removes dependence on cogent's DNA, LoadSeqs, Alignment, DenseAlignment #1497
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Conflicts: qiime/pycogent_backports/blat.py
Conflicts: qiime/adjust_seq_orientation.py qiime/align_seqs.py qiime/assign_taxonomy.py qiime/extract_barcodes.py qiime/filter_alignment.py qiime/parse.py qiime/pycogent_backports/blat.py qiime/pycogent_backports/uclust.py qiime/split_libraries.py qiime/split_libraries_fastq.py qiime/truncate_reverse_primer.py qiime/util.py scripts/adjust_seq_orientation.py tests/test_align_seqs.py tests/test_pick_otus.py tests/test_split_libraries.py
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/806/ |
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@gregcaporaso I'm done reviewing, some mostly minor comments |
… were only used by that code. see biocore#1499 for additional information.
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Ok, this should address everything. I tried to clean up calls of the form:
to: on lines that I touched, and I think I got them all. Cleaning that up generally is outside the scope of this pull request. This is ready for re-review for merge. |
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Oh, also deleted |
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/814/ |
| @@ -181,8 +181,6 @@ Alignment, tree-building, taxonomy assignment, OTU picking, and other data gener | |||
| * cdbtools (`src_cdbtools <ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta/cdbfasta.tar.gz>`_) | |||
| * muscle 3.8.31 (`src_muscle <http://www.drive5.com/muscle/downloads.htm>`_) (Public domain) | |||
| * rtax 0.984 (`src_rtax <http://static.davidsoergel.com/rtax-0.984.tgz>`_) (license: BSD) | |||
| * pplacer 1.1 (`src_pplacer <http://matsen.fhcrc.org/pplacer/builds/pplacer-v1.1-Linux.tar.gz>`_) (license: GPL) | |||
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Should these dependencies also be removed from qiime-deploy? If so, can you please create issues on the qiime-deploy-conf tracker?
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Looks good, just a couple of questions |
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addressed your questions - ready for merge? |
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Thanks @gregcaporaso! |
removes dependence on cogent's DNA, LoadSeqs, Alignment, DenseAlignment
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Thanks for the review! |
NOT READY FOR MERGE$ gc "from cogent.*Alignment" qiime scripts testsqiime/filter_alignment.py:14:from cogent.core.alignment import DenseAlignment#1500scripts/insert_seqs_into_tree.py:18:from cogent.core.alignment import DenseAlignmentadd pipeline for inserting OTU representative sequences into an existing tree #1499$ gc "from cogent.*LoadSeqs" qiime scripts testsqiime/split_libraries.py:49:from cogent import DNA as DNA_cogent, LoadSeqsupdate primer to sequence alignment in split_libraries to use skbio's SSW wrapper #1501tests/test_filter_alignment.py:15:from cogent import LoadSeqsre-write filter_alignment.py to make better use of skbio.core.alignment.Alignment #1500$ gc "from cogent.*DNA" qiime scripts testsqiime/filter_alignment.py:13:from cogent import DNAre-write filter_alignment.py to make better use of skbio.core.alignment.Alignment #1500qiime/split_libraries.py:49:from cogent import DNA as DNA_cogent, LoadSeqsupdate primer to sequence alignment in split_libraries to use skbio's SSW wrapper #1501