diff scripts/patho_typing.py @ 0:c6bab5103a14 draft

"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/patho_typing.py	Mon Mar 21 15:23:09 2022 +0000
@@ -0,0 +1,482 @@
+#!/usr/bin/env python3
+
+# -*- coding: utf-8 -*-
+
+"""
+patho_typing.py - In silico pathogenic typing directly from raw
+Illumina reads
+<https://github.com/B-UMMI/patho_typing/>
+
+Copyright (C) 2018 Miguel Machado <[e-mail]>
+
+Last modified: October 15, 2018
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
[phone] ISS
+In order to use the module within the EURL_WGS_Typer pipeline with a 
+different virulence database for E coli, mapping against the 
+typing_rules.tab was deactivated.
+"""
+
+import argparse
+import os
+import time
+import sys
+from pkg_resources import resource_filename
+
+try:
+    from __init__ import __version__
+
+    import modules.utils as utils
+    import modules.run_rematch as run_rematch
+    import modules.typing as typing
+except ImportError:
+    from pathotyping.__init__ import __version__
+
+    from pathotyping.modules import utils as utils
+    from pathotyping.modules import run_rematch as run_rematch
+    from pathotyping.modules import typing as typing
+
+
+def set_reference(species, outdir, script_path, trueCoverage):
+    reference_file = None
+    trueCoverage_file = None
+    trueCoverage_sequences = None
+    trueCoverage_headers = None
+    trueCoverage_config = None
+    typing_file = None
+    typing_sequences = None
+    typing_headers = None
+    typing_rules = None
+    typing_config = None
+
+    species_folder = os.path.join(os.path.dirname(script_path), 'modules', 'seq_conf',
+                                  '_'.join([s.lower() for s in species]), '')
+
+    if os.path.isdir(species_folder):
+        typing_rules = os.path.join(species_folder, 'typing_rules.tab')
+        typing_file = os.path.join(species_folder, 'typing.fasta')
+        typing_sequences, ignore = utils.get_sequence_information(typing_file, 0)
+        typing_sequences, typing_headers = utils.clean_headers_sequences(typing_sequences)
+        typing_sequences = utils.simplify_sequence_dict(typing_sequences)
+        typing_config = os.path.join(species_folder, 'typing.config')
+        if trueCoverage:
+            if os.path.isfile(os.path.join(species_folder, 'trueCoverage.fasta')):
+                trueCoverage_file = os.path.join(species_folder, 'trueCoverage.fasta')
+                trueCoverage_sequences, ignore = utils.get_sequence_information(trueCoverage_file, 0)
+                trueCoverage_sequences, trueCoverage_headers = utils.clean_headers_sequences(trueCoverage_sequences)
+                trueCoverage_sequences = utils.simplify_sequence_dict(trueCoverage_sequences)
+                trueCoverage_config = os.path.join(species_folder, 'trueCoverage.config')
+
+                trueCoverage_typing_sequences = trueCoverage_sequences.copy()
+                for header in typing_sequences:
+                    if header not in trueCoverage_sequences:
+                        trueCoverage_typing_sequences[header] = typing_sequences[header]
+                    else:
+                        print('Sequence {header} of typing.fasta already present in'
+                              ' trueCoverage.fasta'.format(header=header))
+
+                reference_file = os.path.join(outdir, 'trueCoverage_typing.fasta')
+                write_sequeces(reference_file, trueCoverage_typing_sequences)
+        else:
+            reference_file = os.path.join(outdir, 'typing.fasta')
+            write_sequeces(reference_file, typing_sequences)
+    else:
+        species_present = []
+        seq_conf_folder = os.path.join(os.path.dirname(script_path), 'modules', 'seq_conf', '')
+        species_folder = [d for d in os.listdir(seq_conf_folder) if
+                          not d.startswith('.') and os.path.isdir(os.path.join(seq_conf_folder, d, ''))]
+        for species in species_folder:
+            species = species.split('_')
+            species[0] = species[0][0].upper() + species[0][1:]
+            species_present.append(' '.join(species))
+        sys.exit('Only these species are available:' + '\n' + '\n'.join(species_present))
+
+    return reference_file, trueCoverage_file, trueCoverage_sequences, trueCoverage_headers, trueCoverage_config, \
+           typing_file, typing_sequences, typing_headers, typing_rules, typing_config
+
+
+def index_fasta_samtools(fasta, region_None, region_outfile_none, print_comand_True):
+    command = ['samtools', 'faidx', fasta, '', '', '']
+    shell_true = False
+    if region_None is not None:
+        command[3] = region_None
+    if region_outfile_none is not None:
+        command[4] = '>'
+        command[5] = region_outfile_none
+        shell_true = True
+    run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, shell_true, None, print_comand_True)
+    return run_successfully, stdout
+
+
+def indexSequenceBowtie2(referenceFile, threads):
+    if os.path.isfile(str(referenceFile + '.1.bt2')):
+        run_successfully = True
+    else:
+        command = ['bowtie2-build', '--threads', str(threads), referenceFile, referenceFile]
+        run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
+    return run_successfully
+
+
+def run_bowtie(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc):
+    sam_file = os.path.join(outdir, str('alignment.sam'))
+
+    run_successfully = indexSequenceBowtie2(referenceFile, threads)
+    if run_successfully:
+        command = ['bowtie2', '-k', str(numMapLoc), '-q', '', '--threads', str(threads), '-x', referenceFile, '',
+                   '--no-unal', '-S', sam_file]
+
+        if len(fastq_files) == 1:
+            command[9] = '-U ' + fastq_files[0]
+        elif len(fastq_files) == 2:
+            command[9] = '-1 ' + fastq_files[0] + ' -2 ' + fastq_files[1]
+        else:
+            return False, None
+
+        if conserved_True:
+            command[4] = '--sensitive'
+        else:
+            command[4] = '--very-sensitive-local'
+
+        run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
+
+    if not run_successfully:
+        sam_file = None
+
+    return run_successfully, sam_file
+
+
+def sortAlignment(alignment_file, output_file, sortByName_True, threads):
+    outFormat_string = os.path.splitext(output_file)[1][1:].lower()
+    command = ['samtools', 'sort', '-o', output_file, '-O', outFormat_string, '', '-@', str(threads), alignment_file]
+    if sortByName_True:
+        command[6] = '-n'
+    run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
+    if not run_successfully:
+        output_file = None
+    return run_successfully, output_file
+
+
+def indexAlignment(alignment_file):
+    command = ['samtools', 'index', alignment_file]
+    run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
+    return run_successfully
+
+
+def mapping_reads(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc):
+    print('\n' + 'Mapping the reads' + '\n')
+    run_successfully, sam_file = run_bowtie(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc)
+    bam_file = None
+    if run_successfully:
+        run_successfully, bam_file = sortAlignment(sam_file, str(os.path.splitext(sam_file)[0] + '.bam'), False,
+                                                   threads)
+        if run_successfully:
+            os.remove(sam_file)
+            run_successfully = indexAlignment(bam_file)
+            if run_successfully:
+                index_fasta_samtools(referenceFile, None, None, True)
+    return run_successfully, bam_file
+
+
+def include_rematch_dependencies_path():
+    original_rematch = None
+    command = ['which', 'rematch.py']
+    run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, False)
+    if run_successfully:
+        original_rematch = stdout.splitlines()[0]
+
+    resource_rematch = None
+    try:
+        resource_rematch = resource_filename('ReMatCh', 'rematch.py')
+    except ModuleNotFoundError:
+        resource_rematch = original_rematch
+    else:
+        print('\n'
+              'Using ReMatCh "{resource_rematch}" via "{original_rematch}"\n'.format(resource_rematch=resource_rematch,
+                                                                                     original_rematch=original_rematch))
+
+    if resource_rematch is not None:
+        utils.setPATHvariable(False, resource_rematch)
+    else:
+        sys.exit('ReMatCh not found in the PATH')
+
+    return resource_rematch
+
+
+def split_bam(bam_file, list_sequences, outdir, threads):
+    new_bam = os.path.join(outdir, 'partial.bam')
+    command = ['samtools', 'view', '-b', '-u', '-h', '-o', new_bam, '-@', str(threads), bam_file,
+               ' '.join(list_sequences)]
+    run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
+    return run_successfully, new_bam
+
+
+def parse_config(config_file):
+    config = {'reference_file': None, 'length_extra_seq': None, 'maximum_number_absent_genes': None,
+              'maximum_number_genes_multiple_alleles': None, 'minimum_read_coverage': None,
+              'minimum_depth_presence': None, 'minimum_depth_call': None,
+              'minimum_depth_frequency_dominant_allele': None, 'minimum_gene_coverage': None,
+              'minimum_gene_identity': None}
+
+    with open(config_file, 'rt') as reader:
+        field = None
+        for line in reader:
+            line = line.splitlines()[0]
+            if len(line) > 0:
+                line = line.split(' ')[0]
+                if line.startswith('#'):
+                    line = line[1:].split(' ')[0]
+                    field = line
+                else:
+                    if field is not None:
+                        if field in ['length_extra_seq', 'maximum_number_absent_genes',
+                                     'maximum_number_genes_multiple_alleles', 'minimum_read_coverage',
+                                     'minimum_depth_presence', 'minimum_depth_call', 'minimum_gene_coverage',
+                                     'minimum_gene_identity']:
+                            line = int(line)
+                            if field in ['minimum_gene_coverage', 'minimum_gene_identity']:
+                                if line < 0 or line > 100:
+                                    sys.exit('minimum_gene_coverage in trueCoverage_rematch config file must be an'
+                                             ' integer between 0 and 100')
+                        elif field == 'minimum_depth_frequency_dominant_allele':
+                            line = float(line)
+                            if line < 0 or line > 1:
+                                sys.exit('minimum_depth_frequency_dominant_allele in trueCoverage_rematch config file'
+                                         ' must be a double between 0 and 1')
+                        config[field] = line
+                        field = None
+
+    for field in config:
+        if config[field] is None:
+            sys.exit(field + ' in trueCoverage_rematch config file is missing')
+
+    return config
+
+
+def clean_pathotyping_folder(outdir, reference_file, debug_mode_true):
+    if not debug_mode_true:
+        files = [f for f in os.listdir(outdir) if not f.startswith('.') and os.path.isfile(os.path.join(outdir, f))]
+        for file_found in files:
+            if file_found.startswith(('alignment.', os.path.splitext(os.path.basename(reference_file))[0])):
+                file_found = os.path.join(outdir, file_found)
+                os.remove(file_found)
+
+
+def write_sequeces(out_file, sequences_dict):
+    with open(out_file, 'wt') as writer:
+        for header in sequences_dict:
+            writer.write('>' + header + '\n')
+            writer.write('\n'.join(utils.chunkstring(sequences_dict[header]['sequence'], 80)) + '\n')
+
+
+def main():
+    parser = argparse.ArgumentParser(prog='patho_typing.py',
+                                     description='In silico pathogenic typing directly from raw Illumina reads',
+                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('--version', help='Version information', action='version',
+                        version='{prog} v{version}'.format(prog=parser.prog, version=__version__))
+
+    parser_required = parser.add_argument_group('Required options')
+    parser_required.add_argument('-f', '--fastq', nargs='+', action=utils.required_length((1, 2), '--fastq'),
+                                 type=argparse.FileType('r'), metavar=('/path/to/input/file.fq.gz'),
+                                 help='Path to single OR paired-end fastq files. If two files are passed, they will be'
+                                      ' assumed as being the paired fastq files', required=True)
+    parser_required.add_argument('-s', '--species', nargs=2, type=str, metavar=('Yersinia', 'enterocolitica'),
+                                 help='Species name', required=True)
+
+    parser_optional_general = parser.add_argument_group('General facultative options')
+    parser_optional_general.add_argument('-o', '--outdir', type=str, metavar='/path/to/output/directory/',
+                                         help='Path to the directory where the information will be stored',
+                                         required=False, default='.')
+    parser_optional_general.add_argument('-j', '--threads', type=int, metavar='N', help='Number of threads to use',
+                                         required=False, default=1)
+    parser_optional_general.add_argument('--trueCoverage', action='store_true',
+                                         help='Assess true coverage before continue typing')
+    parser_optional_general.add_argument('--noCheckPoint', action='store_true',
+                                         help='Ignore the true coverage checking point')
+    parser_optional_general.add_argument('--minGeneCoverage', type=int, metavar='N',
+                                         help='Minimum typing percentage of target reference gene sequence covered to'
+                                              ' consider a gene to be present (value between [0, 100])', required=False)
+    parser_optional_general.add_argument('--minGeneIdentity', type=int, metavar='N',
+                                         help='Minimum typing percentage of identity of reference gene sequence covered'
+                                              ' to consider a gene to be present (value between [0, 100]). One INDEL'
+                                              ' will be considered as one difference', required=False)
+    parser_optional_general.add_argument('--minGeneDepth', type=int, metavar='N',
+                                         help='Minimum typing gene average coverage depth of present positions to'
+                                              ' consider a gene to be present (default is 1/3 of average sample'
+                                              ' coverage or 15x)', required=False)
+    parser_optional_general.add_argument('--doNotRemoveConsensus', action='store_true',
+                                         help='Do not remove ReMatCh consensus sequences')
+    parser_optional_general.add_argument('--debug', action='store_true',
+                                         help='DeBug Mode: do not remove temporary files')
+
+    args = parser.parse_args()
+
+    if args.minGeneCoverage is not None and (args.minGeneCoverage < 0 or args.minGeneCoverage > 100):
+        parser.error('--minGeneCoverage should be a value between [0, 100]')
+    if args.minGeneIdentity is not None and (args.minGeneIdentity < 0 or args.minGeneIdentity > 100):
+        parser.error('--minGeneIdentity should be a value between [0, 100]')
+
+    start_time = time.time()
+
+    args.outdir = os.path.abspath(args.outdir)
+    if not os.path.isdir(args.outdir):
+        os.makedirs(args.outdir)
+
+    # Start logger
+    logfile, time_str = utils.start_logger(args.outdir)
+
+    script_path = utils.general_information(logfile, __version__, args.outdir, time_str)
+    print('\n')
+
+    rematch = include_rematch_dependencies_path()
+
+    args.fastq = [fastq.name for fastq in args.fastq]
+
+    reference_file, trueCoverage_file, trueCoverage_sequences, trueCoverage_headers, trueCoverage_config, typing_file, \
+    typing_sequences, typing_headers, typing_rules, typing_config = \
+        set_reference(args.species, args.outdir, script_path, args.trueCoverage)
+    original_reference_file = str(reference_file)
+
+    run_successfully, bam_file = mapping_reads(args.fastq, reference_file, args.threads, args.outdir, False, 1)
+    if run_successfully:
+        rematch_dir = os.path.join(args.outdir, 'rematch', '')
+        if not os.path.isdir(rematch_dir):
+            os.makedirs(rematch_dir)
+
+        if args.trueCoverage:
+            if trueCoverage_file is not None:
+                trueCoverage_dir = os.path.join(rematch_dir, 'trueCoverage', '')
+                if not os.path.isdir(trueCoverage_dir):
+                    os.makedirs(trueCoverage_dir)
+
+                print('\n')
+                run_successfully, trueCoverage_bam = split_bam(bam_file, trueCoverage_headers, trueCoverage_dir,
+                                                               args.threads)
+                if run_successfully:
+                    run_successfully = indexAlignment(trueCoverage_bam)
+                    if run_successfully:
+                        reference_file = os.path.join(trueCoverage_dir, 'reference.fasta')
+                        write_sequeces(reference_file, trueCoverage_sequences)
+                        index_fasta_samtools(reference_file, None, None, True)
+                        config = parse_config(trueCoverage_config)
+                        runtime, run_successfully, sample_data_general, data_by_gene = \
+                            run_rematch.run_rematch(rematch, trueCoverage_dir, reference_file, trueCoverage_bam,
+                                                    args.threads, config['length_extra_seq'],
+                                                    config['minimum_depth_presence'], config['minimum_depth_call'],
+                                                    config['minimum_depth_frequency_dominant_allele'],
+                                                    config['minimum_gene_coverage'], config['minimum_gene_identity'],
+                                                    args.debug, args.doNotRemoveConsensus)
+
+                        if run_successfully and sample_data_general['mean_sample_coverage'] is not None and \
+                                sample_data_general['number_absent_genes'] is not None and \
+                                sample_data_general['number_genes_multiple_alleles'] is not None:
+                            if args.minGeneDepth is None:
+                                args.minGeneDepth = sample_data_general['mean_sample_coverage'] / 3 if \
+                                                    sample_data_general['mean_sample_coverage'] / 3 > 15 else \
+                                                    15
+
+                            exit_info = []
+                            if sample_data_general['mean_sample_coverage'] < config['minimum_read_coverage']:
+                                exit_info.append('Sample coverage ({mean}) lower than the minimum'
+                                                 ' required ({minimum})'
+                                                 ''.format(mean=sample_data_general['mean_sample_coverage'],
+                                                           minimum=config['minimum_read_coverage']))
+                            if sample_data_general['number_absent_genes'] > config['maximum_number_absent_genes']:
+                                exit_info.append('Number of absent genes ({number}) higher than the'
+                                                 ' maximum allowed ({maximum})'
+                                                 ''.format(number=sample_data_general['number_absent_genes'],
+                                                           maximum=config['maximum_number_absent_genes']))
+                            if sample_data_general['number_genes_multiple_alleles'] > \
+                                    config['maximum_number_genes_multiple_alleles']:
+                                exit_info.append('Number of genes with multiple alleles'
+                                                 ' ({number}) higher than the maximum'
+                                                 ' allowed ({maximum})'
+                                                 ''.format(number=sample_data_general['number_genes_multiple_alleles'],
+                                                           maximum=config['maximum_number_genes_multiple_alleles']))
+
+                            if len(exit_info) > 0:
+                                print('\n' + '\n'.join(exit_info) + '\n')
+                                e = 'TrueCoverage requirements not fulfilled'
+                                print('\n' + e + '\n')
+                                if not args.noCheckPoint:
+                                    clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
+                                    _ = utils.runTime(start_time)
+                                    sys.exit(e)
+                        else:
+                            e = 'TrueCoverage module did not run successfully'
+                            print('\n' + e + '\n')
+                            if not args.noCheckPoint:
+                                clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
+                                _ = utils.runTime(start_time)
+                                sys.exit(e)
+
+                        print('\n')
+                        typing_dir = os.path.join(rematch_dir, 'typing', '')
+                        if not os.path.isdir(typing_dir):
+                            os.makedirs(typing_dir)
+                        run_successfully, bam_file = split_bam(bam_file, typing_headers, typing_dir, args.threads)
+                        if run_successfully:
+                            run_successfully = indexAlignment(bam_file)
+                            if run_successfully:
+                                reference_file = os.path.join(typing_dir, 'reference.fasta')
+                                write_sequeces(reference_file, typing_sequences)
+                                index_fasta_samtools(reference_file, None, None, True)
+                                rematch_dir = str(typing_dir)
+                if not run_successfully:
+                    if args.noCheckPoint:
+                        clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
+                        _ = utils.runTime(start_time)
+                        sys.exit('Something in the required TrueCoverage analysis went wrong')
+            else:
+                print('\n'
+                      'WARNING: it was not found trueCoverage target files. trueCoverage will not run.'
+                      '\n')
+
+        if run_successfully:
+            config = parse_config(typing_config)
+            if args.minGeneCoverage is not None:
+                config['minimum_gene_coverage'] = args.minGeneCoverage
+            if args.minGeneIdentity is not None:
+                config['minimum_gene_identity'] = args.minGeneIdentity
+
+            runtime, run_successfully, sample_data_general, data_by_gene = \
+                run_rematch.run_rematch(rematch, rematch_dir, reference_file, bam_file, args.threads,
+                                        config['length_extra_seq'], config['minimum_depth_presence'],
+                                        config['minimum_depth_call'], config['minimum_depth_frequency_dominant_allele'],
+                                        config['minimum_gene_coverage'], config['minimum_gene_identity'],
+                                        args.debug, args.doNotRemoveConsensus)
+            if run_successfully and data_by_gene is not None:
+                if args.minGeneDepth is None:
+                    args.minGeneDepth = sample_data_general['mean_sample_coverage'] / 3 if \
+                                        sample_data_general['mean_sample_coverage'] / 3 > 15 else \
+                                        15
+            else:
+                clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
+                _ = utils.runTime(start_time)
+                sys.exit('ReMatCh run for pathotyping did not run successfully')
+        else:
+            clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
+            _ = utils.runTime(start_time)
+            sys.exit('Something did not run successfully')
+
+    clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
+
+    print('\n')
+    _ = utils.runTime(start_time)
+
+
+if __name__ == "__main__":
+    main()