ENH: adds transformer #161
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thermokarst
added
the
stat:DO-NOT-MERGE
SingleLanePerSampleSingleEndFastqDirFmt -> QIIME1DemuxDirFmt
gregcaporaso
removed
the
stat:DO-NOT-MERGE
thermokarst
suggested changes
Nov 22, 2017
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Thanks @gregcaporaso, one minor change requested inline. Thanks!
| filename = r[1]['filename'] | ||
| if re.search("\s", sample_id) is not None: | ||
| raise ValueError( | ||
| "Sample identifers cannot contain space characters, but " |
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How about something along these lines:
Whitespace was found in the ID for sample %s. Sample identifiers with whitespace are incompatible with FASTQ - please remove the whitespace and try again.
| "an identifier with spaces was found: %s" % sample_id) | ||
| fq_reader = skbio.io.read('%s/%s' % (str(dirfmt), filename), | ||
| format='fastq', constructor=skbio.DNA, | ||
| phred_offset=33, verify=False) |
| @@ -0,0 +1,5 @@ | |||
| # Quantitative Insights Into Kneecaps and Armpits | |||
| sample-id,filename,direction | ||
| Human-Kneecap,Human-Kneecap_S1_L001_R1_001.fastq.gz,forward | ||
| # tab in sample-id | ||
| Human-Armp it,Human-Armpit_S2_L001_R1_001.fastq.gz,forward |
| 'data/absolute_manifests/*', | ||
| 'data/relative_manifests/*', | ||
| 'data/qiime1-demux-format/*', | ||
| 'data/single-end-two-sample-data1/*', |
| absolute=False) | ||
|
|
||
| result = QIIME1DemuxDirFmt() | ||
| fp = os.path.join(str(result), 'seqs.fna') |
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No need to change this, but you can also use the operator overloading support with this object:
fp = result / 'seqs.fna'It will handle sticking in the right path separator. I wouldh't worry about making that change, just more of a neat "TIL" type of thing.
thermokarst
approved these changes
Nov 22, 2017
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SingleLanePerSampleSingleEndFastqDirFmt -> QIIME1DemuxDirFmt