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Switch to a path identifier for yml files to define variants. #6

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Switch to a path identifier for yml files to define variants. #6

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4346410
Update aln2type.py
mattloose Mar 12, 2021
f9188a6
Update cli.py
mattloose Mar 12, 2021
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3 changes: 2 additions & 1 deletion aln2type/aln2type.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
from collections import OrderedDict
import json
import gzip
import glob


def iupac_to_base(base):
Expand Down Expand Up @@ -513,7 +514,7 @@ def go(args):
sys.exit(1)

variant_types = []
for scheme in args.typing_yaml:
for scheme in glob.glob(args.typing_yaml + "**/*.yml", recursive=True):
variant_types.append(read_scheme_yaml(scheme))

typing_summary = []
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2 changes: 1 addition & 1 deletion aln2type/cli.py
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Expand Up @@ -10,7 +10,7 @@ def parse_args():
parser.add_argument("summary_csv_outfile", help="Output summary CSV file")
parser.add_argument("ref_name", help="Name of reference sequence in MSA")
parser.add_argument("msa", help="Path to MSA")
parser.add_argument("typing_yaml", nargs='+', help="Path to Variant definition YAML files")
parser.add_argument("typing_yaml", help="Path to Variant definition YAML files")
args = parser.parse_args()

return args
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