biocore/qiime — pull request #1497 by gregcaporaso (2014-04-09 14:51:31+00:00)
Title: removes dependence on cogent's DNA, LoadSeqs, Alignment, DenseAlignment

**NOT READY FOR MERGE**

$ gc "from cogent.*Alignment" qiime scripts tests
- [ ] qiime/filter_alignment.py:14:from cogent.core.alignment import DenseAlignment
- [ ] qiime/util.py:55:from cogent.core.alignment import Alignment
- [ ] scripts/insert_seqs_into_tree.py:18:from cogent.core.alignment import DenseAlignment
- [ ] tests/test_align_seqs.py:19:from cogent.core.alignment import DenseAlignment, Alignment

$ gc "from cogent.*LoadSeqs" qiime scripts tests
- [ ] qiime/make_phylogeny.py:21:from cogent import LoadSeqs, DNA
- [ ] qiime/pick_otus.py:27:from cogent import LoadSeqs, DNA
- [ ] qiime/split_libraries.py:49:from cogent import DNA as DNA_cogent, LoadSeqs
- [ ] qiime/util.py:52:from cogent import LoadSeqs, Sequence
- [ ] scripts/filter_otus_by_sample.py:19:from cogent import LoadSeqs
- [ ] tests/test_align_seqs.py:18:from cogent import LoadSeqs, DNA
- [ ] tests/test_assign_taxonomy.py:25:from cogent import LoadSeqs
- [ ] tests/test_filter_alignment.py:15:from cogent import LoadSeqs
- [ ] tests/test_filter_otus_by_sample.py:17:from cogent import LoadSeqs
- [ ] tests/test_identify_chimeric_seqs.py:18:from cogent import LoadSeqs, DNA
- [ ] tests/test_make_phylogeny.py:18:from cogent import LoadSeqs, DNA
- [ ] tests/test_parallel/test_assign_taxonomy.py:18:from cogent import LoadSeqs
- [ ] tests/test_parallel/test_blast.py:17:from cogent import LoadSeqs
- [ ] tests/test_parallel/test_identify_chimeric_seqs.py:17:from cogent import LoadSeqs
- [ ] tests/test_parallel/test_util.py:18:from cogent import LoadSeqs
- [ ] tests/test_pick_rep_set.py:17:from cogent import LoadSeqs
- [ ] tests/test_split.py:17:from cogent import LoadSeqs
- [ ] tests/test_workflow/test_pick_open_reference_otus.py:19:from cogent import LoadTree, LoadSeqs
- [ ] tests/test_workflow/test_upstream.py:18:from cogent import LoadTree, LoadSeqs

$ gc "from cogent.*DNA" qiime scripts tests
- [ ] qiime/align_seqs.py:33:from cogent import DNA as DNA_cogent
- [ ] qiime/filter_alignment.py:13:from cogent import DNA
- [ ] qiime/make_phylogeny.py:21:from cogent import LoadSeqs, DNA
- [ ] qiime/pick_otus.py:27:from cogent import LoadSeqs, DNA
- [ ] qiime/split_libraries.py:49:from cogent import DNA as DNA_cogent, LoadSeqs
- [ ] scripts/insert_seqs_into_tree.py:19:from cogent.core.moltype import DNA
- [ ] scripts/insert_seqs_into_tree.py:28:from cogent.core.moltype import DNA
- [ ] tests/test_align_seqs.py:18:from cogent import LoadSeqs, DNA
- [ ] tests/test_identify_chimeric_seqs.py:18:from cogent import LoadSeqs, DNA
- [ ] tests/test_make_phylogeny.py:18:from cogent import LoadSeqs, DNA