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IMP: Add transformer from slpssefdf to Casava #226

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IMP: Add transformer from slpssefdf to Casava #226

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9283fba
IMP: Add transformer from casava to slpssefdf
Oddant1 Aug 26, 2019
dbb860f
SQUASH: Fix linter error
Oddant1 Aug 26, 2019
3f357bc
SQUASH: Make the test actually work
Oddant1 Sep 2, 2019
cd73fa3
SQUASH: Clean up transformer
Oddant1 Sep 9, 2019
37378aa
SQUASH: Addressing @thermokarst's review
Oddant1 Sep 9, 2019
30d45a1
SQUASH: Addressing @thermokarst's review
Oddant1 Sep 10, 2019
734f01c
SQUASH: Clean up linting
Oddant1 Sep 10, 2019
f019e10
SQUASH: Change transformer numbers
Oddant1 Sep 11, 2019
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14 changes: 13 additions & 1 deletion q2_types/per_sample_sequences/_transformer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
import gzip
import shutil
import warnings
import tempfile
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import collections

import skbio
Expand Down Expand Up @@ -94,6 +95,17 @@ def _11(dirfmt: CasavaOneEightLanelessPerSampleDirFmt) \
dirfmt, SingleLanePerSamplePairedEndFastqDirFmt, parse_lane=False)


@plugin.register_transformer
def _12(dirfmt: SingleLanePerSampleSingleEndFastqDirFmt) \
-> CasavaOneEightSingleLanePerSampleDirFmt:
casava = CasavaOneEightSingleLanePerSampleDirFmt(mode='w')
for file in dirfmt.path.iterdir():
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if 'MANIFEST' not in str(file) and 'metadata' not in str(file):
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shutil.copy(os.path.join(str(dirfmt), file), str(casava))
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return casava



@plugin.register_transformer
def _5(dirfmt: SingleLanePerSamplePairedEndFastqDirFmt) \
-> SingleLanePerSampleSingleEndFastqDirFmt:
Expand Down Expand Up @@ -351,7 +363,7 @@ def _9(fmt: PairedEndFastqManifestPhred64) \


@plugin.register_transformer
def _12(dirfmt: SingleLanePerSampleSingleEndFastqDirFmt) \
def _27(dirfmt: SingleLanePerSampleSingleEndFastqDirFmt) \
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DBC: Why not keep this as _12, and name the new one _27? Just so you know, with transformers the names of the functions don't matter, we just took the strategy of naming them _number, but it can be anything

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Honestly, probably just because I saw _10, _11 and was bothered at the idea of the next thing being _27 but I guess the rest isn't in numerical order anyway 😆

-> QIIME1DemuxDirFmt:
with dirfmt.manifest.view(FastqManifestFormat).open() as fh:
input_manifest = _parse_and_validate_manifest(fh, single_end=True,
Expand Down
11 changes: 6 additions & 5 deletions q2_types/per_sample_sequences/tests/test_transformer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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),
Expand Down