1.7.4

CHANGELOG.md

@@ -4,6 +4,9 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project (attempts to) adhere to [Semantic Versioning](http://semver.org/).
 
+## [1.7.4] - 2023-05-16
+- Fix a division by 0 when you don't have any annos detected in a sample
+
 ## [1.7.3] - 2023-05-11
 - Fix but in 1.7.2 that resulted in all 0s with parse_gene_annotations
 

inStrain/_version.py

@@ -1 +1 @@
-__version__ = "1.7.3"
+__version__ = "1.7.4"

inStrain/parse_annotations.py

@@ -422,7 +422,10 @@ def create_annotation_tables2(sdb, s2a2g2vals, **kwargs):
 
         db = metric2table[metric].copy()
         for d in TOTAL_KOS:
-            db[d] = [x / s2norm[s] for x, s in zip(db[d], db['sample'])]
+            if s2norm[s] == 0:
+                db[d] = 0
+            else:
+                db[d] = [x / s2norm[s] for x, s in zip(db[d], db['sample'])]
 
         metric2table[metric + '_fraction'] = db
 

test/tests/test_parse_gene_annotations.py

@@ -1,5 +1,7 @@
+import os
 import glob
 import pandas as pd
+import shutil
 
 from test_utils import BTO
 import test_utils
@@ -121,3 +123,21 @@ def test_PA_4(BTO):
         ori_table = pd.read_csv(outloc + name)
         assert test_utils.compare_dfs2(ori_table, table)
 
+def test_PA_5(BTO):
+    """
+    Test the case where one sample doesn't have any annotations detected
+    """
+    # Heavily edit one of the files
+    new_IS2 = BTO.test_dir + os.path.basename(BTO.IS2)
+    shutil.copytree(BTO.IS2, new_IS2)
+    gloc = os.path.join(new_IS2, 'output/N5_271_010G1_scaffold_min1000.fa-vs-N5_271_010G2.forRC.IS_gene_info.tsv')
+    gdb = pd.read_csv(gloc, sep='\t')
+    gdb = gdb.head(1)
+    gdb.to_csv(gloc, sep='\t', index=False)
+
+    # Run program
+    base = BTO.test_dir + 'testA'
+
+    cmd = f"inStrain parse_annotations -i {BTO.IS1} {new_IS2} -o {base} -a {BTO.anno_loc}"
+    print(cmd)
+    inStrain.parse_annotations.PAController(inStrain.argumentParser.parse_args(cmd.split(' ')[1:])).main()