Add uchime2_denovo to close #92 #100
Conversation
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Hi @colinbrislawn, |
Cool! How does this look for the CLI? (CLI docs for the existing function) qiime vsearch uchime-denovo \
--p-method 'uchime2' \
--p-mindiffs 99 # ignored when running uchime2 and uchime3
--p-mindiv 0.8 # ignored when running uchime2 and uchime3
--p-minh 0.99 # ignored when running uchime2 and uchime3
...What should we do if someone passes settings that are not used by uchime2 and uchime3? |
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Let's add support for |
| # this function only exists to simplify testing | ||
| chimeras = DNAFASTAFormat() | ||
| nonchimeras = DNAFASTAFormat() | ||
| uchime_stats = UchimeStatsFmt() | ||
| with tempfile.NamedTemporaryFile() as fasta_with_sizes: | ||
| _fasta_with_sizes(str(sequences), fasta_with_sizes.name, table) | ||
| cmd = ['vsearch', | ||
| '--uchime_denovo', fasta_with_sizes.name, | ||
| '--' + method + '_denovo', fasta_with_sizes.name, |
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Is there a better way to do this?
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Is The methods are tested with 100% coverage, but the results are not, as I'm not sure how they should work with non-trivial examples. If we want to build a test that shows the difference between these methods, here's commentary on vsearch's implementation: @nbokulich, if you have the time and interest, I would appreciate your review! |
WIP to close #92
Add internal functions and tests to use 'uchime' 'uchime2' or 'uchime3'
Open questions:
--abskewfor some or all of these?