BUG: Laneless casava transformer now writes the correct path (#236)

qiime2 · Jan 29, 2020 · abcfda0 · abcfda0
1 parent adf2699
commit abcfda0
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Showing 3 changed files with 28 additions and 2 deletions.
diff --git a/q2_types/per_sample_sequences/_transformer.py b/q2_types/per_sample_sequences/_transformer.py
@@ -54,7 +54,14 @@ def _single_lane_per_sample_fastq_helper(dirfmt, output_cls, parse_lane=True):
                                     barcode_id=barcode_id,
                                     lane_number=lane_number,
                                     read_number=read_number)
-        manifest_fh.write('%s,%s,%s\n' % (sample_id, path, direction))
+
+        filepath = result.sequences.path_maker(sample_id=sample_id,
+                                               barcode_id=barcode_id,
+                                               lane_number=lane_number,
+                                               read_number=read_number)
+        name = filepath.name
+
+        manifest_fh.write('%s,%s,%s\n' % (sample_id, name, direction))
 
     manifest_fh.close()
     result.manifest.write_data(manifest, FastqManifestFormat)

diff --git a/q2_types/per_sample_sequences/tests/data/Human-Armpit_S2_R1_001.fastq.gz b/q2_types/per_sample_sequences/tests/data/Human-Armpit_S2_R1_001.fastq.gz
diff --git a/q2_types/per_sample_sequences/tests/test_transformer.py b/q2_types/per_sample_sequences/tests/test_transformer.py
@@ -30,7 +30,8 @@
     SingleEndFastqManifestPhred64V2,
     PairedEndFastqManifestPhred33V2,
     PairedEndFastqManifestPhred64V2,
-    QIIME1DemuxDirFmt)
+    QIIME1DemuxDirFmt,
+    FastqGzFormat)
 from q2_types.per_sample_sequences._transformer import (
     _validate_header,
     _validate_single_end_fastq_manifest_directions,
@@ -119,6 +120,24 @@ def test_slpssefdf_to_qiime1demuxdf_bad_sample_ids(self):
                 SingleLanePerSampleSingleEndFastqDirFmt,
                 QIIME1DemuxDirFmt, filenames=filenames)
 
+    def test_casava_one_eight_laneless_per_sample_dirfmt_to_slpspefd(self):
+        filenames = ('Human-Kneecap_S1_R1_001.fastq.gz',
+                     'Human-Armpit_S2_R1_001.fastq.gz')
+
+        input, dirfmt = self.transform_format(
+            CasavaOneEightLanelessPerSampleDirFmt,
+            SingleLanePerSamplePairedEndFastqDirFmt, filenames=filenames
+        )
+        expected_filepaths = ['Human-Kneecap_S1_L001_R1_001.fastq.gz',
+                              'Human-Armpit_S2_L001_R1_001.fastq.gz']
+
+        for path, view in dirfmt.sequences.iter_views(FastqGzFormat):
+            self.assertIn(path.name, expected_filepaths)
+
+        df = dirfmt.manifest.view(pd.DataFrame)
+        for name in df['forward']:
+            self.assertTrue((dirfmt.path / name).exists())
+
     def test_casava_one_eight_single_lane_per_sample_dirfmt_to_slpssefdf(self):
         filenames = ('Human-Kneecap_S1_L001_R1_001.fastq.gz',)
         input, obs = self.transform_format(