def ConstructSubreferences(datasets, reference_file, output_dir, index = None, threads = 1, log = None):
bwa_command = "bin/spades-bwa"
if log == None:
log = logging.getLogger('reference_construction')
log.setLevel(logging.INFO)
console = logging.StreamHandler(sys.stderr)
console.setFormatter(logging.Formatter('%(message)s'))
console.setLevel(logging.INFO)
log.addHandler(console)
support.ensure_dir_existence(output_dir)
if not os.path.exists(output_dir):
os.makedirs(output_dir)
if index == None:
log.info("Constructing index\n")
index = alignment.index_bwa(bwa_command, log, reference_file, os.path.join(output_dir, "bwa_index"), "bwtsw")
sam_dir = os.path.join(output_dir, "alignments")
log.info("Aligning barcodes\n")
sam_files = AlignToReference(datasets, sam_dir, bwa_command, log, index, threads)
subreference_dir = os.path.join(output_dir, "subreferences")
filtered_dir = os.path.join(output_dir, "filtered")
support.recreate_dir(subreference_dir)
support.recreate_dir(filtered_dir)
log.info("Constructing subreferences")
subreferences_list = [(barcode_id, ConstructSubreferenceFromSam(barcode_sam)) for barcode_id, barcode_sam in sam_files]
log.info("Reading reference")
reference = ReadReference(reference_file)
log.info("Printing output")
PrintAll([(barcode, filtered) for barcode, (filtered, subreference) in subreferences_list], reference, filtered_dir)
PrintAll([(barcode, subreference) for barcode, (filtered, subreference) in subreferences_list], reference, subreference_dir)
log.info("Subreference construction finished. See results in " + output_dir)
def main(argv):
options = launch_options.Options(argv, spades_home, truspades_home, spades_version)
support.ensure_dir_existence(options.output_dir)
if options.test and not options.continue_launch:
support.recreate_dir(options.output_dir)
log = create_log(options)
dataset_file = os.path.join(options.output_dir, "dataset.info")
if options.continue_launch:
dataset = barcode_extraction.ReadDataset(dataset_file, log)
elif options.input_dirs is not None:
dataset = generate_dataset(options.input_dirs, log)
if dataset is None:
log.info("Error: could not parse dataset from input directories\n")
sys.exit(1)
barcode_extraction.print_dataset(dataset, dataset_file, log)
log.info("Dataset generated. See result in " + dataset_file)
else:
dataset = barcode_extraction.ReadDataset(options.dataset_file, log)
barcode_extraction.print_dataset(dataset, dataset_file, log)
log_dir = os.path.join(options.output_dir, "logs")
support.ensure_dir_existence(log_dir)
# if options.print_commands:
# verify_exists(options.output_dir)
# print_commands(commands, options)
if options.mode == "run_truspades":
RunTruSPAdes(dataset, log_dir, options, log)
elif options.mode == "construct_subreferences":
reference_construction.ConstructSubreferences(dataset, options.reference, options.output_dir, options.index, options.threads, log = None)
log.info("TruSPAdes launch successfully finished")
if options.test:
CheckTestSuccess(options, log)
def main(argv):
options = launch_options.Options(argv, spades_home, truspades_home, spades_version)
support.ensure_dir_existence(options.output_dir)
if options.test and not options.continue_launch:
support.recreate_dir(options.output_dir)
log = create_log(options)
dataset_file = os.path.join(options.output_dir, "dataset.info")
if options.continue_launch:
dataset = barcode_extraction.ReadDataset(dataset_file, log)
elif options.input_dirs is not None:
dataset = generate_dataset(options.input_dirs, log)
if dataset is None:
log.info("Error: could not parse dataset from input directories\n")
sys.exit(1)
barcode_extraction.print_dataset(dataset, dataset_file, log)
log.info("Dataset generated. See result in " + dataset_file)
else:
dataset = barcode_extraction.ReadDataset(options.dataset_file, log)
barcode_extraction.print_dataset(dataset, dataset_file, log)
log_dir = os.path.join(options.output_dir, "logs")
support.ensure_dir_existence(log_dir)
# if options.print_commands:
# verify_exists(options.output_dir)
# print_commands(commands, options)
if options.mode == "run_truspades":
RunTruSPAdes(dataset, log_dir, options, log)
elif options.mode == "construct_subreferences":
reference_construction.ConstructSubreferences(dataset, options.reference, options.output_dir, options.index, options.threads, log = None)
log.info("TruSPAdes launch successfully finished")
if options.test:
CheckTestSuccess(options, log)
def ConstructSubreferences(datasets, reference_file, output_dir, index = None, threads = 1, log = None):
bwa_command = "bin/bwa-spades"
if log == None:
log = logging.getLogger('reference_construction')
log.setLevel(logging.INFO)
console = logging.StreamHandler(sys.stderr)
console.setFormatter(logging.Formatter('%(message)s'))
console.setLevel(logging.INFO)
log.addHandler(console)
support.ensure_dir_existence(output_dir)
if not os.path.exists(output_dir):
os.makedirs(output_dir)
if index == None:
log.info("Constructing index\n")
index = alignment.index_bwa(bwa_command, log, reference_file, os.path.join(output_dir, "bwa_index"), "bwtsw")
sam_dir = os.path.join(output_dir, "alignments")
log.info("Aligning barcodes\n")
sam_files = AlignToReference(datasets, sam_dir, bwa_command, log, index, threads)
subreference_dir = os.path.join(output_dir, "subreferences")
filtered_dir = os.path.join(output_dir, "filtered")
support.recreate_dir(subreference_dir)
support.recreate_dir(filtered_dir)
log.info("Constructing subreferences")
subreferences_list = [(barcode_id, ConstructSubreferenceFromSam(barcode_sam)) for barcode_id, barcode_sam in sam_files]
log.info("Reading reference")
reference = ReadReference(reference_file)
log.info("Printing output")
PrintAll([(barcode, filtered) for barcode, (filtered, subreference) in subreferences_list], reference, filtered_dir)
PrintAll([(barcode, subreference) for barcode, (filtered, subreference) in subreferences_list], reference, subreference_dir)
log.info("Subreference construction finished. See results in " + output_dir)
def RunBarcodeQuast(barcodes, barcode_quast_dir, reference_dir, threads):
quast_format = " ".join([
"quast", "--min-contig", "1000", "--contig-thresholds",
"5000,8000,12000", "-e", "-R",
os.path.join(reference_dir, "{0}.fasta"), "{1}", "-o",
os.path.join(barcode_quast_dir, "{0}")
])
commands = [(barcode_id, quast_format.format(barcode_id, file_name))
for (barcode_id, file_name) in barcodes]
support.recreate_dir(barcode_quast_dir)
task = parallel_launcher.ExternalCallTask("", "")
errors = parallel_launcher.run_in_parallel(task, commands, threads)
sys.stderr.write(str(errors) + " barcodes failed")