Join paired ends updates #1726
Join paired ends updates #1726
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…ated test code files
…t_join_paired_ends.py as all content is now in test_format.py
…t the bottom of `join_paired_ends.py`
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1256/ |
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1258/ |
| help=' Input format of fastq data. Can be: \'illumina1.3\' or'+ | ||
| ' \'illumina1.8\'. Only used if using the \'-b\' option.' + | ||
| ' Output will always be \'illumina1.8\'. [default: %default] '+ | ||
| 'For more info see: http://en.wikipedia.org/wiki/FASTQ_format', |
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Could you replace that link with this one:
http://scikit-bio.org/docs/latest/generated/skbio.io.fastq.html#format-specification
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retest this please |
…updated help documentation in join_paired_ends.py script
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Done. I went through and updated broken code to relevant skbio code in:
The updated code in these two files pass all unit tests on my local machine. I've also updated the link to the skbio fastq format information as requested in 'join_paired_ends.py' |
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1278/ |
| @@ -601,7 +604,8 @@ def write_Fasta_from_name_seq_pairs(name_seqs, fh): | |||
| raise ValueError("Need open file handle to write to.") | |||
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| for (name, seq) in name_seqs: | |||
| fh.write("%s\n" % BiologicalSequence(seq, id=name).to_fasta()) | |||
| #fh.write("%s\n" % BiologicalSequence(seq, id=name).to_fasta()) | |||
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1437/ |
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retest this please |
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1439/ |
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@mikerobeson, thanks for these edits. @jairideout and I are working on prepping 1.9.0 now, and decided that we're going to not merge this for now, and re-assign for the 2.0.0. Our motivation for this is that this would be the only code in QIIME 1.9.0 that uses the new skbio fastq parsers, and it's not a good idea for the code base to be using different parsers for the same file format due to possible inconsistencies. We'll integrate these changes when we port all of the fastq parsing in QIIME to use the new parsers. Sorry we didn't notice the issue with porting to the new skbio parsers sooner. As always, we really appreciate your contributions to QIIME so thanks again! |
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Was I not supposed to use skbio? I used skbio because the test code warned me of deprecated code and specified that I use skbio. :-( |
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Sorry for the confusion, we're just concerned about having two different parsers in different parts of the codebase because unfortunately we didn't get around to updating the rest of QIIME to use the new parsers. So it's great that it is updated for it, we're mostly just concerned about possible differences with the rest of QIIME (so it's really our fault, not yours, that we're concerned about merging this). |
Moved function
write_synced_barcodes_fastqand its test code toformat.pyandtest_format.pyrespectively as per #1243.Also:
skbio.iocode.test_join_paired_ends.pyas all relevant test code is now intest_format.py