diff --git a/rescript/get_gtdb.py b/rescript/get_gtdb.py index 61cac2a..6b7afd9 100644 --- a/rescript/get_gtdb.py +++ b/rescript/get_gtdb.py @@ -84,7 +84,7 @@ def _assemble_queries(version='214.1', def parse_gtdb_taxonomy(tax_str): - tax = tax_str.split()[0] + tax = ' '.join(tax_str.split()[0:2]) return tax diff --git a/rescript/tests/test_get_gtdb.py b/rescript/tests/test_get_gtdb.py index 38602db..ce619a7 100644 --- a/rescript/tests/test_get_gtdb.py +++ b/rescript/tests/test_get_gtdb.py @@ -9,7 +9,7 @@ import pkg_resources from qiime2.plugin.testing import TestPluginBase from qiime2.plugins import rescript -from rescript.get_gtdb import _assemble_queries +from rescript.get_gtdb import _assemble_queries, parse_gtdb_taxonomy from q2_types.feature_data import (TSVTaxonomyFormat, DNAFASTAFormat) from urllib.request import urlopen @@ -153,3 +153,12 @@ def _makey_fakey_bact(faking_ignore_this): version='214.1', db_type='All') self.assertEqual(str(resc[0].type), 'FeatureData[Taxonomy]') self.assertEqual(str(resc[1].type), 'FeatureData[Sequence]') + + def test_parse_gtdb_taxonomy(self): + tax_in = ('d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;' + 'f__Lactobacillaceae;g__Oenococcus;s__Oenococcus oeni ' + '[locus_tag=NZ_AQVA01000009.1] [location=77871..79431] ' + '[ssu_len=1561] [contig_len=79790]') + exp = ('d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;' + 'f__Lactobacillaceae;g__Oenococcus;s__Oenococcus oeni') + self.assertEqual(parse_gtdb_taxonomy(tax_in), exp)