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Remove merge conflict resolution lines (Fixes #68) #69

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May 6, 2020
Merged

Remove merge conflict resolution lines (Fixes #68) #69

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35 changes: 10 additions & 25 deletions autometa/common/markers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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()


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