Python set_logging_verbosity Examples

Example #1

File: create_snp_list.py Project: austinmarkell/snp-pipeline

        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)

Example #2

File: create_snp_pileup.py Project: lozybean/snp-pipeline

#!/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)