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Fix select taxa chimera bug #83

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Jun 20, 2023
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7 changes: 4 additions & 3 deletions phylofisher/select_taxa.py
Original file line number Diff line number Diff line change
@@ -36,7 +36,8 @@ def make_subset_tsv():
for line in infile:
line = line.strip()
split_line = line.split('\t')
taxa[split_line[0]] = split_line[1:3]
taxa[split_line[0]] = split_line[1:4]


# Add Taxonomic Groups to DataFrame
low_tax_list = [taxa[ind][2] for ind in df.index]
@@ -102,7 +103,7 @@ def gen_chimera(df):
for line in infile:
line = line.strip()
split_line = line.split('\t')
chim_dict[split_line[0]] = split_line[3:]
chim_dict[split_line[0]] = split_line[4:]

for key in chim_dict.keys():
df['int_chim'] = 0
@@ -154,7 +155,7 @@ def update_dataframe(df):
"""))
optional.add_argument('--chimeras', type=str, metavar='chimeras.tsv', default=None,
help=textwrap.dedent("""\
A .tsv containing a Unique ID, higher and lower taxonomic designations,
A .tsv containing a Unique ID, higher and lower taxonomic designations, long name,
and the Unique IDs of the taxa to collapse, for each chimera one per line
"""))

2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
@@ -2,7 +2,7 @@

setup(
name='phylofisher',
version='1.2.7',
version='1.2.9',
packages=find_packages(),
scripts={'phylofisher/fisher.py',
'phylofisher/config.py',