Merge 734f01c into 6dd5ec3

qiime2 · Sep 10, 2019 · 2ff976f · 2ff976f
2 parents 6dd5ec3 + 734f01c
commit 2ff976f
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Showing 2 changed files with 16 additions and 6 deletions.
diff --git a/q2_types/per_sample_sequences/_transformer.py b/q2_types/per_sample_sequences/_transformer.py
@@ -94,6 +94,15 @@ def _11(dirfmt: CasavaOneEightLanelessPerSampleDirFmt) \
         dirfmt, SingleLanePerSamplePairedEndFastqDirFmt, parse_lane=False)
 
 
+@plugin.register_transformer
+def _12(dirfmt: SingleLanePerSampleSingleEndFastqDirFmt) \
+        -> CasavaOneEightSingleLanePerSampleDirFmt:
+    casava = CasavaOneEightSingleLanePerSampleDirFmt(mode='w')
+    for fastq in dirfmt.path.glob('*.fastq.gz'):
+        shutil.copy(os.path.join(str(dirfmt), fastq), str(casava))
+    return casava
+
+
 @plugin.register_transformer
 def _5(dirfmt: SingleLanePerSamplePairedEndFastqDirFmt) \
         -> SingleLanePerSampleSingleEndFastqDirFmt:
@@ -351,7 +360,7 @@ def _9(fmt: PairedEndFastqManifestPhred64) \
 
 
 @plugin.register_transformer
-def _12(dirfmt: SingleLanePerSampleSingleEndFastqDirFmt) \
+def _27(dirfmt: SingleLanePerSampleSingleEndFastqDirFmt) \
         -> QIIME1DemuxDirFmt:
     with dirfmt.manifest.view(FastqManifestFormat).open() as fh:
         input_manifest = _parse_and_validate_manifest(fh, single_end=True,

diff --git a/q2_types/per_sample_sequences/tests/test_transformer.py b/q2_types/per_sample_sequences/tests/test_transformer.py
@@ -138,12 +138,13 @@ def test_casava_one_eight_single_lane_per_sample_dirfmt_to_slpssefdf(self):
         for act, exp in zip(obs, input):
             self.assertEqual(act, exp)
 
-    def test_casava_one_eight_single_lane_per_sample_dirfmt_to_slpspefdf(self):
-        filenames = ('Human-Kneecap_S1_L001_R1_001.fastq.gz',)
+    def test_slpssefdf_to_casava_one_eight_single_lane_per_sample_dirfmt(self):
+        filenames = ('single-end-two-sample-data2/MANIFEST',
+                     'metadata.yml',
+                     'Human-Kneecap_S1_L001_R1_001.fastq.gz')
         input, obs = self.transform_format(
-            CasavaOneEightSingleLanePerSampleDirFmt,
-            SingleLanePerSamplePairedEndFastqDirFmt, filenames=filenames
-        )
+            SingleLanePerSampleSingleEndFastqDirFmt,
+            CasavaOneEightSingleLanePerSampleDirFmt, filenames=filenames)
 
         input = skbio.io.read(
             '%s/Human-Kneecap_S1_L001_R1_001.fastq.gz' % str(input),