From 9283fba30ce411e4eccf896cb6f88b1434263248 Mon Sep 17 00:00:00 2001 From: Anthony Date: Mon, 26 Aug 2019 07:57:58 -0700 Subject: [PATCH 1/2] IMP: Add transformer from casava to slpssefdf --- q2_types/per_sample_sequences/_transformer.py | 8 ++++++- .../tests/test_transformer.py | 21 ++++++++++++++++++- 2 files changed, 27 insertions(+), 2 deletions(-) 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..325134c0 100644 --- a/q2_types/per_sample_sequences/tests/test_transformer.py +++ b/q2_types/per_sample_sequences/tests/test_transformer.py @@ -138,7 +138,7 @@ 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_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( CasavaOneEightSingleLanePerSampleDirFmt, @@ -157,6 +157,25 @@ def test_casava_one_eight_single_lane_per_sample_dirfmt_to_slpspefdf(self): for act, exp in zip(obs, input): self.assertEqual(act, exp) + 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( + SingleLanePerSampleSingleEndFastqDirFmt, + CasavaOneEightSingleLanePerSampleDirFmt, filenames=filenames + ) + + input = skbio.io.read( + '%s/Human-Kneecap_S1_L001_R1_001.fastq.gz' % str(input), + format='fastq', constructor=skbio.DNA + ) + obs = skbio.io.read( + '%s/Human-Kneecap_S1_L001_R1_001.fastq.gz' % str(obs), + format='fastq', constructor=skbio.DNA + ) + + for act, exp in zip(obs, input): + self.assertEqual(act, exp) + def test_miseq_demux_dirfmt_to_slpssefdf(self): input, obs = self.transform_format( CasavaOneEightLanelessPerSampleDirFmt, From dbb860f178d816e2e71476df166113ba8c21d713 Mon Sep 17 00:00:00 2001 From: Anthony Date: Mon, 26 Aug 2019 09:06:25 -0700 Subject: [PATCH 2/2] SQUASH: Fix linter error --- .../tests/test_transformer.py | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/q2_types/per_sample_sequences/tests/test_transformer.py b/q2_types/per_sample_sequences/tests/test_transformer.py index 325134c0..e5faaa6c 100644 --- a/q2_types/per_sample_sequences/tests/test_transformer.py +++ b/q2_types/per_sample_sequences/tests/test_transformer.py @@ -138,25 +138,6 @@ 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_slpssefdf(self): - filenames = ('Human-Kneecap_S1_L001_R1_001.fastq.gz',) - input, obs = self.transform_format( - CasavaOneEightSingleLanePerSampleDirFmt, - SingleLanePerSamplePairedEndFastqDirFmt, filenames=filenames - ) - - input = skbio.io.read( - '%s/Human-Kneecap_S1_L001_R1_001.fastq.gz' % str(input), - format='fastq', constructor=skbio.DNA - ) - obs = skbio.io.read( - '%s/Human-Kneecap_S1_L001_R1_001.fastq.gz' % str(obs), - format='fastq', constructor=skbio.DNA - ) - - for act, exp in zip(obs, input): - self.assertEqual(act, exp) - 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(