BUG: faith PD vector retains #SampleID index name (#67)

Author: lizgehret

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', header=0)
+    df.set_index(df.columns[0], inplace=True)
+    df.index.name = None
+    df.to_csv(str(vec), sep='\t', header=True)
+
     return vec
 
 

q2_diversity_lib/tests/test_alpha.py

@@ -13,6 +13,7 @@
 import pandas as pd
 import pandas.testing as pdt
 import biom
+import os
 
 from qiime2.plugin.testing import TestPluginBase
 from qiime2 import Artifact
@@ -93,6 +94,14 @@ def test_passed_rootonlytree(self):
             obs = self.fn(table=self.tbl, phylogeny=tree)
             self.assertTrue('not a subset of the tree tips' in obs.stderr)
 
+    def test_no_index_name(self):
+        res, = self.fn(table=self.tbl, phylogeny=self.tre)
+        res_dirfmt = res.view(res.format)
+        faithpd_fp = os.path.join(str(res_dirfmt), 'alpha-diversity.tsv')
+        with open(faithpd_fp, 'r') as fh:
+            data = fh.read()
+            self.assertNotIn('#SampleID', data)
+
 
 class ObservedFeaturesTests(TestPluginBase):
     package = 'q2_diversity_lib.tests'