def main():
#initialize the logging
utils_logging.init_logging(logging.INFO)
#Setup options
optparser=_prepare_optparser()
(options,args) = optparser.parse_args()
#verify options
arg_pass=_verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if options.debug:
utils_logging.init_logging(logging.DEBUG)
utils_logging.init_logging(output_level=None,
log_file_name=os.path.join(options.output_dir,"extract_and_assemble.log"))
bam_files=[options.bam_files]
if len(args)>0:
bam_files.extend(args)
all_assembler_to_try = options.assembler_name.split(',')
assembly_function_list=[]
for assembler_name in all_assembler_to_try:
assembly_function=RAD_assemble_read2.get_assembly_function(assembler_name)
assembly_function_list.append(assembly_function)
command_runner.set_command_to_run_localy()
if options.rg_ids:
rg_ids=options.rg_ids.split()
else:
rg_ids=[]
extract_and_assemble(bam_files, options.read1_consensus_file, options.white_list_file, options.output_dir,
assembly_function_list, subsample_nb_read=options.subsample_nb_read, rg_ids=rg_ids,
adapter_file=options.adapter_file)
def main():
# initialize the logging
utils_logging.init_logging(logging.INFO)
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if options.debug:
utils_logging.init_logging(logging.DEBUG)
bam_files = [options.bam_file]
if len(args) > 0:
bam_files.extend(args)
command_runner.set_command_to_run_localy()
if options.output_dir:
list_consensus = read_white_list(options.white_list_file)
extract_reads_from_all_bam_files_set_of_consensus(bam_files, list_consensus, options.output_dir,
genome_loader=None,
all_read1_consensus_file=options.read1_consensus_file)
else:
iter_dir_and_file = split_whitelist(white_list_file=options.white_list_file,
nb_consensus_per_dir=options.nb_consensus_per_dir)
for output_dir, sub_whitelist in iter_dir_and_file:
command = 'python %s -g %s -w %s -o %s -b %s' % (
sys.argv[0], options.read1_consensus_file, sub_whitelist, output_dir, ' '.join(bam_files))
print command
def main():
#initialize the logging
utils_logging.init_logging()
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
utils_logging.change_log_stdout_to_log_stderr()
if options.print_commands:
utils_logging.change_log_stdout_to_log_stderr()
else:
command_runner.set_command_to_run_localy()
run_fine = run_BWA_Command(options.genome_file,
options.fastq_file1,
options.fastq_file2,
options.output_dir,
options.name,
analysis_type=options.analysis,
sort=options.sort,
thread=options.thread,
read_group=options.read_group,
illumina=options.illumina)
if run_fine:
logging.info('Run completed')
else:
logging.error('Run Failed')
sys.exit(1)
def main():
# initialize the logging
utils_logging.init_logging(logging.INFO)
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if options.debug:
utils_logging.init_logging(logging.DEBUG)
bam_files = [options.bam_file]
if len(args) > 0:
bam_files.extend(args)
command_runner.set_command_to_run_localy()
if options.output_dir:
list_consensus = read_white_list(options.white_list_file)
extract_reads_from_all_bam_files_set_of_consensus(
bam_files,
list_consensus,
options.output_dir,
genome_loader=None,
all_read1_consensus_file=options.read1_consensus_file)
else:
iter_dir_and_file = split_whitelist(
white_list_file=options.white_list_file,
nb_consensus_per_dir=options.nb_consensus_per_dir)
for output_dir, sub_whitelist in iter_dir_and_file:
command = 'python %s -g %s -w %s -o %s -b %s' % (
sys.argv[0], options.read1_consensus_file, sub_whitelist,
output_dir, ' '.join(bam_files))
print command
def main():
#initialize the logging
utils_logging.init_logging()
#Setup options
optparser=_prepare_optparser()
(options,args) = optparser.parse_args()
#verify options
arg_pass=_verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
utils_logging.change_log_stdout_to_log_stderr()
if options.print_commands:
utils_logging.change_log_stdout_to_log_stderr()
else:
command_runner.set_command_to_run_localy()
run_fine=run_BWA_Command(options.genome_file, options.fastq_file1, options.fastq_file2,
options.output_dir, options.name,analysis_type=options.analysis,
sort=options.sort, thread=options.thread, read_group=options.read_group,
illumina=options.illumina)
if run_fine:
logging.info('Run completed')
else:
logging.error('Run Failed')
sys.exit(1)
def main():
#initialize the logging
utils_logging.init_logging(logging.INFO)
#utils_logging.init_logging(logging.CRITICAL)
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if options.debug:
utils_logging.init_logging(logging.DEBUG)
if not options.print_command:
command_runner.set_command_to_run_localy()
start_time = time.time()
#comment = '%s: contig_align:%s, mismatches:%s site with 1 contig:%s site with more than 1 contig:%s'
all_assembler_to_try = options.assembler_name.split(',')
assembly_function_list = []
for assembler_name in all_assembler_to_try:
assembly_function = get_assembly_function(assembler_name)
assembly_function_list.append(assembly_function)
if options.rg_ids:
rg_ids = options.rg_ids.split()
else:
rg_ids = []
if options.fastq_dir:
run_all_fastq_files(options.fastq_dir,
assembly_function_list,
options.estimated_size,
options.subsample_nb_read,
rg_ids,
options.force_merge,
adapter_file=options.adapter_file)
elif options.fastq_file:
output_dir = os.path.dirname(options.fastq_file)
name = os.path.basename(options.fastq_file)[:-len("_2.fastq")]
read1_fasta = os.path.join(output_dir, name + "_1.fa")
contig_file = run_one_fastq_file(
options.fastq_file,
output_dir,
assembly_function_list,
estimated_size=options.estimated_size,
subsample_nb_read=options.subsample_nb_read,
read1_fasta=read1_fasta,
name=name,
force_merge=options.force_merge,
adapter_file=options.adapter_file)
logging.info("Elapsed time:%.1f seconds" % (time.time() - start_time))
def main():
#initialize the logging
utils_logging.init_logging()
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
command_runner.set_command_to_run_localy()
mark_duplicate(options.input_bam)
def main():
#initialize the logging
utils_logging.init_logging()
#Setup options
optparser=_prepare_optparser()
(options,args) = optparser.parse_args()
#verify options
arg_pass=_verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
command_runner.set_command_to_run_localy()
mark_duplicate(options.input_bam)
def main():
# initialize the logging
utils_logging.init_logging()
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
command_runner.set_command_to_run_localy()
shift_reads(options.bam_file, options.fasta_file, options.output_file)
def main():
# initialize the logging
utils_logging.init_logging(logging.INFO)
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
command_runner.set_command_to_run_localy()
if options.debug:
utils_logging.init_logging(logging.DEBUG)
run_all_snps_call(options.consensus_dir)
def main():
# initialize the logging
utils_logging.init_logging(logging.INFO)
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
command_runner.set_command_to_run_localy()
if options.debug:
utils_logging.init_logging(logging.DEBUG)
run_all_snps_call(options.consensus_dir)
def main():
#initialize the logging
utils_logging.init_logging(logging.INFO)
#Setup options
optparser=_prepare_optparser()
(options,args) = optparser.parse_args()
#verify options
arg_pass=_verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if not options.print_command:
command_runner.set_command_to_run_localy()
assess_read2_contigs(options.contig_file, options.genome_file,options.sites_file, options.output_sites)
def main():
#initialize the logging
utils_logging.init_logging(logging.INFO)
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if not options.print_command:
command_runner.set_command_to_run_localy()
assess_read2_contigs(options.contig_file, options.genome_file,
options.sites_file, options.output_sites)
def main():
#initialize the logging
utils_logging.init_logging(logging.INFO)
#utils_logging.init_logging(logging.CRITICAL)
#Setup options
optparser=_prepare_optparser()
(options,args) = optparser.parse_args()
#verify options
arg_pass=_verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if options.debug:
utils_logging.init_logging(logging.DEBUG)
if not options.print_command:
command_runner.set_command_to_run_localy()
start_time = time.time()
#comment = '%s: contig_align:%s, mismatches:%s site with 1 contig:%s site with more than 1 contig:%s'
all_assembler_to_try = options.assembler_name.split(',')
assembly_function_list=[]
for assembler_name in all_assembler_to_try:
assembly_function=get_assembly_function(assembler_name)
assembly_function_list.append(assembly_function)
if options.rg_ids:
rg_ids=options.rg_ids.split()
else:
rg_ids=[]
if options.fastq_dir:
run_all_fastq_files(options.fastq_dir, assembly_function_list, options.estimated_size,
options.subsample_nb_read, rg_ids,
options.force_merge, adapter_file=options.adapter_file)
elif options.fastq_file:
output_dir = os.path.dirname(options.fastq_file)
name = os.path.basename(options.fastq_file)[:-len("_2.fastq")]
read1_fasta = os.path.join(output_dir, name + "_1.fa")
contig_file = run_one_fastq_file(options.fastq_file, output_dir, assembly_function_list,
estimated_size=options.estimated_size,
subsample_nb_read=options.subsample_nb_read,
read1_fasta=read1_fasta, name=name, force_merge=options.force_merge,
adapter_file=options.adapter_file)
logging.info("Elapsed time:%.1f seconds"%(time.time()-start_time))
def main():
# initialize the logging
utils_logging.init_logging(logging.INFO)
#utils_logging.init_logging(logging.CRITICAL)
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if options.debug:
utils_logging.init_logging(logging.DEBUG)
if not options.print_command:
command_runner.set_command_to_run_localy()
start_time = time.time()
run_all_fastq_files(options.consensus_dir, readgroup_file=options.readgroup_file, snp_call=options.snp_call)
logging.info("Elapsed time:%.1f seconds" % (time.time() - start_time))
def main():
#initialize the logging
utils_logging.init_logging(logging.INFO)
#Setup options
optparser=_prepare_optparser()
(options,args) = optparser.parse_args()
#verify options
arg_pass=_verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if not options.print_commands:
command_runner.set_command_to_run_localy()
if options.debug:
utils_logging.init_logging(logging.DEBUG)
if options.final_merge:
code = merge_all_results(options.consensus_dir)
else:
code = merge_results(options.consensus_dir)
sys.exit(code)
def main():
#initialize the logging
utils_logging.init_logging(logging.INFO)
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if not options.print_commands:
command_runner.set_command_to_run_localy()
if options.debug:
utils_logging.init_logging(logging.DEBUG)
bam_files = [options.bam_files]
if len(args) > 0:
bam_files.extend(args)
code = merge_bam_files(bam_files, options.output_file, options.genome_file,
options.read_group_file, options.per_sample)
sys.exit(code)
def main():
#initialize the logging
utils_logging.init_logging(logging.INFO)
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if not options.print_commands:
command_runner.set_command_to_run_localy()
if options.debug:
utils_logging.init_logging(logging.DEBUG)
bam_files = [options.bam_files]
if len(args) > 0:
bam_files.extend(args)
code = merge_bam_files(bam_files, options.output_file, options.genome_file, options.read_group_file,
options.per_sample)
sys.exit(code)
def main():
# initialize the logging
utils_logging.init_logging(logging.INFO)
#utils_logging.init_logging(logging.CRITICAL)
#Setup options
optparser = _prepare_optparser()
(options, args) = optparser.parse_args()
#verify options
arg_pass = _verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if options.debug:
utils_logging.init_logging(logging.DEBUG)
if not options.print_command:
command_runner.set_command_to_run_localy()
start_time = time.time()
run_all_fastq_files(options.consensus_dir,
readgroup_file=options.readgroup_file,
snp_call=options.snp_call)
logging.info("Elapsed time:%.1f seconds" % (time.time() - start_time))
logging.info("Merging Failed try extending consensus")
if os.path.exists(merged_fa):
os.remove(merged_fa)
os.remove(alignment_report)
extended_sequence_file = os.path.join(parent_dir, consensus_name + "_1_extended.fa")
if not os.path.exists(extended_sequence_file):
extended_sequence_file = extend_read1_consensus(fastq_1, fastq_2, ">%s_extended"%consensus_name,
extended_sequence_file)
if extended_sequence_file:
return merge_2_contigs(consensus_name, extended_sequence_file, contig_file2, output_dir,
allow_extension=False)
else:
logging.info("Merging Failed")
results = None
if os.path.exists(merged_fa):
os.remove(merged_fa)
os.remove(alignment_report)
return results
if __name__ == "1__main__":
alignment_report = sys.argv[1]
parse_alignment_report(alignment_report)
if __name__ == "1__main__":
utils_logging.init_logging()
command_runner.set_command_to_run_localy()
fasta_file = sys.argv[1]
read_consensus(fasta_file)
parent_dir, consensus_name + "_1_extended.fa")
if not os.path.exists(extended_sequence_file):
extended_sequence_file = extend_read1_consensus(
fastq_1, fastq_2, ">%s_extended" % consensus_name,
extended_sequence_file)
if extended_sequence_file:
return merge_2_contigs(consensus_name,
extended_sequence_file,
contig_file2,
output_dir,
allow_extension=False)
else:
logging.info("Merging Failed")
results = None
if os.path.exists(merged_fa):
os.remove(merged_fa)
os.remove(alignment_report)
return results
if __name__ == "1__main__":
alignment_report = sys.argv[1]
parse_alignment_report(alignment_report)
if __name__ == "1__main__":
utils_logging.init_logging()
command_runner.set_command_to_run_localy()
fasta_file = sys.argv[1]
read_consensus(fasta_file)
