def main():
program_name = 'seq_typing.py'
if sys.version_info[0] < 3:
sys.exit('Must be using Python 3. Try calling "python3 {}"'.format(
program_name))
parser, _, _, _, _ = python_arguments(program_name, __version__)
args = parser.parse_args()
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(script_name=program_name,
logfile=logfile,
version=__version__,
outdir=args.outdir,
time_str=time_str)
del script_path
print('\n')
folders_2_remove = []
# Create modules pickles folder
pickles_folder = os.path.join(args.outdir, 'pickles', '')
if not os.path.isdir(pickles_folder):
os.makedirs(pickles_folder)
folders_2_remove.append(pickles_folder)
# Run functions
folders_2_remove_func, references_results, reference, references_headers = args.func(
args)
folders_2_remove.extend(folders_2_remove_func)
# Parse results
_, _, _, _, _ = parse_results.parse_results(
references_results, reference, references_headers, args.outdir,
args.minGeneCoverage, args.minDepthCoverage, args.typeSeparator)
if not args.debug:
for folder in folders_2_remove:
utils.removeDirectory(folder)
_ = utils.runTime(start_time)
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)
confirm_genes_fasta_rules(typing_headers, typing_rules)
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
_, _, _ = typing.typing(data_by_gene, typing_rules, config['minimum_gene_coverage'],
config['minimum_gene_identity'], args.minGeneDepth, args.outdir)
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)
def runRematch(args):
workdir = os.path.abspath(args.workdir)
if not os.path.isdir(workdir):
os.makedirs(workdir)
asperaKey = 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
utils.general_information(logfile, version, workdir, time_str,
args.doNotUseProvidedSoftware, asperaKey,
args.downloadCramBam)
# Set listIDs
listIDs, searched_fastq_files = getListIDs(
workdir, args.listIDs.name if args.listIDs is not None else None,
args.taxon)
# Run ReMatCh for each sample
print '\n' + 'STARTING ReMatCh' + '\n'
# Clean sequences headers
reference_file, gene_list_reference = clean_headers_reference_file(
os.path.abspath(args.reference.name), workdir, args.extraSeq)
if len(gene_list_reference) == 0:
sys.exit('No sequences left')
# To use in combined report
number_samples_successfully = 0
for sample in listIDs:
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
sequencingInformation = {
'run_accession': None,
'instrument_platform': None,
'instrument_model': None,
'library_layout': None,
'library_source': None,
'extra_run_accession': None,
'date_download': None
}
if not searched_fastq_files:
# Download Files
time_taken_fastq, run_successfully_fastq, fastq_files, sequencingInformation = download.runDownload(
sample, args.downloadLibrariesType, asperaKey, sample_outdir,
args.downloadCramBam, args.threads,
args.downloadInstrumentPlatform)
else:
fastq_files = listIDs[sample]
fileSize = None
run_successfully_rematch_first = None
run_successfully_rematch_second = None
time_taken_rematch_first = 0
time_taken_rematch_second = 0
if run_successfully_fastq is not False:
fileSize = 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 = rematch_module.runRematchModule(
sample, fastq_files, reference_file, args.threads,
sample_outdir, args.extraSeq, args.minCovPresence,
args.minCovCall, args.minFrequencyDominantAllele,
args.minGeneCoverage, args.conservedSeq, args.debug,
args.numMapLoc, args.minGeneIdentity)
if run_successfully_rematch_first:
write_data_by_gene(gene_list_reference, args.minGeneCoverage,
sample, data_by_gene, workdir, time_str,
'first_run', args.minGeneIdentity)
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 = concatenate_extraSeq_2_consensus(
consensus_files['noMatter'], reference_file,
args.extraSeq, rematch_second_outdir)
if len(consensus_concatenated_gene_list) > 0:
time_taken_rematch_second, run_successfully_rematch_second, data_by_gene, sample_data_general_second, consensus_files = rematch_module.runRematchModule(
sample, fastq_files, consensus_concatenated_fasta,
args.threads, rematch_second_outdir, args.extraSeq,
args.minCovPresence, args.minCovCall,
args.minFrequencyDominantAllele,
args.minGeneCoverage, args.conservedSeq,
args.debug, args.numMapLoc, args.minGeneIdentity)
if not args.debug:
os.remove(consensus_concatenated_fasta)
if run_successfully_rematch_second:
write_data_by_gene(gene_list_reference,
args.minGeneCoverage, sample,
data_by_gene, workdir, time_str,
'second_run',
args.minGeneIdentity)
else:
print 'No sequences left after ReMatCh module first run. Second run will not be performed'
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.runTime(sample_start_time)
write_sample_report(
sample, workdir, time_str, fileSize, run_successfully_fastq,
run_successfully_rematch_first, run_successfully_rematch_second,
time_taken_fastq, time_taken_rematch_first,
time_taken_rematch_second, time_taken, sequencingInformation,
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
return number_samples_successfully, len(listIDs)
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():
program_name = 'ecoli_stx_subtyping.py'
if sys.version_info[0] < 3:
sys.exit('Must be using Python 3. Try calling "python3 {}"'.format(
program_name))
parser, parser_reads, _, parser_assembly, _ = python_arguments(
program_name=program_name, version=version)
parser.description = 'Gets E. coli stx subtypes'
# Add specific arguments
parser_reads.add_argument(
'--stx2covered',
type=float,
metavar='N',
help='Minimal percentage of sequence covered to consider extra stx2'
' subtypes (value between [0, 100]) (default: 100)',
required=False,
default=100)
parser_reads.add_argument(
'--stx2identity',
type=float,
metavar='N',
help='Minimal sequence identity to consider extra stx2'
' subtypes (value between [0, 100]) (default: 99.5)',
required=False,
default=99.5)
parser_assembly.add_argument(
'--stx2covered',
type=float,
metavar='N',
help='Minimal percentage of sequence covered to consider extra stx2'
' subtypes (value between [0, 100]) (default: 100)',
required=False,
default=100)
parser_assembly.add_argument(
'--stx2identity',
type=float,
metavar='N',
help='Minimal sequence identity to consider extra stx2'
' subtypes (value between [0, 100]) (default: 99.5)',
required=False,
default=99.5)
args = parser.parse_args()
msg = []
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.stx2covered < 0 or args.stx2covered > 100:
msg.append('--stx2covered should be a value between [0, 100]')
if args.stx2identity < 0 or args.stx2identity > 100:
msg.append('--stx2identity should be a value between [0, 100]')
if args.org != ['stx', 'subtyping']:
msg.append('Use "--org stx subtyping" with {}'.format(program_name))
if len(msg) > 0:
argparse.ArgumentParser(prog='{} options'.format(program_name)).error(
'\n'.join(msg))
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)
_ = utils.general_information(script_name=program_name,
logfile=logfile,
version=version,
outdir=args.outdir,
time_str=time_str)
print('\n')
folders_2_remove = []
# Create modules pickles folder
pickles_folder = os.path.join(args.outdir, 'pickles', '')
if not os.path.isdir(pickles_folder):
os.makedirs(pickles_folder)
folders_2_remove.append(pickles_folder)
# Run functions
folders_2_remove_func, references_results, reference, references_headers = args.func(
args)
folders_2_remove.extend(folders_2_remove_func)
# Parse results
_, _, _, _, _ = parse_results.parse_results(
references_results, reference, references_headers, args.outdir,
args.minGeneCoverage, args.minDepthCoverage, args.typeSeparator)
stx1_result, stx2_result = stx_subtype_parser(
os.path.join(args.outdir, 'seq_typing.report_types.tab'), [
ref_file for ref_file in reference
if 'stx1' in os.path.basename(ref_file).lower()
][0], [
ref_file for ref_file in reference
if 'stx2' in os.path.basename(ref_file).lower()
][0], args.stx2covered, args.stx2identity)
# Rename the file to keep ecoli_stx_subtyping stamp
if os.path.isfile(os.path.join(args.outdir,
'seq_typing.report_types.tab')):
os.rename(
os.path.join(args.outdir, 'seq_typing.report_types.tab'),
os.path.join(args.outdir,
'seq_typing.ecoli_stx_subtyping.report_types.tab'))
# Remove the file to only keep the ecoli_stx_subtyping one
if os.path.isfile(os.path.join(args.outdir, 'seq_typing.report.txt')):
os.remove(os.path.join(args.outdir, 'seq_typing.report.txt'))
print('\n'
'E. coli stx_subtyping - {stx1_result}:{stx2_result}\n'
'\n'.format(stx1_result=stx1_result, stx2_result=stx2_result))
with open(os.path.join(args.outdir, 'seq_typing.ecoli_stx_subtyping.txt'),
'wt') as writer:
writer.write(':'.join([stx1_result, stx2_result]))
if not args.debug:
for folder in folders_2_remove:
utils.removeDirectory(folder)
_ = utils.runTime(start_time)