def main(argv=sys.argv):
description = """Dump .fasta from .bam (identified from .xml dataset).
"""
epilog = """
If you have only '.bam', you will first need to run 'dataset create --type ReferenceSet --generateIndices outdataset inbam*'
to generate the dataset.
"""
parser = argparse.ArgumentParser(
description=description,
epilog=epilog,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
#parser.add_argument('--logging',
# help='.ini or .json config file for Python logging module')
parser.add_argument('in_file',
help='Input dataset XML filename. (Must have .bam resource.)')
parser.add_argument('out_file',
help='Output fasta filename.')
args = parser.parse_args(argv[1:])
#logging.basicConfig()
#log.warning('RUNNING filterbam: {}'.format(repr(args)))
run_bam_to_fasta(args.in_file, args.out_file)
def main(argv=sys.argv):
description = """Dump .fasta from .bam (identified from .xml dataset).
"""
epilog = """
If you have only '.bam', you will first need to run 'dataset create --type ReferenceSet --generateIndices outdataset inbam*'
to generate the dataset.
"""
parser = argparse.ArgumentParser(
description=description,
epilog=epilog,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
#parser.add_argument('--logging',
# help='.ini or .json config file for Python logging module')
parser.add_argument(
'in_file',
help='Input dataset XML filename. (Must have .bam resource.)')
parser.add_argument('out_file', help='Output fasta filename.')
args = parser.parse_args(argv[1:])
#logging.basicConfig()
#log.warning('RUNNING filterbam: {}'.format(repr(args)))
run_bam_to_fasta(args.in_file, args.out_file)
def run_rtc(rtc):
return run_bam_to_fasta(rtc.task.input_files[0],
rtc.task.output_files[0],
tmp_dir=rtc.task.tmpdir_resources[0].path)
def run_args(args):
return run_bam_to_fasta(args.subreads, args.fasta_out)
def run_rtc(rtc):
return run_bam_to_fasta(rtc.task.input_files[0], rtc.task.output_files[0],
tmp_dir=rtc.task.tmpdir_resources[0].path)
def run_args(args):
return run_bam_to_fasta(args.subreads, args.fasta_out)
