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)