BUG: faith PD vector retains #SampleID index name

qiime2 · Jul 2, 2024 · 2695b22 · 2695b22
1 parent 6bc66e3
commit 2695b22
Showing 1 changed file with 9 additions and 0 deletions.
diff --git a/q2_diversity_lib/alpha.py b/q2_diversity_lib/alpha.py
@@ -61,6 +61,15 @@ def faith_pd(table: BIOMV210Format, phylogeny: NewickFormat,
     vec = AlphaDiversityFormat()
     cmd = ['faithpd', '-i', str(table), '-t', str(phylogeny), '-o', str(vec)]
     _omp_cmd_wrapper(threads, cmd)
+
+    # this is needed to prevent #SampleID from being retained as the
+    # index name in the faith PD vector
+    # (consistent with the other diversity outputs)
+    df = pd.read_csv(str(vec), sep='\t')
+    df.set_index('#SampleID', inplace=True)
+    df.index.name = None
+    df.to_csv(str(vec), sep='\t', header=True)
+
     return vec