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[MRG] add query name to CSV output of sbt categorize #421

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merged 3 commits into from
Mar 9, 2018
Merged

[MRG] add query name to CSV output of sbt categorize #421

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ab26d95
add query name to CSV output of sbt categorize
ctb Feb 24, 2018
a69e1c1
Merge branch 'master' into add/names_to_categorize
ctb Mar 9, 2018
64e6116
Merge branch 'master' into add/names_to_categorize
standage Mar 9, 2018
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3 changes: 2 additions & 1 deletion sourmash_lib/commands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -872,7 +872,8 @@ def categorize(args):

if args.csv:
w = csv.writer(args.csv)
w.writerow([queryfile, best_hit_query_name, best_hit_sim])
w.writerow([queryfile, query.name(), best_hit_query_name,
best_hit_sim])

if loader.skipped_ignore:
notify('skipped/ignore: {}', loader.skipped_ignore)
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2 changes: 1 addition & 1 deletion tests/test_sourmash.py
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Expand Up @@ -2873,7 +2873,7 @@ def test_sbt_categorize():
assert 'for s10+s11, found: 0.50 genome-s10.fa.gz' in err

out_csv = open(os.path.join(location, 'out.csv')).read()
assert './4.sig,genome-s10.fa.gz,0.50' in out_csv
assert './4.sig,s10+s11,genome-s10.fa.gz,0.50' in out_csv


def test_sbt_categorize_already_done():
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