diff --git a/neat/bacterial_wrapper/__init__.py b/neat/bacterial_wrapper/__init__.py new file mode 100644 index 00000000..936ca573 --- /dev/null +++ b/neat/bacterial_wrapper/__init__.py @@ -0,0 +1,4 @@ +""" +Load modules needed for other parts of the program +""" +from .runner import * \ No newline at end of file diff --git a/neat/bacterial_wrapper/runner.py b/neat/bacterial_wrapper/runner.py new file mode 100644 index 00000000..b2302822 --- /dev/null +++ b/neat/bacterial_wrapper/runner.py @@ -0,0 +1,203 @@ +import subprocess +import gzip +import shutil +import yaml +import pysam +import unittest +import os + +from pathlib import Path +from typing import List +from Bio import bgzf +from Bio.bgzf import BgzfWriter, BgzfReader + + +# Rearranges the bacterial chromosome by wrapping it around + +def wrapper(seq): + length = len(seq) + + if (length % 2 == 0): + half_index = length // 2 + else: + half_index = (length // 2) + 1 + + first_half = seq[:half_index] + second_half = seq[half_index:] + + new_seq = second_half + first_half + + return new_seq + + +# Writes the newly rearranged chromosome's sequence to a new fasta file + +def write_fasta_file(new_seq, bacteria_name, fasta_header, output_dir_path, type): + fasta_file_name = f"{type}_{bacteria_name}.fna" + fasta_file_path = output_dir_path / fasta_file_name + fasta_file = open(fasta_file_path, "w") + + fasta_file.write(fasta_header + "\n" + new_seq) + + fasta_file.close() + + return fasta_file_path + + +# Writes a yml configuration file for the newly rearranged chromosome's fasta sequence +# Splits the coverage in half for the reference and new config files +# These use default values for all other parameters for NEAT + +def write_config_file(ref_config_file, rearranged_seq_file, orig_seq_file, bacteria_name, output_dir_path): + new_config_file_name = f"new_{bacteria_name}_config_test.yml" + old_config_file_name = f"{bacteria_name}_config_test.yml" + + new_config_file_path = output_dir_path / new_config_file_name + old_config_file_path = output_dir_path / old_config_file_name + + with open(ref_config_file, 'r') as ref_file, open(new_config_file_path, 'w') as new_file, open(old_config_file_path, 'w') as old_file: + for line in ref_file: + if line.find("reference:") != -1: + new_file.write(f"reference: {rearranged_seq_file}\n") + old_file.write(f"reference: {orig_seq_file}\n") + elif line.find("coverage:") != -1: + if line.strip() == "coverage: .": + new_coverage = 5.0 + else: + new_coverage = float((line.split(" "))[1].strip()) // 2 + + new_file.write(f"coverage: {new_coverage}\n") + old_file.write(f"coverage: {new_coverage}\n") + else: + new_file.write(line) + old_file.write(line) + + + ref_file.close() + new_file.close() + old_file.close() + + return old_config_file_path, new_config_file_path + + +# Runs the NEAT read simulator using the given config file + +def run_neat(config_file, output_dir, prefix): + subprocess.run(["neat", "read-simulator", "-c", config_file, "-o", output_dir + "/" + prefix]) + + +# General function for bacterial wrapper that calls all of the functions defined above + +def bacterial_wrapper(reference_file, bacteria_name, ref_config_file, output_dir): + + orig_seq = "" + + f = open(reference_file) + fasta_header = f.readline().strip() + + plasmids = False + + for line in f: + if line[0] != ">": + orig_seq += line.strip() + elif line.lower().find("plasmid") != -1: # exclude plasmids from the sequence to be rearranged + plasmids = True + break + + f.close() + + output_dir_path = Path(output_dir) + + rearranged_seq = wrapper(orig_seq) + rearranged_seq_file = write_fasta_file(rearranged_seq, bacteria_name, fasta_header, output_dir_path, "wrapped") + + orig_seq_file = reference_file + if plasmids: + orig_seq_file = write_fasta_file(orig_seq, bacteria_name, fasta_header, output_dir_path, "orig") + + config_files = write_config_file(ref_config_file, rearranged_seq_file, orig_seq_file, bacteria_name, output_dir_path) + old_config_file = config_files[0] + new_config_file = config_files[1] + + run_neat(old_config_file, output_dir, "Regular") + run_neat(new_config_file, output_dir, "Wrapped") + + +# Stitching all outputs together - Keshav's script + +def concat_fq(input_files: List[Path], dest: Path) -> None: + + if not input_files: + # Nothing to do, and no error to throw + return + + with gzip.open(dest, 'wt') as out_f: + for input_file in input_files: + with gzip.open(input_file, 'rt') as in_f: + shutil.copyfileobj(in_f, out_f) + +def merge_bam(bams: List[Path], dest: Path, threads: int) -> None: + + if not bams: + return + + unsorted = dest.with_suffix(".unsorted.bam") + pysam.merge("--no-PG", "-@", str(threads), "-f", str(unsorted), *map(str, bams)) + pysam.sort("-@", str(threads), "-o", str(dest), str(unsorted)) + unsorted.unlink(missing_ok=True) + +def merge_vcf(vcfs: List[Path], dest: Path) -> None: + if not vcfs: + return + + first, *rest = vcfs + shutil.copy(first, dest) + + with dest.open("ab") as out_f: + for vcf in rest: + with vcf.open("rb") as fh: + for line in fh: + if not line.startswith(b"#"): + out_f.write(line) + +def stitch_all_outputs(files: List[Path], output_dir) -> None: + fq1_list = [] + fq2_list = [] + vcf_list = [] + bam_list = [] + + for file in files: + file_name = file.stem # use stem to differentiate fq1 and fq2 + suffixes = file.suffixes # use suffixes to catch vcf and bam files + + if "r2.fastq" in file_name: + fq2_list.append(file) + elif "r1.fastq" in file_name or ".fastq" in suffixes: + fq1_list.append(file) + elif ".vcf" in suffixes and ".tbi" not in suffixes: + vcf_list.append(file) + elif ".bam" in suffixes and ".bai" not in suffixes: + bam_list.append(file) + + dest_fq1 = Path(f"{output_dir}/stitched_fq1.gz") + dest_bam = Path(f"{output_dir}/stitched.bam") + dest_vcf = Path(f"{output_dir}/stitched.vcf") + + concat_fq(fq1_list, dest_fq1) + + if (fq2_list): + dest_fq2 = Path(f"{output_dir}/stitched_fq2.gz") + concat_fq(fq2_list, dest_fq2) + + merge_bam(bam_list, dest_bam, 2) + merge_vcf(vcf_list, dest_vcf) + + +# Testing functions + +class TestWrapper(unittest.TestCase): + def test_even(self): + self.assertEqual(wrapper("ABBCBB"), "CBBABB") + + def test_odd(self): + self.assertEqual(wrapper("ABBCBBC"), "BBCABBC") \ No newline at end of file diff --git a/neat/cli/commands/bacterial_wrapper.py b/neat/cli/commands/bacterial_wrapper.py new file mode 100644 index 00000000..565d417e --- /dev/null +++ b/neat/cli/commands/bacterial_wrapper.py @@ -0,0 +1,78 @@ +""" +Command line interface for NEAT's bacterial wrapper function +""" + +import argparse +import subprocess +import os +from pathlib import Path + +from ...bacterial_wrapper import bacterial_wrapper +from ...bacterial_wrapper import stitch_all_outputs +from .base import BaseCommand +from .options import output_group + + +class Command(BaseCommand): + """ + Class that generates wrapped bacterial models + """ + name = "bacterial-wrapper" + description = "Generate wrapped bacterial model reads" + + def add_arguments(self, parser: argparse.ArgumentParser): + """ + Add the command's arguments to its parser + + :param parser: The parser to add arguments to + """ + + parser.add_argument('reference', + type=str, + metavar='reference.fa', + help="Reference file for organism in fasta format.") + + parser.add_argument('bacteria_name', + type=str, + metavar='bacteria_name', + help="Name of the bacteria.") + + parser.add_argument( + "-c", "--config", + metavar="config", + type=str, + required=True, + help="Path (including filename) to the configuration file for the reference run." + ) + + output_group.add_to_parser(parser) + + def execute(self, arguments: argparse.Namespace): + """ + Execute the command + + :param arguments: The namespace with arguments and their values. + """ + bacterial_wrapper(arguments.reference, arguments.bacteria_name, arguments.config, arguments.output_dir) + + output_path = Path(arguments.output_dir) + file_list = os.listdir(output_path / "Regular") # same file names for both Regular and Wrapped folders + + output_files = [] + + for file in file_list: + reg_file_path = output_path / "Regular" / file + wrap_file_path = output_path / "Wrapped" / file + + if ("vcf" in file): + subprocess.run(["gzip", "-d", reg_file_path]) + subprocess.run(["gzip", "-d", wrap_file_path]) + + file = file[:-3] + reg_file_path = output_path / "Regular" / file + wrap_file_path = output_path / "Wrapped" / file + + output_files.append(reg_file_path) + output_files.append(wrap_file_path) + + stitch_all_outputs(output_files, arguments.output_dir) \ No newline at end of file diff --git a/neat/read_simulator/utils/options.py b/neat/read_simulator/utils/options.py index 2104dd32..6141ac43 100644 --- a/neat/read_simulator/utils/options.py +++ b/neat/read_simulator/utils/options.py @@ -249,7 +249,6 @@ def from_cli(output_dir: Path, for key, (_, default, _, _) in defs.items(): if key not in input_args: input_args[key] = default - base_options = Options( output_dir=output_dir, output_prefix=output_prefix @@ -257,7 +256,6 @@ def from_cli(output_dir: Path, # Read the config file using the definitions for validation base_options.read_yaml(config_file, defs) - # Merge validated config values over defaults final_args = dict(input_args) for key, val in defs.items(): @@ -299,6 +297,8 @@ def read_yaml(self, config_yaml: Path, args: dict): But I'm not sure how else to accomplish this. """ config = yaml.load(open(config_yaml, 'r'), Loader=Loader) + + for key, value in config.items(): if key in args: type_of_var, default, criteria1, criteria2 = args[key] @@ -447,7 +447,10 @@ def log_configuration(self): if splits_dir.is_dir(): _LOG.info(f'Reusing existing splits {splits_dir}.') else: - _LOG.warning(f'Reused splits set to True, but splits dir not found: {splits_dir}. Creating new splits') + if self.reuse_splits: + raise FileNotFoundError(f'reuse_splits=True') + else: + _LOG.warning(f'Reused splits set to True, but splits dir not found: {splits_dir}. Creating new splits') _LOG.info(f'Preserving splits for next run in directory {self.splits_dir}.') else: splits_dir = self.temp_dir_path / "splits" @@ -509,4 +512,4 @@ def log_configuration(self): _LOG.info(f'Custom average mutation rate for the run: {self.mutation_rate}') if self.mutation_bed: _LOG.info(f'BED of mutation rates of different regions: {self.mutation_bed}') - _LOG.info(f'RNG seed value for run: {self.rng_seed}') + _LOG.info(f'RNG seed value for run: {self.rng_seed}') \ No newline at end of file diff --git a/neat/read_simulator/utils/output_file_writer.py b/neat/read_simulator/utils/output_file_writer.py index 721c5387..4f685e62 100755 --- a/neat/read_simulator/utils/output_file_writer.py +++ b/neat/read_simulator/utils/output_file_writer.py @@ -10,12 +10,16 @@ import os import re +import shutil +import time from struct import pack import logging from typing import Any from Bio import bgzf +from Bio import SeqIO from pathlib import Path +from numpy.random import Generator #gzip for temp outs, bgzip for final outs import gzip diff --git a/neat/read_simulator/utils/stitch_outputs.py b/neat/read_simulator/utils/stitch_outputs.py index 101c50a4..9531be78 100644 --- a/neat/read_simulator/utils/stitch_outputs.py +++ b/neat/read_simulator/utils/stitch_outputs.py @@ -18,6 +18,11 @@ _LOG = logging.getLogger(__name__) def concat(files_to_join: List[Path], dest_file: gzip.GzipFile) -> None: + if not files_to_join: + # Nothing to do, and no error to throw + _LOG.warning(f"Concat called but there are no files to join: {files_to_join}" ) + return + for f in files_to_join: with gzip.open(f, 'rt') as in_f: shutil.copyfileobj(in_f, dest_file) @@ -33,7 +38,7 @@ def merge_vcfs(vcfs: List[Path], ofw: OutputFileWriter) -> None: def merge_bam(bam_files: List[Path], ofw: OutputFileWriter, threads: int): merged_file = ofw.tmp_dir / "temp_merged.bam" intermediate_files = [] - # Note 1000 is abritrary. May need to be a user parameter/adjustable/a function + # Note 1000 is arbitrary. May need to be a user parameter/adjustable/a function for i in range(0, len(bam_files), 500): temp_file = str(ofw.tmp_dir / f"temp_merged_{i}.bam") pysam.merge("--no-PG", "-f", temp_file, *map(str, bam_files[i:i+500])) diff --git a/poetry.lock b/poetry.lock index 35e222d3..58313cd3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. [[package]] name = "biopython" @@ -6,7 +6,6 @@ version = "1.85" description = "Freely available tools for computational molecular biology." optional = false python-versions = ">=3.9" -groups = ["main"] files = [ {file = "biopython-1.85-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a6308053a61f3bdbb11504ece4cf24e264c6f1d6fad278f7e59e6b84b0d9a7b4"}, {file = "biopython-1.85-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:434dd23e972b0c89e128f2ebbd16b38075d609184f4f1fd16368035f923019c2"}, @@ -51,8 +50,6 @@ version = "0.4.6" description = "Cross-platform colored terminal text." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" -groups = ["dev"] -markers = "sys_platform == \"win32\"" files = [ {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, 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