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BUG Fix concatenate_fasta and compression
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luispedro committed Oct 21, 2023
1 parent 1f10823 commit 75bf01a
Showing 1 changed file with 13 additions and 8 deletions.
21 changes: 13 additions & 8 deletions SemiBin/main.py
Original file line number Diff line number Diff line change
Expand Up @@ -263,7 +263,20 @@ def parse_args(args, is_semibin2):
dest='no_write_pre_reclustering_bins',
action='store_true')

p.add_argument('--tag-output',
required=False,
type=str,
dest='output_tag',
default=('SemiBin' if is_semibin2 else None),
help='Tag to add to output file names')

for p in [single_easy_bin,
multi_easy_bin,
generate_cannot_links,
generate_sequence_features_single,
generate_sequence_features_multi,
binning, binning_long,
concatenate_fasta]:
p.add_argument('--compression',
required=False,
type=str,
Expand All @@ -273,14 +286,6 @@ def parse_args(args, is_semibin2):
dest='output_compression',
default=('gz' if is_semibin2 else 'none'))

p.add_argument('--tag-output',
required=False,
type=str,
dest='output_tag',
default=('SemiBin' if is_semibin2 else None),
help='Tag to add to output file names')


for p in [binning, binning_long]:
p.add_argument('--model',
required=False,
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