new demultiplexed illumina formats #111
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…q filename restrictions
…#82 This adds the formats: - SingleEndFastqManifestPhred33 - SingleEndFastqManifestPhred64 - PairedEndFastqManifestPhred33 - PairedEndFastqManifestPhred64
| def test_parse_and_validate_manifest_expand_vars(self): | ||
| with tempfile.NamedTemporaryFile() as fh: | ||
| directory, filename = os.path.split(fh.name) | ||
| os.environ['TESTENVGWAR'] = directory |
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| metadata = YamlFormat() | ||
| metadata.path.write_text(yaml.dump({'phred-offset': 33})) | ||
| result.metadata.write_data(metadata, YamlFormat) |
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Not really worth it (and it looks like the other transformer is doing the same thing as you), but you could define a transformer from object -> YamlFormat then you could drop the line just above this one with:
result.metadata.write_data({'phred-offset': 33}, YamlFormat)
Same could be done for pd.DataFrame -> FastqManifestFormat.
Basically write_data can invoke other transformers (just like Artifact.import_data)
| format_, | ||
| SingleLanePerSampleSingleEndFastqDirFmt) | ||
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| with tempfile.TemporaryDirectory() as tmpdir: |
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use self.temp_dir (derived from TestPluginBase) instead of all of these TemporaryDirectorys. temp_dir will have a reasonable name in case something goes wrong, making cleanup easier on the user.
| _parse_and_validate_manifest(manifest, single_end=True) | ||
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| def test_parse_and_validate_manifest_expand_vars(self): | ||
| with tempfile.NamedTemporaryFile() as fh: |
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Use self.temp_dir with a fixed name like manifest.txt instead.
| for idx, sample_id, input_fastq_fp, direction in \ | ||
| input_manifest.itertuples(): | ||
| output_fastq_fn = \ | ||
| _get_fastq_fn(sample_id, idx, direction) |
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I think you can replace this with result.sequences.path_maker(...).
fixes #82
fixes #98