset in range(start_offset, 272, 32): + design.add_nick(helix, offset, forward=helix % 2 == 1) + + +def add_twist_correction_deletions(design: sc.Design) -> None: + for helix in range(24): + for offset in range(19, 286, 48): + design.add_deletion(helix, offset) + + +def export_idt_plate_file(design: sc.Design) -> None: + for strand in design.strands: + if strand != design.scaffold: + strand.set_default_idt(use_default_idt=True) + design.write_idt_plate_excel_file(use_default_plates=True) + + +if __name__ == '__main__': + main() diff --git a/examples/tutorial-examples/24_helix_rectangle.sc b/examples/tutorial-examples/24_helix_rectangle.sc new file mode 100644 index 00000000..40f3c8fc --- /dev/null +++ b/examples/tutorial-examples/24_helix_rectangle.sc @@ -0,0 +1,2182 @@ +{ + "version": "0.13.4", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]}, + {"grid_position": [0, 2]}, + {"grid_position": [0, 3]}, + {"grid_position": [0, 4]}, + {"grid_position": [0, 5]}, + {"grid_position": [0, 6]}, + {"grid_position": [0, 7]}, + {"grid_position": [0, 8]}, + {"grid_position": [0, 9]}, + {"grid_position": [0, 10]}, + {"grid_position": [0, 11]}, + {"grid_position": [0, 12]}, + {"grid_position": [0, 13]}, + {"grid_position": [0, 14]}, + {"grid_position": [0, 15]}, + {"grid_position": [0, 16]}, + {"grid_position": [0, 17]}, + {"grid_position": [0, 18]}, + {"grid_position": [0, 19]}, + {"grid_position": [0, 20]}, + {"grid_position": [0, 21]}, + {"grid_position": [0, 22]}, + {"grid_position": [0, 23]} + ], + "strands": [ + { + "color": "#0066cc", + "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGT", + "domains": [ + {"helix": 23, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 22, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 21, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 20, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 19, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 18, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 17, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 16, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 15, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 14, "forward": true, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 13, "forward": false, "start": 0, "end": 144, "deletions": [19, 67, 115]}, + {"helix": 12, "forward": true, 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support dropped + """ + :return: The :any:`Strand` that contains this :any:`Loopout`. + """ if self._parent_strand is None: raise ValueError('_parent_strand has not yet been set') return self._parent_strand @@ -1854,6 +1857,14 @@ def from_json(json_map: Dict[str, Any]) -> 'Loopout': # remove quotes when Py3. label = json_map.get(domain_label_key) return Loopout(length=length, name=name, label=label) + def strand(self) -> 'Strand': # remove quotes when Py3.6 support dropped + """ + :return: The :any:`Strand` that contains this :any:`Loopout`. + """ + if self._parent_strand is None: + raise ValueError('_parent_strand has not yet been set') + return self._parent_strand + def __repr__(self) -> str: return f'Loopout(' + \ (f'{self.name}, ' if self.name is not None else '') + \ @@ -2574,20 +2585,7 @@ class Strand(_JSONSerializable, Generic[StrandLabel, DomainLabel]): def __post_init__(self) -> None: self._helix_idx_domain_map = defaultdict(list) - for domain in self.domains: - if isinstance(domain, Domain): - self._helix_idx_domain_map[domain.helix].append(domain) - - for domain in self.domains: - domain._parent_strand = self - - if len(self.domains) == 1: - if isinstance(self.domains[0], Loopout): - raise StrandError(self, 'strand cannot have a single Loopout as its only domain') - - for domain1, domain2 in _pairwise(self.domains): - if isinstance(domain1, Loopout) and isinstance(domain2, Loopout): - raise StrandError(self, 'cannot have two consecutive Loopouts in a strand') + self.set_domains(self.domains) if self.use_default_idt: self.set_default_idt(True) @@ -2750,6 +2748,44 @@ def set_linear(self) -> None: """ self.set_circular(False) + def set_domains(self, domains: Iterable[Union[Domain[DomainLabel], Loopout]]) -> None: + """ + Sets the :any:`Domain`'s/:any:`Loopout`'s of this :any:`Strand` to be `domains`, + which can contain a mix of :any:`Domain`'s and :any:`Loopout`'s, + just like the field :py:data:`Strand.domains`. + + :param domains: + The new sequence of :any:`Domain`'s/:any:`Loopout`'s to use for this :any:`Strand`. + :raises StrandError: + if domains has two consecutive :any:`Loopout`'s, consists of just a single :any:`Loopout`'s, + or starts or ends with a :any:`Loopout` + """ + self.domains = domains + + for domain in self.domains: + if isinstance(domain, Domain): + self._helix_idx_domain_map[domain.helix].append(domain) + + for domain in self.domains: + domain._parent_strand = self + + if len(self.domains) == 1: + if isinstance(self.domains[0], Loopout): + raise StrandError(self, 'strand cannot have a single Loopout as its only domain') + + if len(self.domains) == 0: + raise StrandError(self, 'domains cannot be empty') + + for domain1, domain2 in _pairwise(self.domains): + if isinstance(domain1, Loopout) and isinstance(domain2, Loopout): + raise StrandError(self, 'cannot have two consecutive Loopouts in a strand') + + if isinstance(self.domains[0], Loopout): + raise StrandError(self, 'strand cannot begin with a loopout') + + if isinstance(self.domains[-1], Loopout): + raise StrandError(self, 'strand cannot end with a loopout') + def set_default_idt(self, use_default_idt: bool = True, skip_scaffold: bool = True, unique_names: bool = False) -> None: """ @@ -5426,7 +5462,7 @@ def add_nick(self, helix: int, offset: int, forward: bool, new_color: bool = Tru if strand.circular: # if strand is circular, we modify its domains in place domains = domains_after + domains_before - strand.domains = domains + strand.set_domains(domains) # DNA sequence was rotated, so re-assign it if seq_before_whole is not None and seq_after_whole is not None: @@ -5960,13 +5996,13 @@ class Crossover: forward: bool """direction of :any:`Strand` on `helix` to which to add half crossover""" - offset2: int + offset2: Optional[int] = None """ offset on `helix2` at which to add half crossover. If not specified, defaults to `offset` """ - forward2: bool + forward2: Optional[bool] = None """ direction of :any:`Strand` on `helix2` to which to add half crossover. If not specified, defaults to the negation of `forward` diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 4fefa46b..9d3289f1 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -3496,10 +3496,12 @@ def test_consecutive_domains_loopout(self) -> None: with self.assertRaises(sc.IllegalDesignError): sc.Strand([ss1, ss2, ss3]) - strand = sc.Strand([ss1, ss2]) - strand.domains.append(ss3) - with self.assertRaises(sc.IllegalDesignError): - sc.Design(helices=helices, strands=[strand], grid=sc.square) + #XXX: we used to allow Strands to violate the loopout rules and caught it only at the design level + # now the Strand constructor checks, so that means we can't set up a bad Strand for the Design check + # strand = sc.Strand([ss1, ss2]) + # strand.domains.append(ss3) + # with self.assertRaises(sc.IllegalDesignError): + # sc.Design(helices=helices, strands=[strand], grid=sc.square) def test_singleton_loopout(self) -> None: helices = [sc.Helix(max_offset=10)] @@ -3507,10 +3509,12 @@ def test_singleton_loopout(self) -> None: with self.assertRaises(sc.StrandError): sc.Strand([loopout]) - strand = sc.Strand([]) - strand.domains.append(loopout) - with self.assertRaises(sc.StrandError): - sc.Design(helices=helices, strands=[strand], grid=sc.square) + # XXX: we used to allow Strands to violate the loopout rules and caught it only at the design level + # now the Strand constructor checks, so that means we can't set up a bad Strand for the Design check + # strand = sc.Strand([]) + # strand.domains.append(loopout) + # with self.assertRaises(sc.StrandError): + # sc.Design(helices=helices, strands=[strand], grid=sc.square) def test_strand_offset_beyond_maxbases(self) -> None: helices = [sc.Helix(max_offset=10)] @@ -3864,6 +3868,9 @@ def test_add_nick_to_2_domain_circular_strand_makes_it_linear_nick_first_domain( self.assertEqual(40, d2.start) self.assertEqual(45, d2.end) + for domain in strand.domains: + self.assertIs(strand, domain.strand()) + def test_add_nick_to_2_domain_circular_strand_makes_it_linear_nick_second_domain(self) -> None: # nick strand 5 r''' @@ -3897,6 +3904,9 @@ def test_add_nick_to_2_domain_circular_strand_makes_it_linear_nick_second_domain self.assertEqual(45, d2.start) self.assertEqual(50, d2.end) + for domain in strand.domains: + self.assertIs(strand, domain.strand()) + def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_first_domain(self) -> None: # nick strand 4 r''' @@ -3939,6 +3949,9 @@ def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_first_domain( self.assertEqual(30, d3.start) self.assertEqual(35, d3.end) + for domain in strand.domains: + self.assertIs(strand, domain.strand()) + def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_middle_domain(self) -> None: # nick strand 4 r''' @@ -3981,6 +3994,9 @@ def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_middle_domain self.assertEqual(35, d3.start) self.assertEqual(40, d3.end) + for domain in strand.domains: + self.assertIs(strand, domain.strand()) + def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_last_domain(self) -> None: # nick strand 4 r''' @@ -4023,15 +4039,22 @@ def test_add_nick_to_3_domain_circular_strand_makes_it_linear_nick_last_domain(s self.assertEqual(30, d3.start) self.assertEqual(35, d3.end) + for domain in strand.domains: + self.assertIs(strand, domain.strand()) + def test_ligate_linear_strand_to_itself_makes_it_circular(self) -> None: self.assertFalse(self.design.strands[1].circular) self.assertEqual(3, len(self.design.strands[1].domains)) self.design.ligate(0, 15, True) + strand = self.design.strands[1] self.assertEqual(self.num_strands, len(self.design.strands)) - self.assertTrue(self.design.strands[1].circular) - self.assertEqual(2, len(self.design.strands[1].domains)) + self.assertTrue(strand.circular) + self.assertEqual(2, len(strand.domains)) + + for domain in strand.domains: + self.assertIs(strand, domain.strand()) #TODO: add functionality for removing crossovers and loopouts, and test that here From 5f91962e9aab8e31281b4fea5edc38200d1ab9cf Mon Sep 17 00:00:00 2001 From: Cosmo Date: Tue, 22 Dec 2020 14:46:47 +0000 Subject: [PATCH 15/18] Modifications not needed in circular example --- examples/circular.py | 1 - 1 file changed, 1 deletion(-) diff --git a/examples/circular.py b/examples/circular.py index adabd036..4d563835 100644 --- a/examples/circular.py +++ b/examples/circular.py @@ -1,5 +1,4 @@ import scadnano as sc -import modifications as mod import dataclasses def create_design(): From 4ee5e288d4c94fb57791845b2c5df79f7e7470ed Mon Sep 17 00:00:00 2001 From: Cosmo Date: Tue, 22 Dec 2020 17:31:27 +0000 Subject: [PATCH 16/18] Importing circular strands from cadnano to scadnano is now functional. Two tests added: which come from cadnano Autostaple's output --- examples/output_designs/circular.sc | 2 +- scadnano/scadnano.py | 57 +- tests/scadnano_tests.py | 25 + .../test_circular_auto_staple.json | 6277 +++++++++++++++++ .../test_circular_auto_staple_hex.json | 1 + 5 files changed, 6352 insertions(+), 10 deletions(-) create mode 100644 tests_inputs/cadnano_v2_import/test_circular_auto_staple.json create mode 100644 tests_inputs/cadnano_v2_import/test_circular_auto_staple_hex.json diff --git a/examples/output_designs/circular.sc b/examples/output_designs/circular.sc index 5c4019cd..9a08852c 100644 --- a/examples/output_designs/circular.sc +++ b/examples/output_designs/circular.sc @@ -1,5 +1,5 @@ { - "version": "0.13.1", + "version": "0.13.4", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index ab6df015..c9a17b99 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -283,7 +283,7 @@ def colors(self, newcolors: Iterable[Color]) -> None: default_strand_color = Color(0, 0, 0) """Default color for non-scaffold strand(s).""" - +default_cadnano_strand_color = Color(hex_string='#BFBFBF') # # END Colors ############################################################################## @@ -4024,22 +4024,35 @@ def _cadnano_v2_import_find_5_end(vstrands: VStrands, strand_type: str, helix_nu """ Routine which finds the 5' end of a strand in a cadnano v2 import. It returns the helix and the base of the 5' end. """ - id_from_before = helix_num + id_from_before = helix_num # 'id' stands for helix id base_from_before = base_id + + circular_seen = {} + is_circular = False + while not (id_from == -1 and base_from == -1): + if (id_from,base_from) in circular_seen: + is_circular = True + break + circular_seen[(id_from,base_from)] = True id_from_before = id_from base_from_before = base_from id_from, base_from, _, _ = vstrands[id_from][strand_type][base_from] - return id_from_before, base_from_before + return id_from_before, base_from_before, is_circular @staticmethod def _cadnano_v2_import_find_strand_color(vstrands: VStrands, strand_type: str, strand_5_end_base: int, strand_5_end_helix: int) -> Color: """Routine that finds the color of a cadnano v2 strand.""" - color: Color = default_scaffold_color + color: Color = default_cadnano_strand_color + + if strand_type == 'scaf': + return default_scaffold_color + if strand_type == 'stap': base_id: int stap_color: int + for base_id, stap_color in vstrands[strand_5_end_helix]['stap_colors']: if base_id == strand_5_end_base: color = Color.from_cadnano_v2_int_hex(stap_color) @@ -4083,15 +4096,22 @@ def _cadnano_v2_import_explore_domains(vstrands: VStrands, seen: Dict[Tuple[int, else: end = curr_base + circular_seen = {} while not (curr_helix == -1 and curr_base == -1): + if (curr_helix,curr_base) in circular_seen: + break + circular_seen[(curr_helix,curr_base)] = True + old_helix = curr_helix old_base = curr_base seen[(curr_helix, curr_base)] = True curr_helix, curr_base = vstrands[curr_helix][strand_type][curr_base][2:] # Add crossover # We have a crossover when we jump helix or when order is broken on same helix + # Or circular strand if curr_helix != old_helix or (not direction_forward and curr_base > old_base) or ( - direction_forward and curr_base < old_base): + direction_forward and curr_base < old_base) or (curr_helix == strand_5_end_helix and curr_base == strand_5_end_base): + if direction_forward: end = old_base else: @@ -4114,6 +4134,20 @@ def _cadnano_v2_import_explore_domains(vstrands: VStrands, seen: Dict[Tuple[int, return domains + @staticmethod + def _cadnano_v2_import_circular_strands_merge_first_last_domains(domains: Sequence[Domain]) -> None: + """ When we create domains for circular strands in the cadnano import routine, we may end up + with a fake crossover if first and last domain are on same helix, we have to merge them + if it is the case. + """ + if domains[0].helix != domains[-1].helix: + return + + domains[0].start = min(domains[0].start,domains[-1].start) + domains[0].end = max(domains[0].end,domains[-1].end) + + del domains[-1] + @staticmethod def _cadnano_v2_import_explore_strand(vstrands: VStrands, strand_type: str, seen: Dict[Tuple[int, int], bool], @@ -4128,23 +4162,27 @@ def _cadnano_v2_import_explore_strand(vstrands: VStrands, if (id_from, base_from, id_to, base_to) == (-1, -1, -1, -1): return None - - strand_5_end_helix, strand_5_end_base = Design._cadnano_v2_import_find_5_end(vstrands, + + strand_5_end_helix, strand_5_end_base, is_circular = Design._cadnano_v2_import_find_5_end(vstrands, strand_type, helix_num, base_id, id_from, base_from) + strand_color = Design._cadnano_v2_import_find_strand_color(vstrands, strand_type, strand_5_end_base, strand_5_end_helix) domains: Sequence[Domain] = Design._cadnano_v2_import_explore_domains(vstrands, seen, strand_type, strand_5_end_base, strand_5_end_helix) + # merge first and last domain if circular + if is_circular: + Design._cadnano_v2_import_circular_strands_merge_first_last_domains(domains) domains_loopouts = cast(List[Union[Domain, Loopout]], # noqa domains) # type: ignore strand: Strand = Strand(domains=domains_loopouts, - is_scaffold=(strand_type == 'scaf'), color=strand_color) + is_scaffold=(strand_type == 'scaf'), color=strand_color, circular=is_circular) return strand @@ -4155,7 +4193,7 @@ def from_cadnano_v2(directory: Optional[str] = None, filename: Optional[str] = N """ Creates a Design from a cadnano v2 file. """ - + if json_dict is None and filename is not None and directory is not None: file_path = os.path.join(directory, filename) f = open(file_path, 'r') @@ -4191,6 +4229,7 @@ def from_cadnano_v2(directory: Optional[str] = None, filename: Optional[str] = N strands: List[Strand] = [] cadnano_helices = OrderedDict({}) for cadnano_helix in cadnano_v2_design['vstrands']: + helix_num = cadnano_helix['num'] cadnano_helices[helix_num] = cadnano_helix diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 9d3289f1..3343add8 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -595,6 +595,20 @@ def test_Nature09_monolith(self) -> None: design.write_scadnano_file(directory=self.output_path, filename=f'{file_name}.{sc.default_scadnano_file_extension}') + def test_circular_auto_staple(self) -> None: + file_name = "test_circular_auto_staple" + design = sc.Design.from_cadnano_v2(directory=self.input_path, + filename=file_name + ".json") + design.write_scadnano_file(directory=self.output_path, + filename=f'{file_name}.{sc.default_scadnano_file_extension}') + + def test_circular_auto_staple_hex(self) -> None: + file_name = "test_circular_auto_staple_hex" + design = sc.Design.from_cadnano_v2(directory=self.input_path, + filename=file_name + ".json") + design.write_scadnano_file(directory=self.output_path, + filename=f'{file_name}.{sc.default_scadnano_file_extension}') + class TestExportDNASequences(unittest.TestCase): @@ -961,6 +975,17 @@ def test_16_helix_origami_rectangle_no_twist(self) -> None: design.export_cadnano_v2(directory=self.output_path, filename='test_16_helix_origami_rectangle_no_twist.json') + def test_circular_strand(self) -> None: + # TODO: not working + helices = [sc.Helix(max_offset=24) for _ in range(2)] + design = sc.Design(helices=helices, grid=sc.square) + + design.strand(0,0).move(8).cross(1).move(-8).as_circular() + design.write_scadnano_file(directory=self.input_path, + filename=f'test_circular_strand.{self.ext}') + design.export_cadnano_v2(directory=self.output_path, + filename='test_circular_strand.json') + def test_bad_cases(self) -> None: """ We do not handle Loopouts and design where the parity of the helix does not correspond to the direction. diff --git a/tests_inputs/cadnano_v2_import/test_circular_auto_staple.json b/tests_inputs/cadnano_v2_import/test_circular_auto_staple.json new file mode 100644 index 00000000..8f981f39 --- /dev/null +++ b/tests_inputs/cadnano_v2_import/test_circular_auto_staple.json @@ -0,0 +1,6277 @@ +{ + "name": "test_circular_auto_staple.json", + "vstrands": [ + { + "row": 21, + "col": 17, + "num": 0, + "scaf": [ + [-1, -1, -1, -1], + [-1, -1, -1, -1], + [-1, -1, -1, -1], + [-1, -1, -1, -1], + [-1, -1, -1, -1], + [-1, -1, -1, -1], + [-1, -1, -1, -1], + [-1, -1, -1, -1], + [1, 8, 0, 9], + [0, 8, 0, 10], + [0, 9, 0, 11], + [0, 10, 0, 12], + [0, 11, 0, 13], + [0, 12, 0, 14], + [0, 13, 0, 15], + [0, 14, 0, 16], + [0, 15, 0, 17], + [0, 16, 0, 18], + [0, 17, 0, 19], + [0, 18, 0, 20], + [0, 19, 0, 21], + [0, 20, 0, 22], + [0, 21, 0, 23], + [0, 22, 0, 24], + [0, 23, 0, 25], + [0, 24, 0, 26], + [0, 25, 0, 27], + [0, 26, 0, 28], + [0, 27, 0, 29], + [0, 28, 0, 30], + [0, 29, 0, 31], + [0, 30, 0, 32], + [0, 31, 0, 33], + [0, 32, 0, 34], + [0, 33, 0, 35], + [0, 34, 0, 36], + [0, 35, 0, 37], + [0, 36, 0, 38], + [0, 37, 0, 39], + [0, 38, 0, 40], + [0, 39, 0, 41], + [0, 40, 0, 42], + [0, 41, 0, 43], + [0, 42, 0, 44], + [0, 43, 0, 45], + [0, 44, 0, 46], + [0, 45, 0, 47], + [0, 46, 0, 48], + [0, 47, 0, 49], + [0, 48, 0, 50], + [0, 49, 0, 51], + [0, 50, 0, 52], + [0, 51, 0, 53], + [0, 52, 0, 54], + [0, 53, 0, 55], + [0, 54, 0, 56], + [0, 55, 0, 57], + [0, 56, 0, 58], + [0, 57, 0, 59], + [0, 58, 0, 60], + [0, 59, 0, 61], + [0, 60, 0, 62], + [0, 61, 0, 63], + [0, 62, 0, 64], + [0, 63, 0, 65], + [0, 64, 0, 66], + [0, 65, 0, 67], + [0, 66, 0, 68], + [0, 67, 0, 69], + [0, 68, 0, 70], + [0, 69, 0, 71], + [0, 70, 0, 72], + [0, 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[0, 124, 0, 126], + [0, 125, 0, 127], + [0, 126, 0, 128], + [0, 127, 0, 129], + [0, 128, 0, 130], + [0, 129, 0, 131], + [0, 130, 0, 132], + [0, 131, 0, 133], + [0, 132, 0, 134], + [0, 133, 0, 135], + [0, 134, 0, 136], + [0, 135, 0, 137], + [0, 136, 0, 138], + [0, 137, 0, 139], + [0, 138, 0, 140], + [0, 139, 0, 141], + [0, 140, 0, 142], + [0, 141, 0, 143], + [0, 142, 0, 144], + [0, 143, 0, 145], + [0, 144, 0, 146], + [0, 145, 0, 147], + [0, 146, 0, 148], + [0, 147, 0, 149], + [0, 148, 0, 150], + [0, 149, 0, 151], + [0, 150, 0, 152], + [0, 151, 0, 153], + [0, 152, 0, 154], + [0, 153, 0, 155], + [0, 154, 0, 156], + [0, 155, 0, 157], + [0, 156, 0, 158], + [0, 157, 0, 159], + [0, 158, 0, 160], + [0, 159, 0, 161], + [0, 160, 0, 162], + [0, 161, 0, 163], + [0, 162, 0, 164], + [0, 163, 0, 165], + [0, 164, 0, 166], + [0, 165, 0, 167], + [0, 166, 1, 167], + [-1, -1, -1, -1], + [-1, -1, -1, -1], + [-1, -1, -1, -1], + [-1, -1, -1, -1], + [-1, -1, -1, -1], + [-1, -1, -1, -1], + [-1, -1, -1, -1], + 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\ No newline at end of file From 6e27f5f97ac3defafe3a754c127f7f51211ffdfa Mon Sep 17 00:00:00 2001 From: Cosmo Date: Wed, 23 Dec 2020 00:40:14 +0000 Subject: [PATCH 17/18] Exporting designs with circular strands is working, un ignoring tests_inputs/cadnano_v2_export as some .sc files are not generated but directly read by the tests --- scadnano/scadnano.py | 55 +- tests/scadnano_tests.py | 15 +- tests_inputs/cadnano_v2_export/.gitignore | 1 - ...est_16_helix_origami_rectangle_no_twist.sc | 1878 + ...pe_2_helix_origami_deletions_insertions.sc | 36 + ..._stape_2_helix_origami_extremely_simple.sc | 17 + ...tape_2_helix_origami_extremely_simple_2.sc | 18 + .../test_6_helix_origami_rectangle.sc | 282 + .../test_big_circular_staples.sc | 143 + .../test_big_circular_staples_hex.sc | 1123 + .../cadnano_v2_export/test_circular_strand.sc | 18 + .../test_export_design_with_helix_group.sc | 20 + ...t_design_with_helix_group_not_same_grid.sc | 20 + .../test_32_helix_rectangle.json | 126854 +-------------- 14 files changed, 3614 insertions(+), 126866 deletions(-) delete mode 100644 tests_inputs/cadnano_v2_export/.gitignore create mode 100644 tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.sc create mode 100644 tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.sc create mode 100644 tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.sc create mode 100644 tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.sc create mode 100644 tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.sc create mode 100644 tests_inputs/cadnano_v2_export/test_big_circular_staples.sc create mode 100644 tests_inputs/cadnano_v2_export/test_big_circular_staples_hex.sc create mode 100644 tests_inputs/cadnano_v2_export/test_circular_strand.sc create mode 100644 tests_inputs/cadnano_v2_export/test_export_design_with_helix_group.sc create mode 100644 tests_inputs/cadnano_v2_export/test_export_design_with_helix_group_not_same_grid.sc diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index c9a17b99..be6e83a1 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -4448,6 +4448,36 @@ def _cadnano_v2_place_strand(self, strand: Strand, dct: dict, self._cadnano_v2_place_crossover(which_helix, next_helix, domain, next_domain, strand_type) + # if the strand is circular, we need to close the loop + if strand.circular: + first_domain = strand.domains[0] + first_helix = dct['vstrands'][first_domain.helix] + first_start, first_end, first_forward = first_domain.start, first_domain.end, first_domain.forward + + last_domain = strand.domains[-1] + last_helix = dct['vstrands'][last_domain.helix] + last_start, last_end, last_forward = last_domain.start, last_domain.end, last_domain.forward + + the_base_from = last_end-1 + the_base_to = first_start + + if not last_forward: + the_base_from = last_start + + if not first_forward: + the_base_to = first_end-1 + + if first_helix[strand_type][the_base_to][:2] == [-1,-1]: + first_helix[strand_type][the_base_to][:2] = [last_helix['num'],the_base_from] + else: + first_helix[strand_type][the_base_to][2:] = [last_helix['num'],the_base_from] + + if last_helix[strand_type][the_base_from][:2] == [-1,-1]: + last_helix[strand_type][the_base_from][:2] = [first_helix['num'],the_base_to] + else: + last_helix[strand_type][the_base_from][2:] = [first_helix['num'],the_base_to] + + def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) -> Dict[int, int]: """Creates blank cadnanov2 helices in and initialized all their fields. """ @@ -4527,16 +4557,21 @@ def to_cadnano_v2(self) -> Dict[str, Any]: have the scaffold go backward. ''' - for strand in self.strands: - if hasattr(strand, is_scaffold_key) and strand.is_scaffold: - for domain in strand.domains: - if isinstance(domain, Loopout): - raise ValueError( - 'We cannot handle designs with Loopouts as it is not a cadnano v2 concept') - if domain.helix % 2 != int(not domain.forward): - raise ValueError('We can only convert designs where even helices have the scaffold' - 'going forward and odd helices have the scaffold going backward see ' - f'the spec v2.txt Note 4. {domain}') + for strand in self.strands: + for domain in strand.domains: + if isinstance(domain, Loopout): + raise ValueError( + 'We cannot handle designs with Loopouts as it is not a cadnano v2 concept') + right_direction = False + if hasattr(strand, is_scaffold_key) and strand.is_scaffold: + right_direction = ( domain.helix % 2 == int(not domain.forward) ) + else: + right_direction = not ( domain.helix % 2 == int(not domain.forward) ) + + if not right_direction: + raise ValueError('We can only convert designs where even helices have the scaffold' + 'going forward and odd helices have the scaffold going backward see ' + f'the spec v2.txt Note 4. {domain}') '''Filling the helices with blank. ''' diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 3343add8..777135cc 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -976,16 +976,27 @@ def test_16_helix_origami_rectangle_no_twist(self) -> None: filename='test_16_helix_origami_rectangle_no_twist.json') def test_circular_strand(self) -> None: - # TODO: not working helices = [sc.Helix(max_offset=24) for _ in range(2)] design = sc.Design(helices=helices, grid=sc.square) - design.strand(0,0).move(8).cross(1).move(-8).as_circular() + design.strand(1,0).move(8).cross(0).move(-8).as_circular() design.write_scadnano_file(directory=self.input_path, filename=f'test_circular_strand.{self.ext}') design.export_cadnano_v2(directory=self.output_path, filename='test_circular_strand.json') + def test_big_circular_staples_hex(self) -> None: + design = sc.Design.from_scadnano_file( + os.path.join(self.input_path, f'test_big_circular_staples_hex.{self.ext}')) + design.export_cadnano_v2(directory=self.output_path, + filename='test_big_circular_staples_hex.json') + + def test_big_circular_staples(self) -> None: + design = sc.Design.from_scadnano_file( + os.path.join(self.input_path, f'test_big_circular_staples.{self.ext}')) + design.export_cadnano_v2(directory=self.output_path, + filename='test_big_circular_staples.json') + def test_bad_cases(self) -> None: """ We do not handle Loopouts and design where the parity of the helix does not correspond to the direction. diff --git a/tests_inputs/cadnano_v2_export/.gitignore b/tests_inputs/cadnano_v2_export/.gitignore deleted file mode 100644 index b40fef57..00000000 --- a/tests_inputs/cadnano_v2_export/.gitignore +++ /dev/null @@ -1 +0,0 @@ -*.sc \ No newline at end of file diff --git a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.sc b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.sc new file mode 100644 index 00000000..d0c650b9 --- /dev/null +++ b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.sc @@ -0,0 +1,1878 @@ +{ + "version": "0.13.4", + "grid": "square", + "helices": [ + {"max_offset": 448, "grid_position": [0, 0]}, + {"max_offset": 448, "grid_position": [0, 1]}, + {"max_offset": 448, "grid_position": [0, 2]}, + {"max_offset": 448, "grid_position": [0, 3]}, + {"max_offset": 448, "grid_position": [0, 4]}, + {"max_offset": 448, "grid_position": [0, 5]}, + {"max_offset": 448, "grid_position": [0, 6]}, + {"max_offset": 448, "grid_position": [0, 7]}, + {"max_offset": 448, "grid_position": [0, 8]}, + {"max_offset": 448, "grid_position": [0, 9]}, + {"max_offset": 448, "grid_position": [0, 10]}, + {"max_offset": 448, "grid_position": [0, 11]}, + {"max_offset": 448, "grid_position": [0, 12]}, + {"max_offset": 448, "grid_position": [0, 13]}, + {"max_offset": 448, "grid_position": [0, 14]}, + {"max_offset": 448, "grid_position": [0, 15]} + ], + "strands": [ + { + "color": "#0066cc", + "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGA", + "domains": [ + {"helix": 15, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 14, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 13, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 12, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 11, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 10, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 9, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 8, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 7, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 6, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 5, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 4, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 3, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 2, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 1, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 0, "forward": true, "start": 16, "end": 432, "deletions": [33, 81, 129, 177, 225, 273, 321, 369, 417]}, + {"helix": 1, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 2, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 3, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 4, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 5, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 6, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 7, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 8, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 9, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 10, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 11, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 12, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 13, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 14, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 15, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]} + ], + "is_scaffold": true + }, + { + "color": "#f74308", + "sequence": "GCCGCTTTTGCGGGATTTGCAGGGAGTTAAAG", + "domains": [ + {"helix": 1, "forward": true, "start": 16, "end": 32}, + {"helix": 0, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#57bb00", + "sequence": "CAAGAGTAATCTTGACGCTGGCTGACCTTCAT", + "domains": [ + {"helix": 3, "forward": true, "start": 16, "end": 32}, + {"helix": 2, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#888888", + "sequence": "TGCAAAAGAAGTTTTGAATAGCGAGAGGCTTT", + "domains": [ + {"helix": 5, "forward": true, "start": 16, "end": 32}, + {"helix": 4, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#32b86c", + "sequence": "ACGGTGTCTGGAAGTTAATATGCAACTAAAGT", + "domains": [ + {"helix": 7, "forward": true, "start": 16, "end": 32}, + {"helix": 6, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#333333", + "sequence": "AGTCAAATCACCATCAGAGAAAGGCCGGAGAC", + "domains": [ + {"helix": 9, "forward": true, "start": 16, "end": 32}, + {"helix": 8, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#320096", + "sequence": "GGCGGATTGACCGTAACTCCGTGGGAACAAAC", + "domains": [ + {"helix": 11, "forward": true, "start": 16, "end": 32}, + {"helix": 10, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#03b6a2", + "sequence": "AAATTGTTATCCGCTCAGCTGTTTCCTGTGTG", + "domains": [ + {"helix": 13, "forward": true, "start": 16, "end": 32}, + {"helix": 12, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#7300de", + "sequence": "GAGTCCACTATTAAAGTTCCAGTTTGGAACAA", + "domains": [ + {"helix": 15, "forward": true, "start": 16, "end": 32}, + {"helix": 14, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#aaaa00", + "sequence": "AACCCATGTACCGTAAGCAAGCCCAATAGG", + "domains": [ + {"helix": 0, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 1, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#b8056c", + "sequence": "AGCCAGAATGGAAAGATAAATCCTCATTAA", + "domains": [ + {"helix": 2, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 3, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#007200", + "sequence": "ACTTGAGCCATTTGGTTATCACCGTCACCG", + "domains": [ + {"helix": 4, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 5, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#cc0000", + "sequence": "AACCCACAAGAATTGTAATATCAGAGAGAT", + "domains": [ + {"helix": 6, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 7, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#f7931e", + "sequence": "CATCGTAGGAATCATAGCCGTTTTTATTTT", + "domains": [ + {"helix": 8, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 9, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#f74308", + "sequence": "TAATTACTAGAAAAATAAACACCGGAATCA", + "domains": [ + {"helix": 10, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 11, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#57bb00", + "sequence": "TTAATTACATTTAACATCAAGAAAACAAAA", + "domains": [ + {"helix": 12, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 13, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#888888", + "sequence": "CTTTGCCCGAACGTTAACTCGTATTAAATC", + "domains": [ + {"helix": 14, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 15, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#32b86c", + "sequence": "AGAATAGAAAGGAACAACTAAAGGAATTGCG", + "domains": [ + {"helix": 0, "forward": false, "start": 216, "end": 248, "deletions": [225]} + ] + }, + { + "color": "#333333", + "sequence": "TACCAAGCCTCATCTTTGACCCCCTCAAGAG", + "domains": [ + {"helix": 2, "forward": false, "start": 208, "end": 216}, + {"helix": 1, "forward": true, "start": 208, "end": 232, "deletions": [225]} + ] + }, + { + "color": "#320096", + "sequence": "AAGGATTAAGAGGCTGAGACTCCAGCGATTA", + "domains": [ + {"helix": 1, "forward": true, "start": 232, "end": 240}, + {"helix": 2, "forward": false, "start": 216, "end": 240, "deletions": [225]} + ] + }, + { + "color": "#03b6a2", + "sequence": "AATCTACGACCAGTCAGGACGTTGTTCATAA", + "domains": [ + {"helix": 4, "forward": false, "start": 208, "end": 216}, + {"helix": 3, "forward": true, "start": 208, "end": 232, "deletions": [225]} + ] + }, + { + "color": "#7300de", + "sequence": "TCAAAATCAGCGTTTGCCATCTTGGAAGAAA", + "domains": [ + {"helix": 3, "forward": true, "start": 232, "end": 240}, + {"helix": 4, "forward": false, "start": 216, "end": 240, "deletions": [225]} + ] + }, + { + "color": "#aaaa00", + "sequence": "GCCCGAAATTGCATCAAAAAGATTACGTAGA", + "domains": [ + {"helix": 6, "forward": false, "start": 208, "end": 216}, + {"helix": 5, "forward": true, "start": 208, "end": 232, "deletions": [225]} + ] + }, + { + "color": "#b8056c", + "sequence": "AAATACATGCAGTATGTTAGCAAAAGAGGAA", + "domains": [ + {"helix": 5, "forward": true, "start": 232, "end": 240}, + {"helix": 6, "forward": false, "start": 216, "end": 240, "deletions": [225]} + ] + }, + { + "color": "#007200", + "sequence": "CAAAATTACATACAGGCAAGGCAACCTAATT", + "domains": [ + {"helix": 8, "forward": false, "start": 208, "end": 216}, + {"helix": 7, "forward": true, "start": 208, "end": 232, "deletions": [225]} + ] + }, + { + "color": "#cc0000", + "sequence": "TGCCAGTTAGCGTCTTTCCAGAGAGAATTAG", + "domains": [ + {"helix": 7, "forward": true, "start": 232, "end": 240}, + {"helix": 8, "forward": false, "start": 216, "end": 240, "deletions": [225]} + ] + }, + { + "color": "#f7931e", + "sequence": "TTGTATAAAGAAAAGCCCCAAAAAACAATAA", + "domains": [ + 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8, "forward": false, "start": 320, "end": 336, "deletions": [321]}, + {"helix": 9, "forward": true, "start": 320, "end": 328, "deletions": [321]} + ] + }, + { + "color": "#b8056c", + "sequence": "GTAGAAACCGCCATATTTAACAACTTTTTC", + "domains": [ + {"helix": 9, "forward": true, "start": 328, "end": 336}, + {"helix": 10, "forward": false, "start": 320, "end": 336, "deletions": [321]}, + {"helix": 11, "forward": true, "start": 320, "end": 328, "deletions": [321]} + ] + }, + { + "color": "#007200", + "sequence": "AAATATATTCGTCGCTATTAATTTTCGCCT", + "domains": [ + {"helix": 11, "forward": true, "start": 328, "end": 336}, + {"helix": 12, "forward": false, "start": 320, "end": 336, "deletions": [321]}, + {"helix": 13, "forward": true, "start": 320, "end": 328, "deletions": [321]} + ] + }, + { + "color": "#cc0000", + "sequence": "GATTGCTTTCCTGATTATCAGATTATCTTT", + "domains": [ + {"helix": 13, "forward": true, "start": 328, "end": 336}, + {"helix": 14, "forward": false, "start": 320, "end": 336, "deletions": [321]}, + {"helix": 15, "forward": true, "start": 320, "end": 328, "deletions": [321]} + ] + }, + { + "color": "#f7931e", + "sequence": "AGGAGCACTAACAACTAATAGATTGGAATTAT", + "domains": [ + {"helix": 15, "forward": true, "start": 328, "end": 352}, + {"helix": 14, "forward": false, "start": 344, "end": 352} + ] + }, + { + "color": "#f74308", + "sequence": "TAAGTTTTGAGGTTTAGTACCGCCGTTAGCGT", + "domains": [ + {"helix": 2, "forward": false, "start": 336, "end": 344}, + {"helix": 1, "forward": true, "start": 336, "end": 352}, + {"helix": 0, "forward": false, "start": 344, "end": 352} + ] + }, + { + "color": "#57bb00", + "sequence": "ATCGATAGGAACCACCACCAGAGCACTGGTAA", + "domains": [ + {"helix": 4, "forward": false, "start": 336, "end": 344}, + {"helix": 3, "forward": true, "start": 336, "end": 352}, + {"helix": 2, "forward": false, "start": 344, "end": 352} + ] + }, + { + "color": "#888888", + "sequence": "AAAGTAAGGCCAAAGACAAAAGGGATGAAACC", + "domains": [ + {"helix": 6, "forward": false, "start": 336, "end": 344}, + {"helix": 5, "forward": true, "start": 336, "end": 352}, + {"helix": 4, "forward": false, "start": 344, "end": 352} + ] + }, + { + "color": "#32b86c", + "sequence": "GCGAACCTATAACATAAAAACAGGTTTTAAGA", + "domains": [ + {"helix": 8, "forward": false, "start": 336, "end": 344}, + {"helix": 7, "forward": true, "start": 336, "end": 352}, + {"helix": 6, "forward": false, "start": 344, "end": 352} + ] + }, + { + "color": "#333333", + "sequence": "TTGAGAATCAATCAATAATCGGCTGCGTTTTA", + "domains": [ + {"helix": 10, "forward": false, "start": 336, "end": 344}, + {"helix": 9, "forward": true, "start": 336, "end": 352}, + {"helix": 8, "forward": false, "start": 344, "end": 352} + ] + }, + { + "color": "#320096", + "sequence": "TCTGTAAATTTAGTTAATTTCATCGGGCTTAA", + "domains": [ + {"helix": 12, "forward": false, "start": 336, "end": 344}, + {"helix": 11, "forward": true, "start": 336, "end": 352}, + {"helix": 10, "forward": false, "start": 344, "end": 352} + ] + }, + { + "color": "#03b6a2", + "sequence": "CATCATATTGAATACCAAGTTACAACCTTGCT", + "domains": [ + {"helix": 14, "forward": false, "start": 336, "end": 344}, + {"helix": 13, "forward": true, "start": 336, "end": 352}, + {"helix": 12, "forward": false, "start": 344, "end": 352} + ] + }, + { + "color": "#7300de", + "sequence": "GCATTCCACAGACAGCCCTCATAACCCTCAG", + "domains": [ + {"helix": 0, "forward": false, "start": 352, "end": 376, "deletions": [369]}, + {"helix": 1, "forward": true, "start": 352, "end": 360} + ] + }, + { + "color": "#aaaa00", + "sequence": "AACCGCCAGATGATACAGGAGTGTCGCCGCCA", + "domains": [ + {"helix": 1, "forward": true, "start": 360, "end": 368}, + {"helix": 2, "forward": false, "start": 352, "end": 368}, + {"helix": 3, "forward": true, "start": 352, "end": 360} + ] + }, + { + "color": "#b8056c", + "sequence": "GCATTGACGCCGGAAACGTCACCACGACATTC", + "domains": [ + {"helix": 3, "forward": true, "start": 360, "end": 368}, + {"helix": 4, "forward": false, "start": 352, "end": 368}, + {"helix": 5, "forward": true, "start": 352, "end": 360} + ] + }, + { + "color": "#007200", + "sequence": "AACCGATTATCTTACCGAAGCCCTGAAGCGCA", + "domains": [ + {"helix": 5, "forward": true, "start": 360, "end": 368}, + {"helix": 6, "forward": false, "start": 352, "end": 368}, + {"helix": 7, "forward": true, "start": 352, "end": 360} + ] + }, + { + "color": "#cc0000", + "sequence": "TTAGACGGATTCTAAGAACGCGAGGTCTTTCC", + "domains": [ + {"helix": 7, "forward": true, "start": 360, "end": 368}, + {"helix": 8, "forward": false, "start": 352, "end": 368}, + {"helix": 9, "forward": true, "start": 352, "end": 360} + ] + }, + { + "color": "#f7931e", + "sequence": "TTATCATTCCAACGCTCAACAGTATTCTGACC", + "domains": [ + {"helix": 9, "forward": true, "start": 360, "end": 368}, + {"helix": 10, "forward": false, "start": 352, "end": 368}, + {"helix": 11, "forward": true, "start": 352, "end": 360} + ] + }, + { + "color": "#f74308", + "sequence": "TAAATTTATATATGTGAGTGAATAAAATCGCG", + "domains": [ + {"helix": 11, "forward": true, "start": 360, "end": 368}, + {"helix": 12, "forward": false, "start": 352, "end": 368}, + {"helix": 13, "forward": true, "start": 352, "end": 360} + ] + }, + { + "color": "#57bb00", + "sequence": "CAGAGGCGAACCACCAGAAGGAGCAGAGCCGT", + "domains": [ + {"helix": 13, "forward": true, "start": 360, "end": 368}, + {"helix": 14, "forward": false, "start": 352, "end": 368}, + {"helix": 15, "forward": true, "start": 352, "end": 360} + ] + }, + { + "color": "#888888", + "sequence": "CAATAGATAATACATTTGAGGATTTTGCGGA", + "domains": [ + {"helix": 15, "forward": true, "start": 360, "end": 384, "deletions": [369]}, + {"helix": 14, "forward": false, "start": 376, "end": 384} + ] + }, + { + "color": "#32b86c", + "sequence": "GGCTTTTCCCTCAGAACCGCCACGCCTGTA", + "domains": [ + {"helix": 2, "forward": false, "start": 368, "end": 376, "deletions": [369]}, + {"helix": 1, "forward": true, "start": 368, "end": 384, "deletions": [369]}, + {"helix": 0, "forward": false, "start": 376, "end": 384} + ] + }, + { + "color": "#333333", + "sequence": "TAGCAAGAGGAGGTTGAGGCAGTCATACAT", + "domains": [ + {"helix": 4, "forward": false, "start": 368, "end": 376, "deletions": [369]}, + {"helix": 3, "forward": true, "start": 368, "end": 384, "deletions": [369]}, + {"helix": 2, "forward": false, "start": 376, "end": 384} + ] + }, + { + "color": "#320096", + "sequence": "AATAGCTGAGGGAGGGAAGGTAATTACCAT", + "domains": [ + {"helix": 6, "forward": false, "start": 368, "end": 376, "deletions": [369]}, + {"helix": 5, "forward": true, "start": 368, "end": 384, "deletions": [369]}, + {"helix": 4, "forward": false, "start": 376, "end": 384} + ] + }, + { + "color": "#03b6a2", + "sequence": "ATCCGGTGAGAATTAACTGAACGAAATAGC", + "domains": [ + {"helix": 8, "forward": false, "start": 368, "end": 376, "deletions": [369]}, + {"helix": 7, "forward": true, "start": 368, "end": 384, "deletions": [369]}, + {"helix": 6, "forward": false, "start": 376, "end": 384} + ] + }, + { + "color": "#7300de", + "sequence": "TATAAAGCCAAGAACGGGTATTGAAGGCTT", + "domains": [ + {"helix": 10, "forward": false, "start": 368, "end": 376, "deletions": [369]}, + {"helix": 9, "forward": true, "start": 368, "end": 384, "deletions": [369]}, + {"helix": 8, "forward": false, "start": 376, "end": 384} + ] + }, + { + "color": "#aaaa00", + "sequence": "AAATCAAATGGTTTGAAATACCCTTACCAG", + "domains": [ + {"helix": 12, "forward": false, "start": 368, "end": 376, "deletions": [369]}, + {"helix": 11, "forward": true, "start": 368, "end": 384, "deletions": [369]}, + {"helix": 10, "forward": false, "start": 376, "end": 384} + ] + }, + { + "color": "#b8056c", + "sequence": "ACAAAGAAATTATTCATTTCAACAGTACAT", + "domains": [ + {"helix": 14, "forward": false, "start": 368, "end": 376, "deletions": [369]}, + {"helix": 13, "forward": true, "start": 368, "end": 384, "deletions": [369]}, + {"helix": 12, "forward": false, "start": 376, "end": 384} + ] + }, + { + "color": "#007200", + "sequence": "TTTCGTCACCAGTACAAACTACAACCCTCAGA", + "domains": [ + {"helix": 0, "forward": false, "start": 384, "end": 408}, + {"helix": 1, "forward": true, "start": 384, "end": 392} + ] + }, + { + "color": "#cc0000", + "sequence": "GCCACCACACCGTTCCAGTAAGCGGTCAGACG", + "domains": [ + {"helix": 1, "forward": true, "start": 392, "end": 400}, + {"helix": 2, "forward": false, "start": 384, "end": 400}, + {"helix": 3, "forward": true, "start": 384, "end": 392} + ] + }, + { + "color": "#f7931e", + "sequence": "ATTGGCCTAATCACCAGTAGCACCAATATTGA", + "domains": [ + {"helix": 3, "forward": true, "start": 392, "end": 400}, + {"helix": 4, "forward": false, "start": 384, "end": 400}, + {"helix": 5, "forward": true, "start": 384, "end": 392} + ] + }, + { + "color": "#f74308", + "sequence": "CGGAAATTAAGAGCAAGAAACAATACCCTGAA", + "domains": [ + {"helix": 5, "forward": true, "start": 392, "end": 400}, + {"helix": 6, "forward": false, "start": 384, "end": 400}, + {"helix": 7, "forward": true, "start": 384, "end": 392} + ] + }, + { + "color": "#57bb00", + "sequence": "CAAAGTCAAAGCAAATCAGATATAAAACCAAG", + "domains": [ + {"helix": 7, "forward": true, "start": 392, "end": 400}, + {"helix": 8, "forward": false, "start": 384, "end": 400}, + {"helix": 9, "forward": true, "start": 384, "end": 392} + ] + }, + { + "color": "#888888", + "sequence": "TACCGCACATGCGTTATACAAATTGACCGTGT", + "domains": [ + {"helix": 9, "forward": true, "start": 392, "end": 400}, + {"helix": 10, "forward": false, "start": 384, "end": 400}, + {"helix": 11, "forward": true, "start": 384, "end": 392} + ] + }, + { + "color": "#32b86c", + "sequence": "GATAAATACCTTTTTTAATGGAAATTACCTGA", + "domains": [ + {"helix": 11, "forward": true, "start": 392, "end": 400}, + {"helix": 12, "forward": false, "start": 384, "end": 400}, + {"helix": 13, "forward": true, "start": 384, "end": 392} + ] + }, + { + "color": "#333333", + "sequence": "GCAAAAGATGAGTAACATTATCATTTAGAAGT", + "domains": [ + {"helix": 13, "forward": true, "start": 392, "end": 400}, + {"helix": 14, "forward": false, "start": 384, "end": 400}, + {"helix": 15, "forward": true, "start": 384, "end": 392} + ] + }, + { + "color": "#320096", + "sequence": "ATTAGACTTTACAAACAATTCGACATTAATTT", + "domains": [ + {"helix": 15, "forward": true, "start": 392, "end": 416}, + {"helix": 14, "forward": false, "start": 408, "end": 416} + ] + }, + { + "color": "#03b6a2", + "sequence": "CTGAATTTCCTCATTTTCAGGGATACACTGAG", + "domains": [ + {"helix": 2, "forward": false, "start": 400, "end": 408}, + {"helix": 1, "forward": true, "start": 400, "end": 416}, + {"helix": 0, "forward": false, "start": 408, "end": 416} + ] + }, + { + "color": "#7300de", + "sequence": "GCCAGCAATGATATTCACAAACAACGCAGTCT", + "domains": [ + {"helix": 4, "forward": false, "start": 400, "end": 408}, + {"helix": 3, "forward": true, "start": 400, "end": 416}, + {"helix": 2, "forward": false, "start": 408, "end": 416} + ] + }, + { + "color": "#aaaa00", + "sequence": "CCAATAATATTCATTAAAGGTGAAGAATTAGA", + "domains": [ + {"helix": 6, "forward": false, "start": 400, "end": 408}, + {"helix": 5, "forward": true, "start": 400, "end": 416}, + {"helix": 4, "forward": false, "start": 408, "end": 416} + ] + }, + { + "color": "#b8056c", + "sequence": "CCAATAGCGAGGGTAATTGAGCGCAGTTAAGC", + "domains": [ + {"helix": 8, "forward": false, "start": 400, "end": 408}, + {"helix": 7, "forward": true, "start": 400, "end": 416}, + {"helix": 6, "forward": false, "start": 408, "end": 416} + ] + }, + { + "color": "#007200", + "sequence": "AGTATCATTCATCGAGAACAAGCATACCGCGC", + "domains": [ + {"helix": 10, "forward": false, "start": 400, "end": 408}, + {"helix": 9, "forward": true, "start": 400, "end": 416}, + {"helix": 8, "forward": false, "start": 408, "end": 416} + ] + }, + { + "color": "#cc0000", + "sequence": "TTGAATTAAGGCGTTAAATAAGAAGCCTGTTT", + "domains": [ + {"helix": 12, "forward": false, "start": 400, "end": 408}, + {"helix": 11, "forward": true, "start": 400, "end": 416}, + {"helix": 10, "forward": false, "start": 408, "end": 416} + ] + }, + { + "color": "#f7931e", + "sequence": "TAAAAGTTAGATGATGAAACAAACAATTTCAT", + "domains": [ + {"helix": 14, "forward": false, "start": 400, "end": 408}, + {"helix": 13, "forward": true, "start": 400, "end": 416}, + {"helix": 12, "forward": false, "start": 408, "end": 416} + ] + } + ] +} \ No newline at end of file diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.sc b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.sc new file mode 100644 index 00000000..544932e6 --- /dev/null +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.sc @@ -0,0 +1,36 @@ +{ + "version": "0.13.4", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]} + ], + "strands": [ + { + "color": "#0066cc", + "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", + "domains": [ + {"helix": 1, "forward": false, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, + {"helix": 0, "forward": true, "start": 0, "end": 32, "deletions": [11, 12, 24], "insertions": [[6, 1], [18, 2]]}, + {"helix": 1, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 4]]} + ], + "is_scaffold": true + }, + { + "color": "#f74308", + "sequence": "GTTACGTTACGTTACGTTGTTACGTTACGTTAC", + "domains": [ + {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, + {"helix": 0, "forward": false, "start": 0, "end": 16, "deletions": [11, 12], "insertions": [[6, 1]]} + ] + }, + { + "color": "#57bb00", + "sequence": "ACGTTACGTTACGTTACCGTTACGTTACGTTACGTT", + "domains": [ + {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, + {"helix": 1, "forward": true, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 4]]} + ] + } + ] +} \ No newline at end of file diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.sc b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.sc new file mode 100644 index 00000000..a4981b33 --- /dev/null +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.sc @@ -0,0 +1,17 @@ +{ + "version": "0.13.4", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]} + ], + "strands": [ + { + "color": "#0066cc", + "domains": [ + {"helix": 0, "forward": true, "start": 0, "end": 32} + ], + "is_scaffold": true + } + ] +} \ No newline at end of file diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.sc b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.sc new file mode 100644 index 00000000..fdafae7e --- /dev/null +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.sc @@ -0,0 +1,18 @@ +{ + "version": "0.13.4", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]} + ], + "strands": [ + { + "color": "#0066cc", + "domains": [ + {"helix": 0, "forward": true, "start": 0, "end": 32}, + {"helix": 1, "forward": false, "start": 0, "end": 32} + ], + "is_scaffold": true + } + ] +} \ No newline at end of file diff --git a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.sc b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.sc new file mode 100644 index 00000000..40aa4f93 --- /dev/null +++ b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.sc @@ -0,0 +1,282 @@ +{ + "version": "0.13.4", + "grid": "square", + "helices": [ + {"max_offset": 192, "grid_position": [0, 0]}, + {"max_offset": 192, "grid_position": [0, 1]}, + {"max_offset": 192, "grid_position": [0, 2]}, + {"max_offset": 192, "grid_position": [0, 3]}, + {"max_offset": 192, "grid_position": [0, 4]}, + {"max_offset": 192, "grid_position": [0, 5]} + ], + "strands": [ + { + 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\ No newline at end of file From 675b5428385bb8885cb25ba7ad45a225223608a7 Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 24 Dec 2020 08:37:19 -0800 Subject: [PATCH 18/18] fixed mypy and PEP errors in cadnano import/export code --- scadnano/scadnano.py | 87 ++++++++++++++++++++++---------------------- 1 file changed, 44 insertions(+), 43 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index be6e83a1..b171fed7 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -54,7 +54,7 @@ import re from builtins import ValueError from dataclasses import dataclass, field, InitVar, replace -from typing import Tuple, List, Sequence, Iterable, Set, Dict, Union, Optional, FrozenSet, Type, cast, Any, \ +from typing import Tuple, List, Iterable, Set, Dict, Union, Optional, FrozenSet, Type, cast, Any, \ TypeVar, Generic, Callable from collections import defaultdict, OrderedDict, Counter import sys @@ -284,6 +284,8 @@ def colors(self, newcolors: Iterable[Color]) -> None: """Default color for non-scaffold strand(s).""" default_cadnano_strand_color = Color(hex_string='#BFBFBF') + + # # END Colors ############################################################################## @@ -4020,21 +4022,21 @@ def assign_modifications_to_strands(strands: List[Strand], strand_jsons: List[di @staticmethod def _cadnano_v2_import_find_5_end(vstrands: VStrands, strand_type: str, helix_num: int, base_id: int, id_from: int, - base_from: int) -> Tuple[int, int]: + base_from: int) -> Tuple[int, int, bool]: """ Routine which finds the 5' end of a strand in a cadnano v2 import. It returns the helix and the base of the 5' end. """ - id_from_before = helix_num # 'id' stands for helix id + id_from_before = helix_num # 'id' stands for helix id base_from_before = base_id circular_seen = {} is_circular = False while not (id_from == -1 and base_from == -1): - if (id_from,base_from) in circular_seen: + if (id_from, base_from) in circular_seen: is_circular = True break - circular_seen[(id_from,base_from)] = True + circular_seen[(id_from, base_from)] = True id_from_before = id_from base_from_before = base_from id_from, base_from, _, _ = vstrands[id_from][strand_type][base_from] @@ -4098,9 +4100,9 @@ def _cadnano_v2_import_explore_domains(vstrands: VStrands, seen: Dict[Tuple[int, circular_seen = {} while not (curr_helix == -1 and curr_base == -1): - if (curr_helix,curr_base) in circular_seen: + if (curr_helix, curr_base) in circular_seen: break - circular_seen[(curr_helix,curr_base)] = True + circular_seen[(curr_helix, curr_base)] = True old_helix = curr_helix old_base = curr_base @@ -4110,8 +4112,9 @@ def _cadnano_v2_import_explore_domains(vstrands: VStrands, seen: Dict[Tuple[int, # We have a crossover when we jump helix or when order is broken on same helix # Or circular strand if curr_helix != old_helix or (not direction_forward and curr_base > old_base) or ( - direction_forward and curr_base < old_base) or (curr_helix == strand_5_end_helix and curr_base == strand_5_end_base): - + direction_forward and curr_base < old_base) or ( + curr_helix == strand_5_end_helix and curr_base == strand_5_end_base): + if direction_forward: end = old_base else: @@ -4135,16 +4138,16 @@ def _cadnano_v2_import_explore_domains(vstrands: VStrands, seen: Dict[Tuple[int, return domains @staticmethod - def _cadnano_v2_import_circular_strands_merge_first_last_domains(domains: Sequence[Domain]) -> None: + def _cadnano_v2_import_circular_strands_merge_first_last_domains(domains: List[Domain]) -> None: """ When we create domains for circular strands in the cadnano import routine, we may end up with a fake crossover if first and last domain are on same helix, we have to merge them if it is the case. """ if domains[0].helix != domains[-1].helix: return - - domains[0].start = min(domains[0].start,domains[-1].start) - domains[0].end = max(domains[0].end,domains[-1].end) + + domains[0].start = min(domains[0].start, domains[-1].start) + domains[0].end = max(domains[0].end, domains[-1].end) del domains[-1] @@ -4162,20 +4165,20 @@ def _cadnano_v2_import_explore_strand(vstrands: VStrands, if (id_from, base_from, id_to, base_to) == (-1, -1, -1, -1): return None - + strand_5_end_helix, strand_5_end_base, is_circular = Design._cadnano_v2_import_find_5_end(vstrands, - strand_type, - helix_num, - base_id, - id_from, - base_from) + strand_type, + helix_num, + base_id, + id_from, + base_from) strand_color = Design._cadnano_v2_import_find_strand_color(vstrands, strand_type, strand_5_end_base, strand_5_end_helix) - domains: Sequence[Domain] = Design._cadnano_v2_import_explore_domains(vstrands, seen, strand_type, - strand_5_end_base, - strand_5_end_helix) + domains: List[Domain] = Design._cadnano_v2_import_explore_domains(vstrands, seen, strand_type, + strand_5_end_base, + strand_5_end_helix) # merge first and last domain if circular if is_circular: Design._cadnano_v2_import_circular_strands_merge_first_last_domains(domains) @@ -4193,7 +4196,7 @@ def from_cadnano_v2(directory: Optional[str] = None, filename: Optional[str] = N """ Creates a Design from a cadnano v2 file. """ - + if json_dict is None and filename is not None and directory is not None: file_path = os.path.join(directory, filename) f = open(file_path, 'r') @@ -4229,7 +4232,6 @@ def from_cadnano_v2(directory: Optional[str] = None, filename: Optional[str] = N strands: List[Strand] = [] cadnano_helices = OrderedDict({}) for cadnano_helix in cadnano_v2_design['vstrands']: - helix_num = cadnano_helix['num'] cadnano_helices[helix_num] = cadnano_helix @@ -4450,33 +4452,32 @@ def _cadnano_v2_place_strand(self, strand: Strand, dct: dict, # if the strand is circular, we need to close the loop if strand.circular: - first_domain = strand.domains[0] + first_domain = strand.first_bound_domain() first_helix = dct['vstrands'][first_domain.helix] first_start, first_end, first_forward = first_domain.start, first_domain.end, first_domain.forward - last_domain = strand.domains[-1] + last_domain = strand.last_bound_domain() last_helix = dct['vstrands'][last_domain.helix] last_start, last_end, last_forward = last_domain.start, last_domain.end, last_domain.forward - the_base_from = last_end-1 + the_base_from = last_end - 1 the_base_to = first_start if not last_forward: the_base_from = last_start if not first_forward: - the_base_to = first_end-1 - - if first_helix[strand_type][the_base_to][:2] == [-1,-1]: - first_helix[strand_type][the_base_to][:2] = [last_helix['num'],the_base_from] - else: - first_helix[strand_type][the_base_to][2:] = [last_helix['num'],the_base_from] - - if last_helix[strand_type][the_base_from][:2] == [-1,-1]: - last_helix[strand_type][the_base_from][:2] = [first_helix['num'],the_base_to] + the_base_to = first_end - 1 + + if first_helix[strand_type][the_base_to][:2] == [-1, -1]: + first_helix[strand_type][the_base_to][:2] = [last_helix['num'], the_base_from] else: - last_helix[strand_type][the_base_from][2:] = [first_helix['num'],the_base_to] + first_helix[strand_type][the_base_to][2:] = [last_helix['num'], the_base_from] + if last_helix[strand_type][the_base_from][:2] == [-1, -1]: + last_helix[strand_type][the_base_from][:2] = [first_helix['num'], the_base_to] + else: + last_helix[strand_type][the_base_from][2:] = [first_helix['num'], the_base_to] def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) -> Dict[int, int]: """Creates blank cadnanov2 helices in and initialized all their fields. @@ -4557,21 +4558,21 @@ def to_cadnano_v2(self) -> Dict[str, Any]: have the scaffold go backward. ''' - for strand in self.strands: + for strand in self.strands: for domain in strand.domains: if isinstance(domain, Loopout): raise ValueError( 'We cannot handle designs with Loopouts as it is not a cadnano v2 concept') - right_direction = False + right_direction: bool if hasattr(strand, is_scaffold_key) and strand.is_scaffold: - right_direction = ( domain.helix % 2 == int(not domain.forward) ) + right_direction = (domain.helix % 2 == int(not domain.forward)) else: - right_direction = not ( domain.helix % 2 == int(not domain.forward) ) + right_direction = not (domain.helix % 2 == int(not domain.forward)) if not right_direction: raise ValueError('We can only convert designs where even helices have the scaffold' - 'going forward and odd helices have the scaffold going backward see ' - f'the spec v2.txt Note 4. {domain}') + 'going forward and odd helices have the scaffold going backward see ' + f'the spec v2.txt Note 4. {domain}') '''Filling the helices with blank. '''