diff --git a/q2_types/per_sample_sequences/_transformer.py b/q2_types/per_sample_sequences/_transformer.py index 6e657c67..066ad64f 100644 --- a/q2_types/per_sample_sequences/_transformer.py +++ b/q2_types/per_sample_sequences/_transformer.py @@ -94,6 +94,12 @@ def _11(dirfmt: CasavaOneEightLanelessPerSampleDirFmt) \ dirfmt, SingleLanePerSamplePairedEndFastqDirFmt, parse_lane=False) +@plugin.register_transformer +def _12(dirfmt: SingleLanePerSampleSingleEndFastqDirFmt) \ + -> CasavaOneEightSingleLanePerSampleDirFmt: + return CasavaOneEightSingleLanePerSampleDirFmt(str(dirfmt), mode='r') + + @plugin.register_transformer def _5(dirfmt: SingleLanePerSamplePairedEndFastqDirFmt) \ -> SingleLanePerSampleSingleEndFastqDirFmt: @@ -351,7 +357,7 @@ 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 index 3bc8fbec..e5faaa6c 100644 --- a/q2_types/per_sample_sequences/tests/test_transformer.py +++ b/q2_types/per_sample_sequences/tests/test_transformer.py @@ -138,11 +138,11 @@ 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): + def test_slpssefdf_to_casava_one_eight_single_lane_per_sample_dirfmt(self): filenames = ('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(