eurl_vtec_wgs_pt: scripts/ReMatCh/rematch.py comparison

comparison scripts/ReMatCh/rematch.py @ 0:c6bab5103a14 draft

"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"

author	iss
date	Mon, 21 Mar 2022 15:23:09 +0000
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children

comparison

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--1:000000000000
+:c6bab5103a14
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+rematch.py - Reads mapping against target sequences, checking mapping
+and consensus sequences production
+<https://github.com/B-UMMI/ReMatCh/>
+Copyright (C) 2019 Miguel Machado <mpmachado@medicina.ulisboa.pt>
+Last modified: August 08, 2019
+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/>.
+"""
+import os
+import sys
+import time
+import argparse
+try:
+from __init__ import __version__
+import modules.utils as utils
+import modules.seqFromWebTaxon as seq_from_web_taxon
+import modules.download as download
+import modules.rematch_module as rematch_module
+import modules.checkMLST as check_mlst
+except ImportError:
+from ReMatCh.__init__ import __version__
+from ReMatCh.modules import utils as utils
+from ReMatCh.modules import seqFromWebTaxon as seq_from_web_taxon
+from ReMatCh.modules import download as download
+from ReMatCh.modules import rematch_module as rematch_module
+from ReMatCh.modules import checkMLST as check_mlst
+def search_fastq_files(directory):
+files_extensions = ['.fastq.gz', '.fq.gz']
+pair_end_files_separation = [['_R1_001.f', '_R2_001.f'], ['_1.f', '_2.f']]
+list_ids = {}
+directories = [d for d in os.listdir(directory) if
+not d.startswith('.') and os.path.isdir(os.path.join(directory, d, ''))]
+for directory_found in directories:
+if directory_found != 'pubmlst':
+directory_path = os.path.join(directory, directory_found, '')
+fastq_found = []
+files = [f for f in os.listdir(directory_path) if
+not f.startswith('.') and os.path.isfile(os.path.join(directory_path, f))]
+for file_found in files:
+if file_found.endswith(tuple(files_extensions)):
+fastq_found.append(file_found)
+if len(fastq_found) == 1:
+list_ids[directory_found] = [os.path.join(directory_path, f) for f in fastq_found]
+elif len(fastq_found) >= 2:
+file_pair = []
+# Search pairs
+for pe_separation in pair_end_files_separation:
+for fastq in fastq_found:
+if pe_separation[0] in fastq or pe_separation[1] in fastq:
+file_pair.append(fastq)
+if len(file_pair) == 2:
+break
+else:
+file_pair = []
+# Search single
+if len(file_pair) == 0:
+for pe_separation in pair_end_files_separation:
+for fastq in fastq_found:
+if pe_separation[0] not in fastq or pe_separation[1] not in fastq:
+file_pair.append(fastq)
+if len(file_pair) >= 1:
+file_pair = file_pair[0]
+if len(file_pair) >= 1:
+list_ids[directory_found] = [os.path.join(directory_path, f) for f in file_pair]
+return list_ids
+def get_list_ids_from_file(file_list_ids):
+list_ids = []
+with open(file_list_ids, 'rtU') as lines:
+for line in lines:
+line = line.rstrip('\r\n')
+if len(line) > 0:
+list_ids.append(line)
+if len(list_ids) == 0:
+sys.exit('No runIDs were found in ' + file_list_ids)
+return list_ids
+def get_taxon_run_ids(taxon_name, outputfile):
+seq_from_web_taxon.run_seq_from_web_taxon(taxon_name, outputfile, True, True, True, False)
+run_ids = []
+with open(outputfile, 'rtU') as reader:
+for line in reader:
+line = line.rstrip('\r\n')
+if len(line) > 0:
+if not line.startswith('#'):
+line = line.split('\t')
+run_ids.append(line[0])
+return run_ids
+def get_list_ids(workdir, file_list_ids, taxon_name):
+searched_fastq_files = False
+list_ids = []
+if file_list_ids is None and taxon_name is None:
+list_ids = search_fastq_files(workdir)
+searched_fastq_files = True
+elif file_list_ids is not None:
+list_ids = get_list_ids_from_file(os.path.abspath(file_list_ids))
+elif taxon_name is not None and file_list_ids is None:
+list_ids = get_taxon_run_ids(taxon_name, os.path.join(workdir, 'IDs_list.seqFromWebTaxon.tab'))
+if len(list_ids) == 0:
+sys.exit('No IDs were found')
+return list_ids, searched_fastq_files
+def format_gene_info(gene_specific_info, minimum_gene_coverage, minimum_gene_identity, reported_data_type, summary,
+sample, genes_present):
+info = None
+if gene_specific_info['gene_coverage'] >= minimum_gene_coverage and \
+gene_specific_info['gene_identity'] >= minimum_gene_identity:
+if summary and sample not in genes_present:
+genes_present[sample] = {}
+if gene_specific_info['gene_number_positions_multiple_alleles'] == 0:
+s = str(gene_specific_info[reported_data_type])
+info = str(s)
+if summary:
+genes_present[sample][gene_specific_info['header']] = str(s)
+else:
+s = 'multiAlleles_' + str(gene_specific_info[reported_data_type])
+info = str(s)
+if summary:
+genes_present[sample][gene_specific_info['header']] = str(s)
+else:
+info = 'absent_' + str(gene_specific_info[reported_data_type])
+return info, genes_present
+def write_data_by_gene(gene_list_reference, minimum_gene_coverage, sample, data_by_gene, outdir, time_str, run_times,
+minimum_gene_identity, reported_data_type, summary, genes_present):
+combined_report = \
+os.path.join(outdir,
+'combined_report.data_by_gene.' + run_times + '.' + reported_data_type + '.' + time_str + '.tab')
+if reported_data_type == 'coverage_depth':
+reported_data_type = 'gene_mean_read_coverage'
+elif reported_data_type == 'sequence_coverage':
+reported_data_type = 'gene_coverage'
+combined_report_exist = os.path.isfile(combined_report)
+with open(combined_report, 'at') as writer:
+seq_list = sorted(gene_list_reference.keys())
+if not combined_report_exist:
+writer.write('#sample' + '\t' + '\t'.join([gene_list_reference[seq] for seq in seq_list]) + '\n')
+results = {}
+headers = []
+for i in data_by_gene:
+results[data_by_gene[i]['header']], genes_present = format_gene_info(data_by_gene[i], minimum_gene_coverage,
+minimum_gene_identity,
+reported_data_type, summary, sample,
+genes_present)
+headers.append(data_by_gene[i]['header'])
+if len(headers) != gene_list_reference:
+for gene in gene_list_reference:
+if gene not in headers:
+results[gene] = 'NA'
+writer.write(sample + '\t' + '\t'.join([results[seq] for seq in seq_list]) + '\n')
+return genes_present
+def write_sample_report(sample, outdir, time_str, file_size, run_successfully_fastq, run_successfully_rematch_first,
+run_successfully_rematch_second, time_taken_fastq, time_taken_rematch_first,
+time_taken_rematch_second, time_taken_sample, sequencing_information, sample_data_general_first,
+sample_data_general_second, fastq_used):
+sample_report = os.path.join(outdir, 'sample_report.' + time_str + '.tab')
+report_exist = os.path.isfile(sample_report)
+header_general = ['sample', 'sample_run_successfully', 'sample_run_time', 'files_size', 'download_run_successfully',
+'download_run_time', 'rematch_run_successfully_first', 'rematch_run_time_first',
+'rematch_run_successfully_second', 'rematch_run_time_second']
+header_data_general = ['number_absent_genes', 'number_genes_multiple_alleles', 'mean_sample_coverage']
+header_sequencing = ['run_accession', 'instrument_platform', 'instrument_model', 'library_layout', 'library_source',
+'extra_run_accession', 'nominal_length', 'read_count', 'base_count', 'date_download']
+with open(sample_report, 'at') as writer:
+if not report_exist:
+writer.write('#' + '\t'.join(header_general) + '\t' + '_first\t'.join(header_data_general) + '_first\t' +
+'_second\t'.join(header_data_general) + '_second\t' + '\t'.join(header_sequencing) + '\t' +
+'fastq_used' + '\n')
+writer.write('\t'.join([sample,
+str(all([run_successfully_fastq is not False,
+run_successfully_rematch_first is not False,
+run_successfully_rematch_second is not False])),
+str(time_taken_sample),
+str(file_size),
+str(run_successfully_fastq),
+str(time_taken_fastq),
+str(run_successfully_rematch_first),
+str(time_taken_rematch_first),
+str(run_successfully_rematch_second),
+str(time_taken_rematch_second)]) +
+'\t' + '\t'.join([str(sample_data_general_first[i]) for i in header_data_general]) +
+'\t' + '\t'.join([str(sample_data_general_second[i]) for i in header_data_general]) +
+'\t' + '\t'.join([str(sequencing_information[i]) for i in header_sequencing]) +
+'\t' + ','.join(fastq_used) + '\n')
+def concatenate_extra_seq_2_consensus(consensus_sequence, reference_sequence, extra_seq_length, outdir):
+reference_dict, ignore, ignore = rematch_module.get_sequence_information(reference_sequence, extra_seq_length)
+consensus_dict, genes, ignore = rematch_module.get_sequence_information(consensus_sequence, 0)
+number_consensus_with_sequences = 0
+for k, values_consensus in list(consensus_dict.items()):
+for values_reference in list(reference_dict.values()):
+if values_reference['header'] == values_consensus['header']:
+if len(set(consensus_dict[k]['sequence'])) > 1:
+number_consensus_with_sequences += 1
+if extra_seq_length <= len(values_reference['sequence']):
+right_extra_seq = \
+'' if extra_seq_length == 0 else values_reference['sequence'][-extra_seq_length:]
+consensus_dict[k]['sequence'] = \
+values_reference['sequence'][:extra_seq_length] + \
+consensus_dict[k]['sequence'] + \
+right_extra_seq
+consensus_dict[k]['length'] += extra_seq_length + len(right_extra_seq)
+consensus_concatenated = os.path.join(outdir, 'consensus_concatenated_extraSeq.fasta')
+with open(consensus_concatenated, 'wt') as writer:
+for i in consensus_dict:
+writer.write('>' + consensus_dict[i]['header'] + '\n')
+fasta_sequence_lines = rematch_module.chunkstring(consensus_dict[i]['sequence'], 80)
+for line in fasta_sequence_lines:
+writer.write(line + '\n')
+return consensus_concatenated, genes, consensus_dict, number_consensus_with_sequences
+def clean_headers_reference_file(reference_file, outdir, extra_seq):
+problematic_characters = ["|", " ", ",", ".", "(", ")", "'", "/", ":"]
+print('Checking if reference sequences contain ' + str(problematic_characters) + '\n')
+# headers_changed = False
+new_reference_file = str(reference_file)
+sequences, genes, headers_changed = rematch_module.get_sequence_information(reference_file, extra_seq)
+if headers_changed:
+print('At least one of the those characters was found. Replacing those with _' + '\n')
+new_reference_file = \
+os.path.join(outdir, os.path.splitext(os.path.basename(reference_file))[0] + '.headers_renamed.fasta')
+with open(new_reference_file, 'wt') as writer:
+for i in sequences:
+writer.write('>' + sequences[i]['header'] + '\n')
+fasta_sequence_lines = rematch_module.chunkstring(sequences[i]['sequence'], 80)
+for line in fasta_sequence_lines:
+writer.write(line + '\n')
+return new_reference_file, genes, sequences
+def write_mlst_report(sample, run_times, consensus_type, st, alleles_profile, loci_order, outdir, time_str):
+mlst_report = os.path.join(outdir, 'mlst_report.' + time_str + '.tab')
+mlst_report_exist = os.path.isfile(mlst_report)
+with open(mlst_report, 'at') as writer:
+if not mlst_report_exist:
+writer.write('\t'.join(['#sample', 'ReMatCh_run', 'consensus_type', 'ST'] + loci_order) + '\n')
+writer.write('\t'.join([sample, run_times, consensus_type, str(st)] + alleles_profile.split(',')) + '\n')
+def run_get_st(sample, mlst_dicts, consensus_sequences, mlst_consensus, run_times, outdir, time_str):
+if mlst_consensus == 'all':
+for consensus_type in consensus_sequences:
+print('Searching MLST for ' + consensus_type + ' consensus')
+st, alleles_profile = check_mlst.get_st(mlst_dicts, consensus_sequences[consensus_type])
+write_mlst_report(sample, run_times, consensus_type, st, alleles_profile, mlst_dicts[2], outdir, time_str)
+print('ST found: ' + str(st) + ' (' + alleles_profile + ')')
+else:
+st, alleles_profile = check_mlst.get_st(mlst_dicts, consensus_sequences[mlst_consensus])
+write_mlst_report(sample, run_times, mlst_consensus, st, alleles_profile, mlst_dicts[2], outdir, time_str)
+print('ST found for ' + mlst_consensus + ' consensus: ' + str(st) + ' (' + alleles_profile + ')')
+def write_summary_report(outdir, reported_data_type, time_str, gene_list_reference, genes_present):
+with open(os.path.join(outdir,
+'summary.{reported_data_type}.{time_str}.tab'.format(reported_data_type=reported_data_type,
+time_str=time_str)), 'wt') as writer:
+seq_list = []
+for info in list(genes_present.values()):
+seq_list.extend(list(info.keys()))
+seq_list = list(set(seq_list))
+writer.write('#sample' + '\t' + '\t'.join([gene_list_reference[seq] for seq in sorted(seq_list)]) + '\n')
+for sample, info in list(genes_present.items()):
+data = []
+for seq in sorted(seq_list):
+if seq in info:
+data.append(info[seq])
+else:
+data.append('NF')
+writer.write(sample + '\t' + '\t'.join(data) + '\n')
+def run_rematch(args):
+workdir = os.path.abspath(args.workdir)
+if not os.path.isdir(workdir):
+os.makedirs(workdir)
+aspera_key = os.path.abspath(args.asperaKey.name) if args.asperaKey is not None else None
+# Start logger
+logfile, time_str = utils.start_logger(workdir)
+# Get general information
+script_path = utils.general_information(logfile, __version__, workdir, time_str, args.doNotUseProvidedSoftware,
+aspera_key, args.downloadCramBam, args.SRA, args.SRAopt)
+# Set list_ids
+list_ids, searched_fastq_files = get_list_ids(workdir, args.listIDs.name if args.listIDs is not None else None,
+args.taxon)
+mlst_sequences = None
+mlst_dicts = None
+if args.mlst is not None:
+time_taken_pub_mlst, mlst_dicts, mlst_sequences = check_mlst.download_pub_mlst_xml(args.mlst,
+args.mlstSchemaNumber,
+workdir)
+args.softClip_recodeRun = 'first'
+if args.reference is None:
+if args.mlst is not None:
+reference_file = check_mlst.check_existing_schema(args.mlst, args.mlstSchemaNumber, script_path)
+args.extraSeq = 200
+if reference_file is None:
+print('It was not found provided MLST scheme sequences for ' + args.mlst)
+print('Trying to obtain reference MLST sequences from PubMLST')
+if len(mlst_sequences) > 0:
+reference_file = check_mlst.write_mlst_reference(args.mlst, mlst_sequences, workdir, time_str)
+args.extraSeq = 0
+else:
+sys.exit('It was not possible to download MLST sequences from PubMLST!')
+else:
+print('Using provided scheme as referece: ' + reference_file)
+else:
+sys.exit('Need to provide at least one of the following options: "--reference" and "--mlst"')
+else:
+reference_file = os.path.abspath(args.reference.name)
+# Run ReMatCh for each sample
+print('\n' + 'STARTING ReMatCh' + '\n')
+# Clean sequences headers
+reference_file, gene_list_reference, reference_dict = clean_headers_reference_file(reference_file, workdir,
+args.extraSeq)
+if args.mlst is not None:
+problem_genes = False
+for header in mlst_sequences:
+if header not in gene_list_reference:
+print('MLST gene {header} not found between reference sequences'.format(header=header))
+problem_genes = True
+if problem_genes:
+sys.exit('Missing MLST genes from reference sequences (at least sequences names do not match)!')
+if len(gene_list_reference) == 0:
+sys.exit('No sequences left')
+# To use in combined report
+number_samples_successfully = 0
+genes_present_coverage_depth = {}
+genes_present_sequence_coverage = {}
+for sample in list_ids:
+sample_start_time = time.time()
+print('\n\n' + 'Sample ID: ' + sample)
+# Create sample outdir
+sample_outdir = os.path.join(workdir, sample, '')
+if not os.path.isdir(sample_outdir):
+os.mkdir(sample_outdir)
+run_successfully_fastq = None
+time_taken_fastq = 0
+sequencing_information = {'run_accession': None, 'instrument_platform': None, 'instrument_model': None,
+'library_layout': None, 'library_source': None, 'extra_run_accession': None,
+'nominal_length': None, 'read_count': None, 'base_count': None, 'date_download': None}
+if not searched_fastq_files:
+# Download Files
+time_taken_fastq, run_successfully_fastq, fastq_files, sequencing_information = \
+download.run_download(sample, args.downloadLibrariesType, aspera_key, sample_outdir,
+args.downloadCramBam, args.threads, args.downloadInstrumentPlatform, args.SRA,
+args.SRAopt)
+else:
+fastq_files = list_ids[sample]
+file_size = None
+run_successfully_rematch_first = None
+run_successfully_rematch_second = None
+time_taken_rematch_first = 0
+time_taken_rematch_second = 0
+sample_data_general_first = None
+sample_data_general_second = None
+if run_successfully_fastq is not False:
+file_size = sum(os.path.getsize(fastq) for fastq in fastq_files)
+# Run ReMatCh
+time_taken_rematch_first, run_successfully_rematch_first, data_by_gene, sample_data_general_first, \
+consensus_files, consensus_sequences = \
+rematch_module.run_rematch_module(sample, fastq_files, reference_file, args.threads, sample_outdir,
+args.extraSeq, args.minCovPresence, args.minCovCall,
+args.minFrequencyDominantAllele, args.minGeneCoverage,
+args.debug, args.numMapLoc, args.minGeneIdentity,
+'first', args.softClip_baseQuality, args.softClip_recodeRun,
+reference_dict, args.softClip_cigarFlagRecode,
+args.bowtieAlgo, args.bowtieOPT,
+gene_list_reference, args.notWriteConsensus, clean_run=True)
+if run_successfully_rematch_first:
+if args.mlst is not None and (args.mlstRun == 'first' or args.mlstRun == 'all'):
+run_get_st(sample, mlst_dicts, consensus_sequences, args.mlstConsensus, 'first', workdir, time_str)
+genes_present_coverage_depth = write_data_by_gene(gene_list_reference, args.minGeneCoverage, sample,
+data_by_gene, workdir, time_str, 'first_run',
+args.minGeneIdentity, 'coverage_depth', args.summary,
+genes_present_coverage_depth)
+if args.reportSequenceCoverage:
+genes_present_sequence_coverage = write_data_by_gene(gene_list_reference, args.minGeneCoverage,
+sample, data_by_gene, workdir, time_str,
+'first_run', args.minGeneIdentity,
+'sequence_coverage', args.summary,
+genes_present_sequence_coverage)
+if args.doubleRun:
+rematch_second_outdir = os.path.join(sample_outdir, 'rematch_second_run', '')
+if not os.path.isdir(rematch_second_outdir):
+os.mkdir(rematch_second_outdir)
+consensus_concatenated_fasta, consensus_concatenated_gene_list, consensus_concatenated_dict, \
+number_consensus_with_sequences = \
+concatenate_extra_seq_2_consensus(consensus_files['noMatter'], reference_file, args.extraSeq,
+rematch_second_outdir)
+if len(consensus_concatenated_gene_list) > 0:
+if args.mlst is None or \
+(args.mlst is not None and number_consensus_with_sequences == len(gene_list_reference)):
+time_taken_rematch_second, run_successfully_rematch_second, data_by_gene, \
+sample_data_general_second, consensus_files, consensus_sequences = \
+rematch_module.run_rematch_module(sample, fastq_files, consensus_concatenated_fasta,
+args.threads, rematch_second_outdir, args.extraSeq,
+args.minCovPresence, args.minCovCall,
+args.minFrequencyDominantAllele, args.minGeneCoverage,
+args.debug, args.numMapLoc,
+args.minGeneIdentity, 'second',
+args.softClip_baseQuality, args.softClip_recodeRun,
+consensus_concatenated_dict,
+args.softClip_cigarFlagRecode,
+args.bowtieAlgo, args.bowtieOPT,
+gene_list_reference, args.notWriteConsensus,
+clean_run=True)
+if not args.debug:
+os.remove(consensus_concatenated_fasta)
+if run_successfully_rematch_second:
+if args.mlst is not None and (args.mlstRun == 'second' or args.mlstRun == 'all'):
+run_get_st(sample, mlst_dicts, consensus_sequences, args.mlstConsensus, 'second',
+workdir, time_str)
+_ = write_data_by_gene(gene_list_reference, args.minGeneCoverage, sample, data_by_gene,
+workdir, time_str, 'second_run', args.minGeneIdentity,
+'coverage_depth', False, {})
+if args.reportSequenceCoverage:
+_ = write_data_by_gene(gene_list_reference, args.minGeneCoverage, sample,
+data_by_gene, workdir, time_str, 'second_run',
+args.minGeneIdentity, 'sequence_coverage', False, {})
+else:
+print('Some sequences missing after ReMatCh module first run. Second run will not be'
+' performed')
+if os.path.isfile(consensus_concatenated_fasta):
+os.remove(consensus_concatenated_fasta)
+if os.path.isdir(rematch_second_outdir):
+utils.remove_directory(rematch_second_outdir)
+else:
+print('No sequences left after ReMatCh module first run. Second run will not be performed')
+if os.path.isfile(consensus_concatenated_fasta):
+os.remove(consensus_concatenated_fasta)
+if os.path.isdir(rematch_second_outdir):
+utils.remove_directory(rematch_second_outdir)
+if not searched_fastq_files and not args.keepDownloadedFastq and fastq_files is not None:
+for fastq in fastq_files:
+if os.path.isfile(fastq):
+os.remove(fastq)
+time_taken = utils.run_time(sample_start_time)
+write_sample_report(sample, workdir, time_str, file_size, run_successfully_fastq,
+run_successfully_rematch_first, run_successfully_rematch_second, time_taken_fastq,
+time_taken_rematch_first, time_taken_rematch_second, time_taken, sequencing_information,
+sample_data_general_first if run_successfully_rematch_first else
+{'number_absent_genes': None, 'number_genes_multiple_alleles': None,
+'mean_sample_coverage': None},
+sample_data_general_second if run_successfully_rematch_second else
+{'number_absent_genes': None, 'number_genes_multiple_alleles': None,
+'mean_sample_coverage': None},
+fastq_files if fastq_files is not None else '')
+if all([run_successfully_fastq is not False,
+run_successfully_rematch_first is not False,
+run_successfully_rematch_second is not False]):
+number_samples_successfully += 1
+if args.summary:
+write_summary_report(workdir, 'coverage_depth', time_str, gene_list_reference, genes_present_coverage_depth)
+if args.reportSequenceCoverage:
+write_summary_report(workdir, 'sequence_coverage', time_str, gene_list_reference,
+genes_present_sequence_coverage)
+return number_samples_successfully, len(list_ids)
+def main():
+if sys.version_info[0] < 3:
+sys.exit('Must be using Python 3. Try calling "python3 rematch.py"')
+parser = argparse.ArgumentParser(prog='rematch.py',
+description='Reads mapping against target sequences, checking mapping and'
+' consensus sequences production',
+formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+parser.add_argument('--version', help='Version information', action='version',
+version='{prog} v{version}'.format(prog=parser.prog, version=__version__))
+parser_optional_general = parser.add_argument_group('General facultative options')
+parser_optional_general.add_argument('-r', '--reference', type=argparse.FileType('r'),
+metavar='/path/to/reference_sequence.fasta',
+help='Fasta file containing reference sequences', required=False)
+parser_optional_general.add_argument('-w', '--workdir', type=str, metavar='/path/to/workdir/directory/',
+help='Path to the directory where ReMatCh will run and produce the outputs'
+' with reads (ended with fastq.gz/fq.gz and, in case of PE data, pair-end'
+' direction coded as _R1_001 / _R2_001 or _1 / _2) already'
+' present (organized in sample folders) or to be downloaded',
+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('--mlst', type=str, metavar='"Streptococcus agalactiae"',
+help='Species name (same as in PubMLST) to be used in MLST'
+' determination. ReMatCh will use Bowtie2 very-sensitive-local mapping'
+' parameters and will recode the soft clip CIGAR flags of the first run',
+required=False)
+parser_optional_general.add_argument('--doNotUseProvidedSoftware', action='store_true',
+help='Tells ReMatCh to not use Bowtie2, Samtools and Bcftools that are'
+' provided with it')
+parser_optional_download_exclusive = parser.add_mutually_exclusive_group()
+parser_optional_download_exclusive.add_argument('-l', '--listIDs', type=argparse.FileType('r'),
+metavar='/path/to/list_IDs.txt',
+help='Path to list containing the IDs to be'
+' downloaded (one per line)', required=False)
+parser_optional_download_exclusive.add_argument('-t', '--taxon', type=str, metavar='"Streptococcus agalactiae"',
+help='Taxon name for which ReMatCh will download fastq files',
+required=False)
+parser_optional_rematch = parser.add_argument_group('ReMatCh module facultative options')
+parser_optional_rematch.add_argument('--extraSeq', type=int, metavar='N',
+help='Sequence length added to both ends of target sequences (usefull to'
+' improve reads mapping to the target one) that will be trimmed in'
+' ReMatCh outputs', required=False, default=0)
+parser_optional_rematch.add_argument('--minCovPresence', type=int, metavar='N',
+help='Reference position minimum coverage depth to consider the position to be'
+' present in the sample', required=False, default=5)
+parser_optional_rematch.add_argument('--minCovCall', type=int, metavar='N',
+help='Reference position minimum coverage depth to perform a base call. Lower'
+' coverage will be coded as N', required=False, default=10)
+parser_optional_rematch.add_argument('--minFrequencyDominantAllele', type=float, metavar='0.6',
+help='Minimum relative frequency of the dominant allele coverage depth (value'
+' between [0, 1]). Positions with lower values will be considered as'
+' having multiple alleles (and will be coded as N)', required=False,
+default=0.6)
+parser_optional_rematch.add_argument('--minGeneCoverage', type=int, metavar='N',
+help='Minimum percentage of target reference gene sequence covered'
+' by --minCovPresence to consider a gene to be present (value'
+' between [0, 100])', required=False, default=70)
+parser_optional_rematch.add_argument('--minGeneIdentity', type=int, metavar='N',
+help='Minimum percentage of identity of reference gene sequence covered'
+' by --minCovCall to consider a gene to be present (value'
+' between [0, 100]). One INDEL will be considered as one difference',
+required=False, default=80)
+parser_optional_rematch.add_argument('--numMapLoc', type=int, metavar='N', help=argparse.SUPPRESS, required=False,
+default=1)
+# parser_optional_rematch.add_argument('--numMapLoc', type=int, metavar='N', help='Maximum number of locations to which a read can map (sometimes useful when mapping against similar sequences)', required=False, default=1)
+parser_optional_rematch.add_argument('--doubleRun', action='store_true',
+help='Tells ReMatCh to run a second time using as reference the noMatter'
+' consensus sequence produced in the first run. This will improve'
+' consensus sequence determination for sequences with high percentage of'
+' target reference gene sequence covered')
+parser_optional_rematch.add_argument('--reportSequenceCoverage', action='store_true',
+help='Produce an extra combined_report.data_by_gene with the sequence coverage'
+' instead of coverage depth')
+parser_optional_rematch.add_argument('--summary', action='store_true',
+help='Produce extra report files containing only sequences present in at least'
+' one sample (usefull when using a large number of reference'
+' sequences, and only for first run)')
+parser_optional_rematch.add_argument('--notWriteConsensus', action='store_true',
+help='Do not write consensus sequences')
+parser_optional_rematch.add_argument('--bowtieAlgo', type=str, metavar='"--very-sensitive-local"',
+help='Bowtie2 alignment mode. It can be an end-to-end alignment (unclipped'
+' alignment) or local alignment (soft clipped alignment). Also, can'
+' choose between fast or sensitive alignments. Please check Bowtie2'
+' manual for extra'
+' information: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml .'
+' This option should be provided between quotes and starting with'
+' an empty space (like --bowtieAlgo " --very-fast") or using equal'
+' sign (like --bowtieAlgo="--very-fast")',
+required=False, default='--very-sensitive-local')
+parser_optional_rematch.add_argument('--bowtieOPT', type=str, metavar='"--no-mixed"',
+help='Extra Bowtie2 options. This option should be provided between quotes and'
+' starting with an empty space (like --bowtieOPT " --no-mixed") or using'
+' equal sign (like --bowtieOPT="--no-mixed")',
+required=False)
+parser_optional_rematch.add_argument('--debug', action='store_true',
+help='DeBug Mode: do not remove temporary files')
+parser_optional_mlst = parser.add_argument_group('MLST facultative options')
+parser_optional_rematch.add_argument('--mlstReference', action='store_true',
+help='If the curated scheme for MLST alleles is available, tells ReMatCh to'
+' use these as reference (force Bowtie2 to run with very-sensitive-local'
+' parameters, and sets --extraSeq to 200), otherwise ReMatCh uses the'
+' first alleles of each MLST gene fragment in PubMLST as reference'
+' sequences (force Bowtie2 to run with very-sensitive-local parameters,'
+' and sets --extraSeq to 0)')
+parser_optional_mlst.add_argument('--mlstSchemaNumber', type=int, metavar='N',
+help='Number of the species PubMLST schema to be used in case of multiple schemes'
+' available (by default will use the first schema)', required=False)
+parser_optional_mlst.add_argument('--mlstConsensus', choices=['noMatter', 'correct', 'alignment', 'all'], type=str,
+metavar='noMatter',
+help='Consensus sequence to be used in MLST'
+' determination (available options: %(choices)s)', required=False,
+default='noMatter')
+parser_optional_mlst.add_argument('--mlstRun', choices=['first', 'second', 'all'], type=str, metavar='first',
+help='ReMatCh run outputs to be used in MLST determination (available'
+' options: %(choices)s)', required=False, default='all')
+parser_optional_download = parser.add_argument_group('Download facultative options')
+parser_optional_download.add_argument('-a', '--asperaKey', type=argparse.FileType('r'),
+metavar='/path/to/asperaweb_id_dsa.openssh',
+help='Tells ReMatCh to download fastq files from ENA using Aspera'
+' Connect. With this option, the path to Private-key file'
+' asperaweb_id_dsa.openssh must be provided (normaly found in'
+' ~/.aspera/connect/etc/asperaweb_id_dsa.openssh).', required=False)
+parser_optional_download.add_argument('-k', '--keepDownloadedFastq', action='store_true',
+help='Tells ReMatCh to keep the fastq files downloaded')
+parser_optional_download.add_argument('--downloadLibrariesType', type=str, metavar='PAIRED',
+help='Tells ReMatCh to download files with specific library'
+' layout (available options: %(choices)s)',
+choices=['PAIRED', 'SINGLE', 'BOTH'], required=False, default='BOTH')
+parser_optional_download.add_argument('--downloadInstrumentPlatform', type=str, metavar='ILLUMINA',
+help='Tells ReMatCh to download files with specific library layout (available'
+' options: %(choices)s)', choices=['ILLUMINA', 'ALL'], required=False,
+default='ILLUMINA')
+parser_optional_download.add_argument('--downloadCramBam', action='store_true',
+help='Tells ReMatCh to also download cram/bam files and convert them to fastq'
+' files')
+parser_optional_sra = parser.add_mutually_exclusive_group()
+parser_optional_sra.add_argument('--SRA', action='store_true',
+help='Tells getSeqENA.py to download reads in fastq format only from NCBI SRA'
+' database (not recommended)')
+parser_optional_sra.add_argument('--SRAopt', action='store_true',
+help='Tells getSeqENA.py to download reads from NCBI SRA if the download from ENA'
+' fails')
+parser_optional_soft_clip = parser.add_argument_group('Soft clip facultative options')
+parser_optional_soft_clip.add_argument('--softClip_baseQuality', type=int, metavar='N',
+help='Base quality phred score in reads soft clipped regions',
+required=False,
+default=7)
+parser_optional_soft_clip.add_argument('--softClip_recodeRun', type=str, metavar='first',
+help='ReMatCh run to recode soft clipped regions (available'
+' options: %(choices)s)', choices=['first', 'second', 'both', 'none'],
+required=False, default='none')
+parser_optional_soft_clip.add_argument('--softClip_cigarFlagRecode', type=str, metavar='M',
+help='CIGAR flag to recode CIGAR soft clip (available options: %(choices)s)',
+choices=['M', 'I', 'X'], required=False, default='X')
+args = parser.parse_args()
+msg = []
+if args.reference is None and not args.mlstReference:
+msg.append('At least --reference or --mlstReference should be provided')
+elif args.reference is not None and args.mlstReference:
+msg.append('Only --reference or --mlstReference should be provided')
+else:
+if args.mlstReference:
+if args.mlst is None:
+msg.append('Please provide species name using --mlst')
+if args.minFrequencyDominantAllele < 0 or args.minFrequencyDominantAllele > 1:
+msg.append('--minFrequencyDominantAllele should be a value between [0, 1]')
+if args.minGeneCoverage < 0 or args.minGeneCoverage > 100:
+msg.append('--minGeneCoverage should be a value between [0, 100]')
+if args.minGeneIdentity < 0 or args.minGeneIdentity > 100:
+msg.append('--minGeneIdentity should be a value between [0, 100]')
+if args.notWriteConsensus and args.doubleRun:
+msg.append('--notWriteConsensus and --doubleRun cannot be used together.'
+' Maybe you only want to use --doubleRun')
+if len(msg) > 0:
+argparse.ArgumentParser.error('\n'.join(msg))
+start_time = time.time()
+number_samples_successfully, samples_total_number = run_rematch(args)
+print('\n' + 'END ReMatCh')
+print('\n' +
+str(number_samples_successfully) + ' samples out of ' + str(samples_total_number) + ' run successfully')
+time_taken = utils.run_time(start_time)
+del time_taken
+if number_samples_successfully == 0:
+sys.exit('No samples run successfully!')
+if __name__ == "__main__":
+main()

Mercurial > repos > iss > eurl_vtec_wgs_pt

comparison scripts/ReMatCh/rematch.py @ 0:c6bab5103a14 draft