Merge pull request #98 from UC-Davis-molecular-computing/dev

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UC-Davis-molecular-computing · Jul 3, 2020 · 92d2a44 · 92d2a44
2 parents 9b32874 + fed5149
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diff --git a/.gitignore b/.gitignore
@@ -21,3 +21,4 @@ examples/run_all_examples.xls
 __pycache__/
 tests_outputs/
 .vscode/
+dist/
diff --git a/README.md b/README.md
@@ -8,10 +8,10 @@ The scadnano Python module is a library for describing synthetic DNA nanostructu
 
 If you find scadnano useful in a scientific project, please cite its associated paper:
 
-> scadnano: A browser-based, easily scriptable tool for designing DNA nanostructures.  
+> <ins>scadnano: A browser-based, scriptable tool for designing DNA nanostructures</ins>.  
   David Doty, Benjamin L Lee, and Tristan Stérin.  
-  *Technical Report 2005.11841, arXiv*, 2020.  
-  [ [arXiv paper](https://arxiv.org/abs/2005.11841) | [BibTeX](https://web.cs.ucdavis.edu/~doty/papers/scadnano.bib) ]
+  DNA 2020: *Proceedings of the 26th International Conference on DNA Computing and Molecular Programming*
+  [ [paper](https://arxiv.org/abs/2005.11841) | [BibTeX](https://web.cs.ucdavis.edu/~doty/papers/scadnano.bib) ]
 
 
 ## Overview
@@ -64,7 +64,7 @@ Once Python is installed, there are two ways you can install the scadnano Python
     * *optional*: [origami_rectangle.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/origami_rectangle.py); This can help create origami rectangles, but it is not necessary to use scadnano.
     * *optional*: [_version.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/_version.py) This ensures that the current version number is written into any `.dna` files written by the library; otherwise it may be out of date. (Which should not matter for the most part.)
     
-    The scadnano package uses the Python package [xlwt](https://pypi.org/project/xlwt/) to write Excel files, so in order to call the method [`DNADesign.write_idt_plate_excel_file()`](https://scadnano-python-package.readthedocs.io/#scadnano.scadnano.DNADesign.write_idt_plate_excel_file) to export an Excel file with DNA sequences, xlwt must be installed. To install, type `pip install xlwt` at the command line.
+    The scadnano package uses the Python package [xlwt](https://pypi.org/project/xlwt/) to write Excel files, so in order to call the method [`DNADesign.write_idt_plate_excel_file()`](https://scadnano-python-package.readthedocs.io/#scadnano.DNADesign.write_idt_plate_excel_file) to export an Excel file with DNA sequences, xlwt must be installed. To install, type `pip install xlwt` at the command line.
 
 
 

diff --git a/dist/scadnano-0.1.0.tar.gz b/dist/scadnano-0.1.0.tar.gz
diff --git a/dist/scadnano-0.1.1.tar.gz b/dist/scadnano-0.1.1.tar.gz
diff --git a/dist/scadnano-0.1.2.tar.gz b/dist/scadnano-0.1.2.tar.gz
diff --git a/dist/scadnano-0.2.0.tar.gz b/dist/scadnano-0.2.0.tar.gz
diff --git a/dist/scadnano-0.3.0.tar.gz b/dist/scadnano-0.3.0.tar.gz
diff --git a/dist/scadnano-0.4.0.tar.gz b/dist/scadnano-0.4.0.tar.gz
diff --git a/dist/scadnano-0.5.0.tar.gz b/dist/scadnano-0.5.0.tar.gz
diff --git a/dist/scadnano-0.6.0.tar.gz b/dist/scadnano-0.6.0.tar.gz
diff --git a/dist/scadnano-0.6.1.tar.gz b/dist/scadnano-0.6.1.tar.gz
diff --git a/dist/scadnano-0.6.2.tar.gz b/dist/scadnano-0.6.2.tar.gz
diff --git a/dist/scadnano-0.6.3.tar.gz b/dist/scadnano-0.6.3.tar.gz
diff --git a/dist/scadnano-0.6.4.tar.gz b/dist/scadnano-0.6.4.tar.gz
diff --git a/dist/scadnano-0.6.5.tar.gz b/dist/scadnano-0.6.5.tar.gz
diff --git a/dist/scadnano-0.6.6.tar.gz b/dist/scadnano-0.6.6.tar.gz
diff --git a/dist/scadnano-0.6.7.tar.gz b/dist/scadnano-0.6.7.tar.gz
diff --git a/dist/scadnano-0.6.8.tar.gz b/dist/scadnano-0.6.8.tar.gz
diff --git a/dist/scadnano-0.7.0.tar.gz b/dist/scadnano-0.7.0.tar.gz
diff --git a/dist/scadnano-0.7.1.tar.gz b/dist/scadnano-0.7.1.tar.gz
diff --git a/dist/scadnano-0.7.2.tar.gz b/dist/scadnano-0.7.2.tar.gz
diff --git a/dist/scadnano-0.7.3.tar.gz b/dist/scadnano-0.7.3.tar.gz
diff --git a/dist/scadnano-0.7.4.tar.gz b/dist/scadnano-0.7.4.tar.gz
diff --git a/dist/scadnano-0.8.0.tar.gz b/dist/scadnano-0.8.0.tar.gz
diff --git a/dist/scadnano-0.8.1.tar.gz b/dist/scadnano-0.8.1.tar.gz
diff --git a/dist/scadnano-0.8.2.tar.gz b/dist/scadnano-0.8.2.tar.gz
diff --git a/dist/scadnano-0.8.3.tar.gz b/dist/scadnano-0.8.3.tar.gz
diff --git a/dist/scadnano-0.9.0.tar.gz b/dist/scadnano-0.9.0.tar.gz
diff --git a/dist/scadnano-0.9.1.tar.gz b/dist/scadnano-0.9.1.tar.gz
diff --git a/dist/scadnano-0.9.2.tar.gz b/dist/scadnano-0.9.2.tar.gz
diff --git a/dist/scadnano-0.9.3.tar.gz b/dist/scadnano-0.9.3.tar.gz
diff --git a/scadnano/_version.py b/scadnano/_version.py
@@ -3,4 +3,4 @@
 
 # The following line *must* be the last in the module, exactly as formatted:
 # XXX: REMEMBER TO CHANGE VERSION IN scadnano.py also, for users who do not install from PyPI
-__version__ = "0.9.3"
+__version__ = "0.9.4"
diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py
@@ -13,10 +13,10 @@
 
 If you find scadnano useful in a scientific project, please cite its associated paper:
 
- | scadnano: A browser-based, easily scriptable tool for designing DNA nanostructures.
+ | scadnano: A browser-based, scriptable tool for designing DNA nanostructures.
  | David Doty, Benjamin L Lee, and Tristan Stérin.
- | *Technical Report 2005.11841, arXiv*, 2020.
- | [ `arXiv paper <https://arxiv.org/abs/2005.11841>`_ | `BibTeX <https://web.cs.ucdavis.edu/~doty/papers/scadnano.bib>`_ ]
+ | DNA 2020: *Proceedings of the 26th International Conference on DNA Computing and Molecular Programming*
+ | [ `paper <https://arxiv.org/abs/2005.11841>`_ | `BibTeX <https://web.cs.ucdavis.edu/~doty/papers/scadnano.bib>`_ ]
 
 This library uses typing hints from the Python typing library.
 (https://docs.python.org/3/library/typing.html)
@@ -63,7 +63,7 @@
     from ._version import __version__
 except ImportError:
     # this is so scadnano.py file works without _version.py being present, in case user downloads it
-    __version__ = "0.9.3"
+    __version__ = "0.9.4"
 
 StrandLabel = TypeVar('StrandLabel')
 DomainLabel = TypeVar('DomainLabel')
@@ -1224,6 +1224,10 @@ def __str__(self):
     def strand(self) -> Strand:
         return self._parent_strand
 
+    def set_label(self, label: StrandLabel):
+        """Sets label of this :any:`Domain`."""
+        self.label = label
+
     def _check_start_end(self):
         if self.start >= self.end:
             raise StrandError(self._parent_strand,
@@ -1907,6 +1911,44 @@ def with_domain_sequence(self, sequence: str, assign_complement: bool = True) ->
                                assign_complement=assign_complement)
         return self
 
+    def with_label(self, label: StrandLabel) -> StrandBuilder:
+        """
+        Assigns `label` as label of the :any:`Strand` being built.
+
+        .. code-block:: Python
+
+            design.strand(0, 0).to(10).cross(1).to(5).with_label('scaffold')
+
+        :param label: label to assign to the :any:`Strand`
+        :return: self
+        """
+        self.strand.set_label(label)
+        return self
+
+    def with_domain_label(self, label: DomainLabel) -> StrandBuilder:
+        """
+        Assigns `label` as DNA sequence of the most recently created :any:`Domain` in
+        the :any:`Strand` being built. This should be called immediately after a :any:`Domain` is created
+        via a call to
+        :py:meth:`StrandBuilder.to`,
+        :py:meth:`StrandBuilder.update_to`,
+        or
+        :py:meth:`StrandBuilder.loopout`, e.g.,
+
+        .. code-block:: Python
+
+            design.strand(0, 5).to(8).with_domain_label('domain 1')\
+                .cross(1).to(5).with_domain_label('domain 2')\
+                .loopout(2, 4).with_domain_label('domain 3')\
+                .to(10).with_domain_label('domain 4')
+
+        :param label: label to assign to the :any:`Domain`
+        :return: self
+        """
+        last_domain = self.strand.domains[-1]
+        last_domain.set_label(label)
+        return self
+
 
 @dataclass
 class Strand(_JSONSerializable, Generic[StrandLabel, DomainLabel]):

diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py
@@ -2202,8 +2202,9 @@ def test_domain_labels(self):
         self.assertEqual(dom11_expected.label, dom11.label)
 
     def test_nondefault_geometry(self):
-        geometry_expected = sc.Geometry(rise_per_base_pair=10.0, helix_radius=4.0, bases_per_turn=11.0, minor_groove_angle=10.0,
-                               inter_helix_gap=5.0)
+        geometry_expected = sc.Geometry(rise_per_base_pair=10.0, helix_radius=4.0, bases_per_turn=11.0,
+                                        minor_groove_angle=10.0,
+                                        inter_helix_gap=5.0)
         design = sc.DNADesign(helices=[], strands=[], geometry=geometry_expected)
         json_str = design.to_json()
         design_from_json = sc.DNADesign.from_scadnano_json_str(json_str)
@@ -2738,6 +2739,7 @@ def test_strand_references_nonexistent_helix(self):
         with self.assertRaises(sc.IllegalDNADesignError):
             sc.DNADesign(grid=sc.square, helices=[h1, h2], strands=strands)
 
+
 class TestInsertRemoveDomains(unittest.TestCase):
 
     def setUp(self) -> None:
@@ -2762,7 +2764,7 @@ def test_insert_domain_with_sequence(self):
             sc.Domain(0, True, 0, 3),
             sc.Domain(1, False, 0, 3),
             sc.Domain(3, True, 0, 3),
-        ]) #, dna_sequence='ACA TCT GTG'.replace(' ', ''))
+        ])  # , dna_sequence='ACA TCT GTG'.replace(' ', ''))
         self.assertEqual(expected_strand_before, design.strands[0])
 
         domain = sc.Domain(2, True, 0, 3)
@@ -2783,7 +2785,7 @@ def test_append_domain_with_sequence(self):
             sc.Domain(1, False, 0, 3),
             sc.Domain(2, True, 0, 3),
             sc.Domain(3, False, 0, 3),
-        ], dna_sequence='ACA TCT GTG ???'.replace(' ',''))
+        ], dna_sequence='ACA TCT GTG ???'.replace(' ', ''))
         self.assertEqual(expected_strand, self.strand)
 
     def test_remove_first_domain_with_sequence(self):
@@ -2811,6 +2813,69 @@ def test_remove_last_domain_with_sequence(self):
         self.assertEqual(expected_strand, self.strand)
 
 
+class TestLabels(unittest.TestCase):
+
+    def setUp(self) -> None:
+        helices = [sc.Helix(max_offset=100) for _ in range(10)]
+        self.design = sc.DNADesign(helices=helices, strands=[], grid=sc.square)
+
+    def test_with_label__str(self):
+        label = 'abc'
+        self.design.strand(0, 0).to(5).cross(1).to(0).with_label(label)
+        actual_strand = self.design.strands[0]
+        expected_strand = sc.Strand(domains=[
+            sc.Domain(0, True, 0, 5),
+            sc.Domain(0, False, 0, 5),
+        ], label=label)
+
+        self.assertEqual(expected_strand.label, actual_strand.label)
+
+    def test_with_label__dict(self):
+        label = {'name': 'abc', 'type': 3}
+        self.design.strand(0, 0).to(5).cross(1).to(0).with_label(label)
+        actual_strand = self.design.strands[0]
+        expected_strand = sc.Strand(domains=[
+            sc.Domain(0, True, 0, 5),
+            sc.Domain(0, False, 0, 5),
+        ], label=label)
+
+        self.assertDictEqual(expected_strand.label, actual_strand.label)
+
+    def test_with_domain_label(self):
+        label0 = 'abc'
+        label1 = {'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=[
+            sc.Domain(0, True, 0, 5, label=label0),
+            sc.Domain(0, False, 0, 5, label=label1),
+        ])
+
+        self.assertEqual(expected_strand.domains[0].label, actual_strand.domains[0].label)
+        self.assertDictEqual(expected_strand.domains[1].label, actual_strand.domains[1].label)
+
+    def test_with_domain_label__and__with_label(self):
+        strand_label = 'xyz'
+        label0 = 'abc'
+        label1 = {'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]
+        expected_strand = sc.Strand(domains=[
+            sc.Domain(0, True, 0, 5, label=label0),
+            sc.Domain(0, False, 0, 5, label=label1),
+        ], label=strand_label)
+
+        self.assertEqual(expected_strand.label, actual_strand.label)
+        self.assertEqual(expected_strand.domains[0].label, actual_strand.domains[0].label)
+        self.assertDictEqual(expected_strand.domains[1].label, actual_strand.domains[1].label)
+
+
+def set_colors_black(*strands):
+    for strand in strands:
+        strand.set_color(sc.Color(r=0, g=0, b=0))
+
+
 class TestAddStrand(unittest.TestCase):
 
     def test_add_strand__with_loopout(self):
@@ -3461,16 +3526,16 @@ def test_assign_dna__wildcards_multiple_overlaps(self):
          098   765   432   109   876   543   210
         """
         self.design.assign_dna(self.strand_top_big9, 'AACTTC')
-        self.assertEqual('??? ??? ??? GTT ??? GAA ???'.replace(' ',''), self.strand_bot.dna_sequence)
+        self.assertEqual('??? ??? ??? GTT ??? GAA ???'.replace(' ', ''), self.strand_bot.dna_sequence)
 
         self.design.assign_dna(self.strand_top_small12, 'TGC')
-        self.assertEqual('??? ??? GCA GTT ??? GAA ???'.replace(' ',''), self.strand_bot.dna_sequence)
+        self.assertEqual('??? ??? GCA GTT ??? GAA ???'.replace(' ', ''), self.strand_bot.dna_sequence)
 
         self.design.assign_dna(self.strand_top_small0, 'ACG')
-        self.assertEqual('??? ??? GCA GTT ??? GAA CGT'.replace(' ',''), self.strand_bot.dna_sequence)
+        self.assertEqual('??? ??? GCA GTT ??? GAA CGT'.replace(' ', ''), self.strand_bot.dna_sequence)
 
         self.design.assign_dna(self.strand_top_big6, 'GGATTGGCA')
-        self.assertEqual('TGC CAA GCA GTT TCC GAA CGT'.replace(' ',''), self.strand_bot.dna_sequence)
+        self.assertEqual('TGC CAA GCA GTT TCC GAA CGT'.replace(' ', ''), self.strand_bot.dna_sequence)
 
     def test_assign_dna__domain_sequence_too_long_error(self):
         with self.assertRaises(sc.IllegalDNADesignError):
@@ -3499,8 +3564,8 @@ def test_assign_dna__to_individual_domains__wildcards_multiple_overlaps(self):
          098   765   432   109   876   543   210
         """
         self.design.assign_dna(self.strand_top_big9, 'AAC', domain=self.dom_top9)
-        self.assertEqual('AAC ???'.replace(' ',''), self.strand_top_big9.dna_sequence)
-        self.assertEqual('??? ??? ??? GTT ??? ??? ???'.replace(' ',''), self.strand_bot.dna_sequence)
+        self.assertEqual('AAC ???'.replace(' ', ''), self.strand_top_big9.dna_sequence)
+        self.assertEqual('??? ??? ??? GTT ??? ??? ???'.replace(' ', ''), self.strand_bot.dna_sequence)
 
         """
          012   345   678   901   234   567   890
@@ -3513,8 +3578,8 @@ def test_assign_dna__to_individual_domains__wildcards_multiple_overlaps(self):
          098   765   432   109   876   543   210
         """
         self.design.assign_dna(self.strand_top_big9, 'TTC', domain=self.dom_top3)
-        self.assertEqual('AAC TTC'.replace(' ',''), self.strand_top_big9.dna_sequence)
-        self.assertEqual('??? ??? ??? GTT ??? GAA ???'.replace(' ',''), self.strand_bot.dna_sequence)
+        self.assertEqual('AAC TTC'.replace(' ', ''), self.strand_top_big9.dna_sequence)
+        self.assertEqual('??? ??? ??? GTT ??? GAA ???'.replace(' ', ''), self.strand_bot.dna_sequence)
 
         """
          012   345   678   901   234   567   890
@@ -3542,7 +3607,7 @@ def test_assign_dna__to_individual_domains__wildcards_multiple_overlaps(self):
         """
         self.design.assign_dna(self.strand_top_small0, 'ACG')
         self.assertEqual('ACG', self.strand_top_small0.dna_sequence)
-        self.assertEqual('??? ??? GCA GTT ??? GAA CGT'.replace(' ',''), self.strand_bot.dna_sequence)
+        self.assertEqual('??? ??? GCA GTT ??? GAA CGT'.replace(' ', ''), self.strand_bot.dna_sequence)
 
         """
          012   345   678   901   234   567   890
@@ -3555,8 +3620,8 @@ def test_assign_dna__to_individual_domains__wildcards_multiple_overlaps(self):
          098   765   432   109   876   543   210
         """
         self.design.assign_dna(self.strand_top_big6, 'TTG', domain=self.dom_top15)
-        self.assertEqual('??? TTG ???'.replace(' ',''), self.strand_top_big6.dna_sequence)
-        self.assertEqual('??? CAA GCA GTT ??? GAA CGT'.replace(' ',''), self.strand_bot.dna_sequence)
+        self.assertEqual('??? TTG ???'.replace(' ', ''), self.strand_top_big6.dna_sequence)
+        self.assertEqual('??? CAA GCA GTT ??? GAA CGT'.replace(' ', ''), self.strand_bot.dna_sequence)
 
         """
          012   345   678   901   234   567   890
@@ -3569,8 +3634,8 @@ def test_assign_dna__to_individual_domains__wildcards_multiple_overlaps(self):
          098   765   432   109   876   543   210
         """
         self.design.assign_dna(self.strand_top_big6, 'GCA', domain=self.dom_top18)
-        self.assertEqual('??? TTG GCA'.replace(' ',''), self.strand_top_big6.dna_sequence)
-        self.assertEqual('TGC CAA GCA GTT ??? GAA CGT'.replace(' ',''), self.strand_bot.dna_sequence)
+        self.assertEqual('??? TTG GCA'.replace(' ', ''), self.strand_top_big6.dna_sequence)
+        self.assertEqual('TGC CAA GCA GTT ??? GAA CGT'.replace(' ', ''), self.strand_bot.dna_sequence)
 
         """
          012   345   678   901   234   567   890
@@ -3583,8 +3648,8 @@ def test_assign_dna__to_individual_domains__wildcards_multiple_overlaps(self):
          098   765   432   109   876   543   210
         """
         self.design.assign_dna(self.strand_top_big6, 'GGA', domain=self.dom_top6)
-        self.assertEqual('GGA TTG GCA'.replace(' ',''), self.strand_top_big6.dna_sequence)
-        self.assertEqual('TGC CAA GCA GTT TCC GAA CGT'.replace(' ',''), self.strand_bot.dna_sequence)
+        self.assertEqual('GGA TTG GCA'.replace(' ', ''), self.strand_top_big6.dna_sequence)
+        self.assertEqual('TGC CAA GCA GTT TCC GAA CGT'.replace(' ', ''), self.strand_bot.dna_sequence)
 
     def test_method_chaining_with_domain_sequence(self):
         """
@@ -3649,7 +3714,6 @@ def test_method_chaining_with_domain_sequence(self):
         self.assertEqual('AAC TTC'.replace(' ', ''), design.strands[-1].dna_sequence)
         self.assertEqual('??? ??? GCA GTT ??? GAA ???'.replace(' ', ''), design.strands[0].dna_sequence)
 
-
         """
          012   345   678   901   234   567   890
               +---------------+
@@ -3660,19 +3724,17 @@ def test_method_chaining_with_domain_sequence(self):
         <???---AAG---CCT---TTG---ACG---AAC---CGT-
          098   765   432   109   876   543   210
         """
-        design.strand(0, 6).to(9)\
-            .with_domain_sequence('GGA')\
-            .cross(0, offset=15)\
-            .to(18)\
-            .with_domain_sequence('TTG')\
-            .to(21)\
+        design.strand(0, 6).to(9) \
+            .with_domain_sequence('GGA') \
+            .cross(0, offset=15) \
+            .to(18) \
+            .with_domain_sequence('TTG') \
+            .to(21) \
             .with_domain_sequence('GCA')
         self.assertEqual('GGA TTG GCA'.replace(' ', ''), design.strands[-1].dna_sequence)
         self.assertEqual('TGC CAA GCA GTT TCC GAA ???'.replace(' ', ''), design.strands[0].dna_sequence)
 
 
-
-
 TEST_OFFSETS_AT_DELETION_INSERTIONS = False