From 39fc4c992297dca2d6cb4c2df5e97abd71199025 Mon Sep 17 00:00:00 2001 From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com> Date: Mon, 27 Nov 2023 14:46:28 +0100 Subject: [PATCH] Update command line parameters (#32) * working multiprocessing * counter and control_window_length are now computed in advance of _run_one_window() * [test] test_run_one_window had to be adapted as it has now also the control_window_length as input * [test] test_run_one_window had to be adapted as it has now also the control_window_length as input * [test] correct expected output * [test] computation control_window_length * fixed: problem with hash not being deterministic which caused problems in the multi-threading, now using a determinisitc version * clean up * correct indent * random hash to deterministic hash * update multiprocessing modules that are needed * fix: computation control window length * delete empty log file * delete empty log file * shotgun command to run command * update log file naming * [README] add channels to conda enviroment installation] * updated readme with new commands * update imported packages to viloca, and other naming * update viloca naming here * update viloca naming here * [unit tests] update commands * update author * build is needed for libshorah * updated readme --- README.md | 20 +- poetry.lock | 631 +++++++++++++----- pyproject.toml | 8 +- tests/data_1/shotgun_test.sh | 2 +- tests/data_5/shotgun_prepare.sh | 2 +- tests/test_b2w.py | 2 +- tests/test_b2w_mapping.py | 24 +- tests/test_envp_post.py | 2 +- tests/test_pooled_post.py | 4 +- tests/test_pooled_pre.py | 4 +- tests/test_shorah_snv.py | 4 +- tests/test_tiling.py | 2 +- {shorah => viloca}/__init__.py | 0 {shorah => viloca}/__main__.py | 2 +- {shorah => viloca}/b2w.py | 449 ++++++++----- {shorah => viloca}/cli.py | 18 +- {shorah => viloca}/envp_post.py | 0 .../learn_error_params/__init__.py | 0 .../learn_error_params/analyze_results.py | 0 .../learn_error_params/cavi.py | 0 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{shorah => viloca}/local_haplotype_inference/learn_error_params/__init__.py (100%) rename {shorah => viloca}/local_haplotype_inference/learn_error_params/analyze_results.py (100%) rename {shorah => viloca}/local_haplotype_inference/learn_error_params/cavi.py (100%) rename {shorah => viloca}/local_haplotype_inference/learn_error_params/elbo_eqs.py (100%) rename {shorah => viloca}/local_haplotype_inference/learn_error_params/initialization.py (100%) rename {shorah => viloca}/local_haplotype_inference/learn_error_params/preparation.py (100%) rename {shorah => viloca}/local_haplotype_inference/learn_error_params/run_dpm_mfa.py (97%) rename {shorah => viloca}/local_haplotype_inference/learn_error_params/update_eqs.py (100%) rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/__init__.py (100%) rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/analyze_results.py (100%) rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/cavi.py (100%) rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/elbo_eqs.py (100%) rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/initialization.py (100%) rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/preparation.py (100%) rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py (98%) rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/update_eqs.py (100%) rename {shorah => viloca}/pooled_post.py (100%) rename {shorah => viloca}/pooled_pre.py (100%) rename {shorah => viloca}/shorah_snv.py (100%) rename {shorah => viloca}/shotgun.py (99%) rename {shorah => viloca}/tiling.py (100%) diff --git a/README.md b/README.md index 3c25d77..412dd01 100755 --- a/README.md +++ b/README.md @@ -1,9 +1,5 @@ VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data =============== -[![Build Status](https://travis-ci.org/cbg-ethz/shorah.svg?branch=master)](https://travis-ci.org/cbg-ethz/shorah) -[![Bioconda package](https://img.shields.io/conda/dn/bioconda/shorah.svg?label=Bioconda)](https://bioconda.github.io/recipes/shorah/README.html) -[![Docker container](https://quay.io/repository/biocontainers/shorah/status)](https://quay.io/repository/biocontainers/shorah) - VILOCA is an open source project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools @@ -17,22 +13,26 @@ genetic variants present in a mixed sample. For installation miniconda is recommended: https://docs.conda.io/en/latest/miniconda.html. We recommend to install VILOCA in a clean conda environment: ``` -conda create --name env_viloca libshorah +conda create --name env_viloca --channel conda-forge --channel bioconda libshorah conda activate env_viloca -pip install git+https://github.com/LaraFuhrmann/VILOCA@master +pip install git+https://github.com/cbg-ethz/VILOCA@master ``` ### Example -To test your installation, we recommend running the program on `tests/data_1`. +To test your installation run VILOCA `tests/data_1`: +``` +viloca run -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode use_quality_scores +``` + If the sequencing amplicon strategy is known, we recommend using the amplicon-mode of the program, which takes as input the `.insert.bed` - file: -`shorah shotgun -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode use_quality_scores` +`viloca run -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode use_quality_scores` If the sequencing quality scores are not trustable, the sequencing error parameters can also be learned: -`shorah shotgun -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode learn_error_params`. +`viloca run -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode learn_error_params`. If there is no information on the sequencing amplicon strategy available, run: -`shorah shotgun -b test_aln.cram -f test_ref.fasta --mode use_quality_scores` +`viloca run -b test_aln.cram -f test_ref.fasta --mode use_quality_scores` ### Parameters There are several parameters available: diff --git a/poetry.lock b/poetry.lock index c304ed1..5aa4b8b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,153 +1,383 @@ +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. + [[package]] name = "atomicwrites" version = "1.4.1" description = "Atomic file writes." -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +files = [ + {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"}, +] [[package]] name = "attrs" -version = "22.2.0" +version = "23.1.0" description = "Classes Without Boilerplate" -category = "dev" optional = false -python-versions = ">=3.6" 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"ShoRAH" +name = "VILOCA" version = "0.1.0" description = "SHOrt Reads Assembly into Haplotypes" license = "GPL-3.0-only" -authors = ["Benjamin Langer "] +authors = ["Benjamin Langer , Lara Fuhrmann "] build = "build.py" packages = [ - { include = "shorah" } + { include = "viloca" } ] [tool.poetry.scripts] -shorah = 'shorah.cli:main' +viloca = 'viloca.cli:main' [tool.poetry.dependencies] python = ">=3.9.9,<3.11" diff --git a/tests/data_1/shotgun_test.sh b/tests/data_1/shotgun_test.sh index 0ac3749..77925d3 100755 --- a/tests/data_1/shotgun_test.sh +++ b/tests/data_1/shotgun_test.sh @@ -1,4 +1,4 @@ #!/bin/bash -shorah shotgun -a 0.1 -w 201 -x 100000 -p 0.9 -c 0 \ +viloca run -a 0.1 -w 201 -x 100000 -p 0.9 -c 0 \ -r HXB2:2469-3713 -R 42 -f test_ref.fasta -b test_aln.cram --out_format csv "$@" diff --git a/tests/data_5/shotgun_prepare.sh b/tests/data_5/shotgun_prepare.sh index 81564db..0ce7749 100755 --- a/tests/data_5/shotgun_prepare.sh +++ b/tests/data_5/shotgun_prepare.sh @@ -1,3 +1,3 @@ #!/bin/bash -shorah shotgun -a 0.1 -w 42 -x 100000 -p 0.9 -c 0 -r REF:43-273 -R 42 -b test_aln.cram -f ref.fasta +viloca run -a 0.1 -w 42 -x 100000 -p 0.9 -c 0 -r REF:43-273 -R 42 -b test_aln.cram -f ref.fasta diff --git a/tests/test_b2w.py b/tests/test_b2w.py index c41609a..7a3dd8e 100644 --- a/tests/test_b2w.py +++ b/tests/test_b2w.py @@ -2,7 +2,7 @@ import filecmp import os import glob -from shorah import b2w, tiling +from viloca import b2w, tiling import math import libshorah diff --git a/tests/test_b2w_mapping.py b/tests/test_b2w_mapping.py index 0fc3b9c..6a0fb84 100644 --- a/tests/test_b2w_mapping.py +++ b/tests/test_b2w_mapping.py @@ -1,7 +1,8 @@ from array import array import pytest from cigar import Cigar -from shorah import b2w +from viloca import b2w +import hashlib class MockAlignedSegment: def __init__(self, query_name: str, reference_start: int, query_sequence: str, cigarstring: str): @@ -35,10 +36,10 @@ def add_indels(self, indels_map): cnt = self.reference_start for i in self.cigartuples: if i[0] == 1: # insert TODO Justify -1 - indels_map.append((self.query_name, self.reference_start, hash(self.cigarstring), cnt-1, i[1], 0)) # cnt-1 + indels_map.append((self.query_name, self.reference_start, hashlib.sha1(self.cigarstring.encode()).hexdigest(), cnt-1, i[1], 0)) # cnt-1 elif i[0] == 2: # del for k in range(i[1]): - indels_map.append((self.query_name, self.reference_start, hash(self.cigarstring), cnt+k, 0, 1)) + indels_map.append((self.query_name, self.reference_start, hashlib.sha1(self.cigarstring.encode()).hexdigest(), cnt+k, 0, 1)) cnt += i[1] else: cnt += i[1] @@ -326,11 +327,22 @@ def test_run_one_window(mArr, spec, window_length, window_start, extended_window mock_dict = mocker.MagicMock() mock_dict.__getitem__.return_value = 42 - arr, _, _, _, _, _ = b2w._run_one_window( + # added by Lara + original_window_length = window_length + control_window_length = window_length + + if extended_window_mode: + for pos, val in max_indel_at_pos.items(): + if window_start <= pos < window_start + original_window_length: + control_window_length += val + + + arr, _, _, _, = b2w._run_one_window( mock_samfile, - window_start, + window_start, # 0 based "HXB2-does-not-matter", window_length, + control_window_length, 0, mock_dict, 0, @@ -343,4 +355,4 @@ def test_run_one_window(mArr, spec, window_length, window_start, extended_window print(arr) for idx, el in enumerate(arr): - assert el.split("\n")[1] == spec[idx] \ No newline at end of file + assert el.split("\n")[1] == spec[idx] diff --git a/tests/test_envp_post.py b/tests/test_envp_post.py index 205ed05..d4b4fb3 100644 --- a/tests/test_envp_post.py +++ b/tests/test_envp_post.py @@ -1,5 +1,5 @@ from unittest.mock import patch, mock_open -from shorah import envp_post +from viloca import envp_post DEFAULT_MOCK_DATA = "default mock data" diff --git a/tests/test_pooled_post.py b/tests/test_pooled_post.py index f491ba5..7baf31c 100644 --- a/tests/test_pooled_post.py +++ b/tests/test_pooled_post.py @@ -1,5 +1,5 @@ from unittest.mock import patch, mock_open -from shorah import pooled_post +from viloca import pooled_post import numpy as np DEFAULT_MOCK_DATA = "default mock data" @@ -48,4 +48,4 @@ def open_side_effect(name): # open("debug/w-HXB2-2938-3138.dbg"), # open("support/w-HXB2-2938-3138.reads-support.fas"), # open("corrected/w-HXB2-2938-3138.reads-cor.fas"), -# "shorah") # TODO \ No newline at end of file +# "shorah") # TODO diff --git a/tests/test_pooled_pre.py b/tests/test_pooled_pre.py index ce36024..dbe59ab 100644 --- a/tests/test_pooled_pre.py +++ b/tests/test_pooled_pre.py @@ -1,6 +1,6 @@ import pysam import os -from shorah import pooled_pre +from viloca import pooled_pre def test__annotate_alignment_file(): out = "out.bam" @@ -48,4 +48,4 @@ def test_pre_process_pooled(): os.remove(out + ".bai") assert a[0] == a[1] != 0 - assert a[2] == 0 \ No newline at end of file + assert a[2] == 0 diff --git a/tests/test_shorah_snv.py b/tests/test_shorah_snv.py index 56b0166..4967b55 100644 --- a/tests/test_shorah_snv.py +++ b/tests/test_shorah_snv.py @@ -1,5 +1,5 @@ import pytest -from shorah.shorah_snv import _compare_ref_to_read, SNP_id, SNV +from viloca.shorah_snv import _compare_ref_to_read, SNP_id, SNV @pytest.mark.parametrize("ref, seq, spec", [ @@ -39,4 +39,4 @@ def test_compare_ref_to_read(ref, seq, spec): assert snp == spec - assert tot_snv == len(snp) \ No newline at end of file + assert tot_snv == len(snp) diff --git a/tests/test_tiling.py b/tests/test_tiling.py index f44d66f..89e38fc 100644 --- a/tests/test_tiling.py +++ b/tests/test_tiling.py @@ -1,4 +1,4 @@ -from shorah import tiling +from viloca import tiling import pytest def test_equispaced(): diff --git a/shorah/__init__.py b/viloca/__init__.py similarity index 100% rename from shorah/__init__.py rename to viloca/__init__.py diff --git a/shorah/__main__.py b/viloca/__main__.py similarity index 92% rename from shorah/__main__.py rename to viloca/__main__.py index 42e6c65..50ed2a3 100644 --- a/shorah/__main__.py +++ b/viloca/__main__.py @@ -8,7 +8,7 @@ - https://docs.python.org/2/using/cmdline.html#cmdoption-m - https://docs.python.org/3/using/cmdline.html#cmdoption-m """ -from shorah.cli import main +from viloca.cli import main if __name__ == "__main__": main() diff --git a/shorah/b2w.py b/viloca/b2w.py similarity index 61% rename from shorah/b2w.py rename to viloca/b2w.py index ce7d571..505dd9a 100644 --- a/shorah/b2w.py +++ b/viloca/b2w.py @@ -1,9 +1,12 @@ import pysam from typing import Optional -from shorah.tiling import TilingStrategy, EquispacedTilingStrategy +from viloca.tiling import TilingStrategy, EquispacedTilingStrategy import numpy as np import math import logging +from multiprocessing import Process, cpu_count +import os +import hashlib def _write_to_file(lines, file_name): with open(file_name, "w") as f: @@ -38,7 +41,8 @@ def _calc_via_pileup(samfile, reference_name, maximum_reads): indel_map.add(( pileupread.alignment.query_name, # TODO is unique? pileupread.alignment.reference_start, # TODO is unique? - hash(pileupread.alignment.cigarstring), # TODO is unique? + hashlib.sha1(pileupread.alignment.cigarstring.encode()).hexdigest(), + #hash(pileupread.alignment.cigarstring), # TODO is unique? pileupcolumn.reference_pos, pileupread.indel, pileupread.is_del @@ -127,7 +131,7 @@ def _build_one_full_read(full_read: list[str], full_qualities: list[int]|list[st return full_read, full_qualities # TODO return same data type twice -def _run_one_window(samfile, window_start, reference_name, window_length, +def _run_one_window(samfile, window_start, reference_name, window_length,control_window_length, minimum_overlap, permitted_reads_per_location, counter, exact_conformance_fix_0_1_basing_in_reads, indel_map, max_ins_at_pos, extended_window_mode, exclude_non_var_pos_threshold): @@ -142,11 +146,16 @@ def _run_one_window(samfile, window_start, reference_name, window_length, window_start + window_length # arg exclusive as per pysam convention ) + # TODO: minimum_overlap + # TODO: original_window_length + # TODO: window_length original_window_length = window_length + window_length = control_window_length if extended_window_mode: - for pos, val in max_ins_at_pos.items(): - if window_start <= pos < window_start + original_window_length: - window_length += val + # this is now done intilaly for all windows + #for pos, val in max_ins_at_pos.items(): + # if window_start <= pos < window_start + original_window_length: + # window_length += val minimum_overlap *= window_length/original_window_length if exclude_non_var_pos_threshold > 0: @@ -154,7 +163,6 @@ def _run_one_window(samfile, window_start, reference_name, window_length, base_pair_distr_in_window = np.zeros((window_length, len(alphabet)), dtype=int) for read in iter: - if (read.reference_start is None) or (read.reference_end is None): continue first_aligned_pos = read.reference_start # this is 0-based @@ -183,15 +191,16 @@ def _run_one_window(samfile, window_start, reference_name, window_length, if ct_idx != 0 and ct_idx != len(read.cigartuples)-1: raise ValueError("Soft clipping only possible on the edges of a read.") elif ct[0] == 5: # 5 = BAM_CHARD_CLIP - #logging.debug(f"[b2w] Hard clipping detected in {read.query_name}") + #logging.debug(f"[b2w] Hard clipping detected in {read.query_name}") # commented out because this happens too often pass else: raise NotImplementedError("CIGAR op code found that is not implemented:", ct[0]) full_read, full_qualities = _build_one_full_read(full_read, full_qualities, - read.query_name, hash(read.cigarstring), first_aligned_pos, last_aligned_pos, + read.query_name, hashlib.sha1(read.cigarstring.encode()).hexdigest(), first_aligned_pos, last_aligned_pos, indel_map, max_ins_at_pos, extended_window_mode, "-") + if (first_aligned_pos + minimum_overlap < window_start + 1 + window_length and last_aligned_pos >= window_start + minimum_overlap - 2 # TODO justify 2 and len(full_read) >= minimum_overlap): @@ -232,12 +241,11 @@ def _run_one_window(samfile, window_start, reference_name, window_length, cut_out_read = (-start_cut_out + num_inserts_left_of_read) * "N" + cut_out_read if full_qualities is not None: cut_out_qualities = (-start_cut_out + num_inserts_left_of_read) * [2] + cut_out_qualities - if len(cut_out_read) != window_length: - breakpoint() + assert len(cut_out_read) == window_length, ( "read unequal window size", - read.query_name, first_aligned_pos, cut_out_read, window_start, window_length, read.reference_end + read.query_name, first_aligned_pos, cut_out_read, window_start, window_length, read.reference_end, len(cut_out_read) ) if cut_out_qualities is not None: assert len(cut_out_qualities) == window_length, ( @@ -276,7 +284,216 @@ def _run_one_window(samfile, window_start, reference_name, window_length, # TODO move out of this function convert_to_printed_fmt = lambda x: [f'>{k[0]} {k[1]}\n{"".join(k[2])}' for k in x] - return convert_to_printed_fmt(arr), arr_read_qualities_summary, arr_read_summary, counter, window_length, pos_filter +# return convert_to_printed_fmt(arr), arr_read_qualities_summary, arr_read_summary, counter, window_length, pos_filter + return convert_to_printed_fmt(arr), arr_read_qualities_summary, arr_read_summary, pos_filter + + +def parallel_run_one_window( + reference_filename, + minimum_reads, + tiling, + region_end, + idx, + window_start, + window_length, + control_window_length, + alignment_file, + reference_name, + win_min_ext, + permitted_reads_per_location, + counter, + exact_conformance_fix_0_1_basing_in_reads, + indel_map, + max_ins_at_pos, + extended_window_mode, + exclude_non_var_pos_threshold +): + """ + build one window. + """ + reffile = pysam.FastaFile(reference_filename) + + samfile = pysam.AlignmentFile( + alignment_file, + "r", # auto-detect bam/cram (rc) + reference_filename=reference_filename, + threads=1 + ) + + reads = open(f"reads_{idx}.fas", "w") + + logging.info(f"Working on window (1-based) @ {window_start+1}") + +# (arr, arr_read_qualities_summary, arr_read_summary, +# counter, control_window_length, pos_filter) = _run_one_window( + (arr, arr_read_qualities_summary, arr_read_summary, + pos_filter) = _run_one_window( + samfile, + window_start - 1, # make 0 based + reference_name, + window_length, + control_window_length, + math.floor(win_min_ext * window_length), + dict(permitted_reads_per_location), # copys dict ("pass by value") + counter, + exact_conformance_fix_0_1_basing_in_reads, + indel_map, + max_ins_at_pos, + extended_window_mode, + exclude_non_var_pos_threshold + ) + + logging.debug(f"Window length: {control_window_length}") + + window_end = window_start + window_length - 1 + file_name = f'w-{reference_name}-{window_start}-{window_end}' + + # TODO solution for backward conformance + if len(tiling) > 1: + end_extended_by_a_window = region_end + (tiling[1][0]-tiling[0][0])*3 + else: + end_extended_by_a_window = region_end + window_length*3 + + for read in arr_read_summary: + if idx == len(tiling) - 1 and read[1] > end_extended_by_a_window: + continue + # TODO reads.fas not FASTA conform, +-0/1 mixed + # TODO global end does not really make sense, only for conformance + # read name, global start, global end, read start, read end, read + reads.write( + f'{read[0]}\t{tiling[0][0]-1}\t{end_extended_by_a_window}\t{read[1]}\t{read[2]}\t{read[3]}\n' + ) + + reads.close() + + if (idx != len(tiling) - 1 # except last + and len(arr) > 0) or len(tiling) == 1: # suppress output if window empty + + _write_to_file(arr, file_name + '.reads.fas') + if arr_read_qualities_summary is not None: + with open(file_name + '.qualities.npy', 'wb') as f: + np.save(f, np.asarray(arr_read_qualities_summary, dtype=np.int64), allow_pickle=True) + + ref = reffile.fetch(reference=reference_name, start=window_start-1, end=window_end) + + if extended_window_mode: + for file_name_comp, char in [("extended-ref", "X"), ("ref", "-")]: + res_ref = _build_one_full_read( + list(ref), list(ref), None, None, + window_start-1, window_end-1, + indel_map, max_ins_at_pos, extended_window_mode, char + )[0] + + k = max(0, control_window_length - len(res_ref)) + res_ref += k * "N" + assert_condition = control_window_length == len(res_ref) + + if exclude_non_var_pos_threshold > 0 and file_name_comp == "ref": + _write_to_file([ + f'>{reference_name} {window_start}\n' + res_ref + ], file_name + '.envp-full-ref.fas') + + envp_ref = np.array(list(res_ref)) + envp_ref[~pos_filter] = "=" + _write_to_file([ + f'>{reference_name} {window_start}\n' + "".join(envp_ref) + ], file_name + '.envp-ref.fas') + + reduced_ref = np.array(list(res_ref))[pos_filter] + res_ref = "".join(reduced_ref) + assert_condition = (control_window_length == + len(reduced_ref) + len(pos_filter) - pos_filter.sum()) + + _write_to_file([ + f'>{reference_name} {window_start}\n' + res_ref + ], f'{file_name}.{file_name_comp}.fas') + + assert assert_condition, ( + f""" + Reference ({file_name_comp}) does not have same length as the window. + Location: {file_name} + Ref: {len(res_ref)} + Win: {control_window_length} + """ + ) + + else: + k = max(0, control_window_length - len(ref)) + ref += k * "N" + + if exclude_non_var_pos_threshold > 0: + full_file_name = file_name + '.envp-full-ref.fas' + else: + full_file_name = file_name + '.ref.fas' + + _write_to_file([ + f'>{reference_name} {window_start}\n' + ref + ], full_file_name) + + assert control_window_length == len(ref), ( + f""" + Reference does not have same length as the window. + Location: {file_name} + Ref: {len(ref)} + Win: {control_window_length} + """ + ) + + if exclude_non_var_pos_threshold > 0: + envp_ref = np.array(list(ref)) + envp_ref[~pos_filter] = "=" + _write_to_file([ + f'>{reference_name} {window_start}\n' + "".join(envp_ref) + ], file_name + '.envp-ref.fas') + reduced_ref = np.array(list(ref))[pos_filter] + _write_to_file([ + f'>{reference_name} {window_start}\n' + "".join(reduced_ref) + ], file_name + '.ref.fas') + + assert (control_window_length == len(envp_ref) and + control_window_length == len(reduced_ref) + len(pos_filter) - pos_filter.sum()), ( + f""" + Reference does not have same length as the window. + Location: {file_name} + Envp Ref: {len(envp_ref)} + Ref: {len(reduced_ref)} + Win: {control_window_length} + """ + ) + + if len(arr) > minimum_reads: + line = ( + f'{file_name}.reads.fas\t{reference_name}\t{window_start}\t' + f'{window_end}\t{len(arr)}' + ) + _write_to_file([line], f"coverage_{idx}.txt") + + + +def update_tiling(tiling, extended_window_mode, max_ins_at_pos): + """ + input tiling: + window_start is 1-based + max_ins_at_pos is 0-based + + return: tiling = [ + (window_start, original_window_length, control_window_length) + for each window + ] + """ + updated_tiling = [] + + for idx, (window_start, window_length) in enumerate(tiling): + original_window_length = window_length + if extended_window_mode: + for pos, val in max_ins_at_pos.items(): + if window_start - 1 <= pos < window_start - 1 + original_window_length: + window_length += val + updated_tiling.append((window_start,original_window_length, window_length)) + else: + updated_tiling.append((window_start,original_window_length, window_length)) + + return updated_tiling def build_windows(alignment_file: str, tiling_strategy: TilingStrategy, @@ -284,7 +501,8 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy, reference_filename: str, exact_conformance_fix_0_1_basing_in_reads: Optional[bool] = False, extended_window_mode: Optional[bool] = False, - exclude_non_var_pos_threshold: Optional[float] = -1) -> None: + exclude_non_var_pos_threshold: Optional[float] = -1, + maxthreads: Optional[int] = 1) -> None: """Summarizes reads aligned to reference into windows. Three products are created: #. Multiple FASTA files (one for each window position) @@ -314,6 +532,10 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy, positions are excluded. Set to -1 if no position should be excluded (the default). """ + max_proc = min(max(cpu_count() - 1, 1), maxthreads) + logging.info('CPU(s) count %u, will run %u build_windows', cpu_count(), max_proc) + + assert 0 <= win_min_ext <= 1 assert (0 <= exclude_non_var_pos_threshold <= 1 or exclude_non_var_pos_threshold == -1) @@ -323,13 +545,10 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy, alignment_file, "r", # auto-detect bam/cram (rc) reference_filename=reference_filename, - threads=1 + threads=max_proc #1 ) - reffile = pysam.FastaFile(reference_filename) - - cov_arr = [] - reads = open("reads.fas", "w") - counter = 0 + #reffile = pysam.FastaFile(reference_filename) --> we need to read it in each child process + #counter = 0 #--> counter is now coputed initially for all windows reference_name = tiling_strategy.get_reference_name() tiling = tiling_strategy.get_window_tilings() region_end = tiling_strategy.get_region_end() @@ -340,151 +559,65 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy, maximum_reads ) - for idx, (window_start, window_length) in enumerate(tiling): - logging.info(f"Working on window (1-based) @ {window_start+1}") - (arr, arr_read_qualities_summary, arr_read_summary, - counter, control_window_length, pos_filter) = _run_one_window( - samfile, - window_start - 1, # make 0 based - reference_name, - window_length, - math.floor(win_min_ext * window_length), - dict(permitted_reads_per_location), # copys dict ("pass by value") - counter, - exact_conformance_fix_0_1_basing_in_reads, - indel_map, - max_ins_at_pos, - extended_window_mode, - exclude_non_var_pos_threshold - ) - logging.debug(f"Window length: {control_window_length}") - - window_end = window_start + window_length - 1 - file_name = f'w-{reference_name}-{window_start}-{window_end}' - - # TODO solution for backward conformance - if len(tiling) > 1: - end_extended_by_a_window = region_end + (tiling[1][0]-tiling[0][0])*3 - else: - end_extended_by_a_window = region_end + window_length*3 - - for read in arr_read_summary: - if idx == len(tiling) - 1 and read[1] > end_extended_by_a_window: - continue - # TODO reads.fas not FASTA conform, +-0/1 mixed - # TODO global end does not really make sense, only for conformance - # read name, global start, global end, read start, read end, read - reads.write( - f'{read[0]}\t{tiling[0][0]-1}\t{end_extended_by_a_window}\t{read[1]}\t{read[2]}\t{read[3]}\n' + tiling = update_tiling(tiling, extended_window_mode, max_ins_at_pos) + + # generate counter for each window + # counter = window_start - 1 + control_window_length, # make 0 based + counter_list = [0] + [window_start - 1 + control_window_length for (window_start, window_length, control_window_length) in tiling] + + all_processes = [] + for idx, (window_start, window_length, control_window_length) in enumerate(tiling): + counter = counter_list[idx] + p = Process( + target=parallel_run_one_window, + args=( + reference_filename, + minimum_reads, + tiling, + region_end, + idx, + window_start, # 1-based + window_length, + control_window_length, + alignment_file, + reference_name, + win_min_ext, + permitted_reads_per_location, + counter, # 0-based + exact_conformance_fix_0_1_basing_in_reads, + indel_map, + max_ins_at_pos, # 0-based + extended_window_mode, + exclude_non_var_pos_threshold, + ) ) + all_processes.append(p) - if (idx != len(tiling) - 1 # except last - and len(arr) > 0) or len(tiling) == 1: # suppress output if window empty - - _write_to_file(arr, file_name + '.reads.fas') - if arr_read_qualities_summary is not None: - with open(file_name + '.qualities.npy', 'wb') as f: - np.save(f, np.asarray(arr_read_qualities_summary, dtype=np.int64), allow_pickle=True) - - ref = reffile.fetch(reference=reference_name, start=window_start-1, end=window_end) - - if extended_window_mode: - for file_name_comp, char in [("extended-ref", "X"), ("ref", "-")]: - res_ref = _build_one_full_read( - list(ref), list(ref), None, None, - window_start-1, window_end-1, - indel_map, max_ins_at_pos, extended_window_mode, char - )[0] - - k = max(0, control_window_length - len(res_ref)) - res_ref += k * "N" - assert_condition = control_window_length == len(res_ref) - - if exclude_non_var_pos_threshold > 0 and file_name_comp == "ref": - _write_to_file([ - f'>{reference_name} {window_start}\n' + res_ref - ], file_name + '.envp-full-ref.fas') - - envp_ref = np.array(list(res_ref)) - envp_ref[~pos_filter] = "=" - _write_to_file([ - f'>{reference_name} {window_start}\n' + "".join(envp_ref) - ], file_name + '.envp-ref.fas') - - reduced_ref = np.array(list(res_ref))[pos_filter] - res_ref = "".join(reduced_ref) - assert_condition = (control_window_length == - len(reduced_ref) + len(pos_filter) - pos_filter.sum()) - - _write_to_file([ - f'>{reference_name} {window_start}\n' + res_ref - ], f'{file_name}.{file_name_comp}.fas') - - assert assert_condition, ( - f""" - Reference ({file_name_comp}) does not have same length as the window. - Location: {file_name} - Ref: {len(res_ref)} - Win: {control_window_length} - """ - ) - - else: - k = max(0, control_window_length - len(ref)) - ref += k * "N" - - if exclude_non_var_pos_threshold > 0: - full_file_name = file_name + '.envp-full-ref.fas' - else: - full_file_name = file_name + '.ref.fas' - - _write_to_file([ - f'>{reference_name} {window_start}\n' + ref - ], full_file_name) - - assert control_window_length == len(ref), ( - f""" - Reference does not have same length as the window. - Location: {file_name} - Ref: {len(ref)} - Win: {control_window_length} - """ - ) + for p in all_processes: + p.start() - if exclude_non_var_pos_threshold > 0: - envp_ref = np.array(list(ref)) - envp_ref[~pos_filter] = "=" - _write_to_file([ - f'>{reference_name} {window_start}\n' + "".join(envp_ref) - ], file_name + '.envp-ref.fas') - reduced_ref = np.array(list(ref))[pos_filter] - _write_to_file([ - f'>{reference_name} {window_start}\n' + "".join(reduced_ref) - ], file_name + '.ref.fas') - - assert (control_window_length == len(envp_ref) and - control_window_length == len(reduced_ref) + len(pos_filter) - pos_filter.sum()), ( - f""" - Reference does not have same length as the window. - Location: {file_name} - Envp Ref: {len(envp_ref)} - Ref: {len(reduced_ref)} - Win: {control_window_length} - """ - ) - - if len(arr) > minimum_reads: - line = ( - f'{file_name}.reads.fas\t{reference_name}\t{window_start}\t' - f'{window_end}\t{len(arr)}' - ) - cov_arr.append(line) + for p in all_processes: + p.join() samfile.close() - reads.close() - _write_to_file(cov_arr, "coverage.txt") + with open('reads.fas', 'w') as output_file: + for file_path in [f"reads_{idx}.fas" for idx in range(len(tiling))]: + with open(file_path, 'r') as input_file: + for line in input_file: + output_file.write(line) + os.remove(file_path) + cov_arr = [] + with open("coverage.txt", 'w') as output_file: + for file_path in [f"coverage_{idx}.txt" for idx in range(len(tiling))]: + try: + with open(file_path, 'r') as input_file: + for line in input_file: + output_file.write(line) + os.remove(file_path) + except Exception: + pass if __name__ == "__main__": import argparse diff --git a/shorah/cli.py b/viloca/cli.py similarity index 95% rename from shorah/cli.py rename to viloca/cli.py index de7caf1..902ebd9 100644 --- a/shorah/cli.py +++ b/viloca/cli.py @@ -39,12 +39,12 @@ import argparse import logging import logging.handlers -from shorah import shotgun, shorah_snv +from viloca import shotgun, shorah_snv # FIXME can we remove this? @Ivan -> version tag (get through poetry in the future) use_pkg_resources = False all_dirs = os.path.abspath(__file__).split(os.sep) -base_dir = os.sep.join(all_dirs[:-all_dirs[::-1].index('shorah')]) +base_dir = os.sep.join(all_dirs[:-all_dirs[::-1].index('viloca')]) version_fname = os.path.join(base_dir, '.version') if os.path.exists(version_fname): # probably installed using Autotools, e.g: bioconda package - the current recommended way @@ -54,7 +54,7 @@ # probably installed using setup.py from pkg_resources import (get_distribution, DistributionNotFound) try: - __version__ = get_distribution('shorah').version + __version__ = get_distribution('viloca').version except DistributionNotFound: __version__ = 'unknown' print("cannot find version", file=sys.stderr) @@ -66,8 +66,8 @@ if __name__ == '__main__': if __package__ is None: os.sys.path.insert(1, parent_dir) - mod = __import__('shorah') - sys.modules["shorah"] = mod + mod = __import__('viloca') + sys.modules["viloca"] = mod #from common import hcv_map, hiv_map, org_dict, wobbles #from stats import (genome_coverage, start_stop_coverage) # else: @@ -89,13 +89,13 @@ def snv_run(args): def main(): """Parse command line, run default functions.""" # logging configuration - logging.basicConfig(filename='shorah.log', level=logging.DEBUG, + logging.basicConfig(filename='viloca.log', level=logging.DEBUG, format='%(levelname)s %(asctime)s %(filename)s: %(funcName)s() %(lineno)d: \t%(message)s', datefmt='%Y/%m/%d %H:%M:%S', force=True) logging.info(' '.join(sys.argv)) - logging.info('shorah version:%s', __version__) + logging.info('viloca version:%s', __version__) # parse command line # create the top-level parser @@ -151,7 +151,7 @@ def main(): parser = argparse.ArgumentParser( usage='%(prog)s [options]', - epilog="Run `shorah subcommand -h` for more help", + epilog="Run `viloca subcommand -h` for more help", parents=[version_parser]) subparsers = parser.add_subparsers( @@ -159,7 +159,7 @@ def main(): # create the parser for command "shotgun" parser_shotgun = subparsers.add_parser( - 'shotgun', help='run local analysis in shotgun mode', parents=[version_parser, parent_parser, coverage_parser]) + 'run', help='run viloca', parents=[version_parser, parent_parser, coverage_parser]) parser_shotgun.add_argument("-w", "--windowsize", metavar='INT', required=False, type=int, dest="w", default=201, help="window size") diff --git a/shorah/envp_post.py b/viloca/envp_post.py similarity index 100% rename from shorah/envp_post.py rename to viloca/envp_post.py diff --git a/shorah/local_haplotype_inference/learn_error_params/__init__.py b/viloca/local_haplotype_inference/learn_error_params/__init__.py similarity index 100% rename from shorah/local_haplotype_inference/learn_error_params/__init__.py rename to viloca/local_haplotype_inference/learn_error_params/__init__.py diff --git a/shorah/local_haplotype_inference/learn_error_params/analyze_results.py b/viloca/local_haplotype_inference/learn_error_params/analyze_results.py similarity index 100% rename from shorah/local_haplotype_inference/learn_error_params/analyze_results.py rename to viloca/local_haplotype_inference/learn_error_params/analyze_results.py diff --git a/shorah/local_haplotype_inference/learn_error_params/cavi.py b/viloca/local_haplotype_inference/learn_error_params/cavi.py similarity index 100% rename from shorah/local_haplotype_inference/learn_error_params/cavi.py rename to viloca/local_haplotype_inference/learn_error_params/cavi.py diff --git a/shorah/local_haplotype_inference/learn_error_params/elbo_eqs.py b/viloca/local_haplotype_inference/learn_error_params/elbo_eqs.py similarity index 100% rename from shorah/local_haplotype_inference/learn_error_params/elbo_eqs.py rename to viloca/local_haplotype_inference/learn_error_params/elbo_eqs.py diff --git a/shorah/local_haplotype_inference/learn_error_params/initialization.py b/viloca/local_haplotype_inference/learn_error_params/initialization.py similarity index 100% rename from shorah/local_haplotype_inference/learn_error_params/initialization.py rename to viloca/local_haplotype_inference/learn_error_params/initialization.py diff --git a/shorah/local_haplotype_inference/learn_error_params/preparation.py b/viloca/local_haplotype_inference/learn_error_params/preparation.py similarity index 100% rename from shorah/local_haplotype_inference/learn_error_params/preparation.py rename to viloca/local_haplotype_inference/learn_error_params/preparation.py diff --git a/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py b/viloca/local_haplotype_inference/learn_error_params/run_dpm_mfa.py similarity index 97% rename from shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py rename to viloca/local_haplotype_inference/learn_error_params/run_dpm_mfa.py index 29332f4..a66e988 100644 --- a/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py +++ b/viloca/local_haplotype_inference/learn_error_params/run_dpm_mfa.py @@ -11,7 +11,7 @@ from . import cavi logging.basicConfig( - filename="shorah_inference.log", encoding="utf-8", level=logging.INFO + filename="viloca_inference.log", encoding="utf-8", level=logging.INFO ) @@ -69,7 +69,7 @@ def main(freads_in, fref_in, output_dir, n_starts, K, alpha0, alphabet="ACGT-", 0, output_name, )] - + logging.info("len(result_list) " + str(len(result_list))) logging.info("reference " + fref_in) logging.info("reads " + freads_in) diff --git a/shorah/local_haplotype_inference/learn_error_params/update_eqs.py b/viloca/local_haplotype_inference/learn_error_params/update_eqs.py similarity index 100% rename from shorah/local_haplotype_inference/learn_error_params/update_eqs.py rename to viloca/local_haplotype_inference/learn_error_params/update_eqs.py diff --git a/shorah/local_haplotype_inference/use_quality_scores/__init__.py b/viloca/local_haplotype_inference/use_quality_scores/__init__.py similarity index 100% rename from shorah/local_haplotype_inference/use_quality_scores/__init__.py rename to viloca/local_haplotype_inference/use_quality_scores/__init__.py diff --git a/shorah/local_haplotype_inference/use_quality_scores/analyze_results.py b/viloca/local_haplotype_inference/use_quality_scores/analyze_results.py similarity index 100% rename from shorah/local_haplotype_inference/use_quality_scores/analyze_results.py rename to viloca/local_haplotype_inference/use_quality_scores/analyze_results.py diff --git a/shorah/local_haplotype_inference/use_quality_scores/cavi.py b/viloca/local_haplotype_inference/use_quality_scores/cavi.py similarity index 100% rename from shorah/local_haplotype_inference/use_quality_scores/cavi.py rename to viloca/local_haplotype_inference/use_quality_scores/cavi.py diff --git a/shorah/local_haplotype_inference/use_quality_scores/elbo_eqs.py b/viloca/local_haplotype_inference/use_quality_scores/elbo_eqs.py similarity index 100% rename from shorah/local_haplotype_inference/use_quality_scores/elbo_eqs.py rename to viloca/local_haplotype_inference/use_quality_scores/elbo_eqs.py diff --git a/shorah/local_haplotype_inference/use_quality_scores/initialization.py b/viloca/local_haplotype_inference/use_quality_scores/initialization.py similarity index 100% rename from shorah/local_haplotype_inference/use_quality_scores/initialization.py rename to viloca/local_haplotype_inference/use_quality_scores/initialization.py diff --git a/shorah/local_haplotype_inference/use_quality_scores/preparation.py b/viloca/local_haplotype_inference/use_quality_scores/preparation.py similarity index 100% rename from shorah/local_haplotype_inference/use_quality_scores/preparation.py rename to viloca/local_haplotype_inference/use_quality_scores/preparation.py diff --git a/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py b/viloca/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py similarity index 98% rename from shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py rename to viloca/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py index 552f228..27285ab 100644 --- a/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py +++ b/viloca/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py @@ -13,7 +13,7 @@ from . import cavi logging.basicConfig( - filename="shorah_inference.log", encoding="utf-8", level=logging.INFO + filename="viloca_inference.log", encoding="utf-8", level=logging.INFO ) @@ -96,7 +96,7 @@ def main( ] # sort list of tuple by ELBO value sort_elbo.sort(key=lambda x: x[1], reverse=True) - + best_run_idx = sort_elbo[0][0] best_run_elbo = sort_elbo[0][1] logging.info("Maximal ELBO " + str(best_run_elbo) + "in run " + str(best_run_idx)) diff --git a/shorah/local_haplotype_inference/use_quality_scores/update_eqs.py b/viloca/local_haplotype_inference/use_quality_scores/update_eqs.py similarity index 100% rename from shorah/local_haplotype_inference/use_quality_scores/update_eqs.py rename to viloca/local_haplotype_inference/use_quality_scores/update_eqs.py diff --git a/shorah/pooled_post.py b/viloca/pooled_post.py similarity index 100% rename from shorah/pooled_post.py rename to viloca/pooled_post.py diff --git a/shorah/pooled_pre.py b/viloca/pooled_pre.py similarity index 100% rename from shorah/pooled_pre.py rename to viloca/pooled_pre.py diff --git a/shorah/shorah_snv.py b/viloca/shorah_snv.py similarity index 100% rename from shorah/shorah_snv.py rename to viloca/shorah_snv.py diff --git a/shorah/shotgun.py b/viloca/shotgun.py similarity index 99% rename from shorah/shotgun.py rename to viloca/shotgun.py index 127d85b..81d5698 100644 --- a/shorah/shotgun.py +++ b/viloca/shotgun.py @@ -469,7 +469,8 @@ def main(args): cov_thrd, in_fasta, extended_window_mode=extended_window_mode, - exclude_non_var_pos_threshold=exclude_non_var_pos_threshold + exclude_non_var_pos_threshold=exclude_non_var_pos_threshold, + maxthreads=maxthreads ) logging.info('finished b2w') diff --git a/shorah/tiling.py b/viloca/tiling.py similarity index 100% rename from shorah/tiling.py rename to viloca/tiling.py