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Printing correct default values.
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pdec committed Sep 24, 2020
1 parent 7595ff1 commit e184944
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4 changes: 2 additions & 2 deletions PhiSpyModules/helper_functions.py
Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@ def get_args():
' to be called. [Default: %(default)d]')
parser.add_argument('-u', '--min_contig_size', default=5000, type=int,
help='Minimum contig size (in bp) to be included in the analysis. Smaller contigs will ' +
'be dropped. [Default: 30]')
'be dropped. [Default: %(default)d]')
parser.add_argument('-w', '--window_size', default=30, type=int,
help='Window size of consecutive genes to look through to find phages. [Default: %(default)d]')
parser.add_argument('-g', '--nonprophage_genegaps', default=10, type=int,
Expand All @@ -109,7 +109,7 @@ def get_args():
parser.add_argument('--expand_slope', action='store_true', default=False,
help='Use the product of the slope of the Shannon scores in making test sets')
parser.add_argument('--kmers_type', default='all', choices=['all', 'codon', 'simple'], type=str,
help='Type of kmers used for calculating Shannon scores. [Default: all]')
help='Type of kmers used for calculating Shannon scores. [Default: %(default)s]')
parser.add_argument('--phmms', type=str,
help='Phage HMM profile database (like pVOGs) will be mapped against the genome of ' +
'interest and used as additional feature to identify prophages.\nNote that this ' +
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2 changes: 1 addition & 1 deletion VERSION
Original file line number Diff line number Diff line change
@@ -1 +1 @@
4.2.5
4.2.6

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