diff --git a/autometa/common/markers.py b/autometa/common/markers.py index 4bc5afbb8..bd994e9ba 100644 --- a/autometa/common/markers.py +++ b/autometa/common/markers.py @@ -251,38 +251,23 @@ def main(): import argparse import logging as logger logger.basicConfig( - format='%(asctime)s : %(name)s : %(levelname)s : %(message)s', + format='[%(asctime)s %(levelname)s] %(name)s: %(message)s', datefmt='%m/%d/%Y %I:%M:%S %p', level=logger.DEBUG) parser = argparse.ArgumentParser( - description='Annotate ORFs with kingdom-marker information') + description='Annotate ORFs with kingdom-marker information', + formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('orfs', - help='Path to a fasta file containing amino acid sequences of open reading frames') - parser.add_argument('kingdom', help='kingdom to search for markers', - choices=['bacteria', 'archaea'], default='bacteria') + help='Path to a fasta file containing amino acid sequences of open reading frames') + parser.add_argument('--kingdom', help='kingdom to search for markers', + choices=['bacteria', 'archaea'], default='bacteria') parser.add_argument('--dbdir', - help=f'Path to directory containing the single-copy marker HMM databases.', - default=MARKERS_DIR) - args = parser.parse_args() - markers = Markers(orfs_fpath=args.orfs, - kingdom=args.kingdom, dbdir=args.dbdir) - - -== == == = - description = 'Annotate ORFs with kingdom-marker information', - formatter_class = argparse.ArgumentDefaultsHelpFormatter) - parser.add_argument('orfs', - help = 'Path to a fasta file containing amino acid sequences of open reading frames') - parser.add_argument('--kingdom', help = 'kingdom to search for markers', - choices = ['bacteria', 'archaea'], default = 'bacteria') - parser.add_argument('--dbdir', - help = 'Path to directory containing the single-copy marker HMM databases.', - default = MARKERS_DIR) + help='Path to directory containing the single-copy marker HMM databases.', + default=MARKERS_DIR) args=parser.parse_args() - markers=Markers(orfs_fpath = args.orfs, - kingdom = args.kingdom, dbdir = args.dbdir) ->> >>>> > 962121fba54cc9c3bff74322b3a6fd734f4c5f12 + markers=Markers(orfs_fpath=args.orfs, kingdom=args.kingdom, dbdir=args.dbdir) + markers.get()