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fix parsing of priorities tsv file to allow spaces in sequence IDs #668

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merged 4 commits into from
Feb 12, 2021
Merged

fix parsing of priorities tsv file to allow spaces in sequence IDs #668

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6043010
fix parsing of priorities tsv file to allow spaces in sequence IDs
tomkinsc Feb 3, 2021
9891eac
in filter.py::read_priority_scores(), only split by tab if a tab is p…
tomkinsc Feb 11, 2021
8ce21a4
split on tabs if tabs are present as more common case
tomkinsc Feb 11, 2021
190ae73
add unit test for parsing tab-delimited priorities file
tomkinsc Feb 12, 2021
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2 changes: 1 addition & 1 deletion augur/filter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ def read_priority_scores(fname):
with open(fname, encoding='utf-8') as pfile:
return defaultdict(float, {
elems[0]: float(elems[1])
for elems in (line.strip().split() for line in pfile.readlines())
for elems in (line.strip().split('\t') if '\t' in line else line.strip().split() for line in pfile.readlines())
})
except Exception as e:
print(f"ERROR: missing or malformed priority scores file {fname}", file=sys.stderr)
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