From 11ea8d6b0b51574d0c4a17f82aba13ee0ae963c5 Mon Sep 17 00:00:00 2001 From: Robert Jones Date: Tue, 20 Jun 2023 14:12:51 -0400 Subject: [PATCH 1/2] fixes chimera bug --- phylofisher/select_taxa.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/phylofisher/select_taxa.py b/phylofisher/select_taxa.py index ddee9a2..696a1bc 100644 --- a/phylofisher/select_taxa.py +++ b/phylofisher/select_taxa.py @@ -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 """)) From 3e1fae63228fbb5708b4467ab8534c1aaa427cfe Mon Sep 17 00:00:00 2001 From: Robert Jones Date: Tue, 20 Jun 2023 14:18:22 -0400 Subject: [PATCH 2/2] bumps version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 5ee1b43..6439855 100644 --- a/setup.py +++ b/setup.py @@ -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',