dest='vcfFileName',
type=str,
default='var.flt.vcf',
metavar='NAME',
help=
'File name of the VCF files which must exist in each of the sample directories'
)
parser.add_argument(
'-o',
'--output',
dest='snpListFile',
type=str,
default='snplist.txt',
metavar='FILE',
help='Output file. Relative or absolute path to the SNP list file')
parser.add_argument('-v',
'--verbose',
dest='verbose',
type=int,
default=1,
metavar='0..5',
help='Verbose message level (0=no info, 5=lots)')
parser.add_argument('--version',
action='version',
version='%(prog)s version ' + __version__)
args_dict = vars(parser.parse_args())
utils.set_logging_verbosity(args_dict)
snppipeline.set_logging_verbosity(args_dict)
snppipeline.create_snp_list(args_dict)
#!/usr/bin/env python
import argparse
from snppipeline import __version__
from snppipeline import snppipeline
from snppipeline import utils
#==============================================================================
# Command line driver
#==============================================================================
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="""Create the SNP pileup file for a sample -- the pileup file
at the positions where SNPs were called in any of the samples.""",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-f', '--force', dest='forceFlag', action='store_true', help='Force processing even when result file already exists and is newer than inputs')
parser.add_argument('-l', '--snpListFile', dest='snpListFile', type=str, default='snplist.txt', metavar='FILE', help='Relative or absolute path to the SNP list file across all samples')
parser.add_argument('-a', '--allPileupFile', dest='allPileupFile', type=str, default='reads.all.pileup', metavar='FILE', help='Relative or absolute path to the genome-wide pileup file for this sample')
parser.add_argument('-o', '--output', dest='snpPileupFile', type=str, default='reads.snp.pileup', metavar='FILE', help='Output file. Relative or absolute path to the sample SNP pileup file')
parser.add_argument('-v', '--verbose', dest='verbose', type=int, default=1, metavar='0..5', help='Verbose message level (0=no info, 5=lots)')
parser.add_argument('--version', action='version', version='%(prog)s version ' + __version__)
args_dict = vars(parser.parse_args())
utils.set_logging_verbosity(args_dict)
snppipeline.set_logging_verbosity(args_dict)
snppipeline.create_snp_pileup(args_dict)