ENH: output closed-ref OTU picking stats

[nbokulich]

Improvement Description
Simply: % reads that match ref, but maybe other information could be relevant. (does vsearch output anything by default that we could just propagate here?)

This could be as simple as a report written to stdout, or could attempt to mirror what dada2/deblur do. (I'd lean toward the former, given the relative simplicity of OTU picking)

References
forum xref

[colinbrislawn]

This command...

vsearch --usearch_global all-sequences.fasta --id 0.97 \
--db /people/bris469/bin/databases/97_otus.fasta \
--log closed-ref.log --uc closed-ref.uc --threads 4

... prints this to stdout...

vsearch v2.8.0_linux_x86_64, 62.8GB RAM, 48 cores
https://github.com/torognes/vsearch

Reading file /people/bris469/bin/databases/97_otus.fasta 100%  
142290491 nt in 99322 seqs, min 1254, max 2353, avg 1433
Masking 100%  
Counting k-mers 100%  
Creating k-mer index 100%  
Searching 100%  

... and writes this into the --log file:

vsearch v2.8.0_linux_x86_64, 62.8GB RAM, 48 cores
vsearch --usearch_global all-sequences.fasta --id 0.97 --db /people/bris469/bin/databases/97_otus.fasta --log closed-ref.log --uc closed-ref.uc --threads 4
Started  Thu Jul 26 09:54:19 2018
142290491 nt in 99322 seqs, min 1254, max 2353, avg 1433

Matching query sequences: 700 of 723 (96.82%)

Finished Thu Jul 26 09:54:46 2018
Elapsed time 00:27
Max memory 472.4MB

Simply: % reads that match ref,

Found it! 😉

[colinbrislawn]

Should we add this as an output, like this?
--o-log ARTIFACT Log file from vsearch.

Or should I figure how how to get this written into standard out from --verbose?

EDIT: To be clear, vsearch does not include a --verbose flag. It has a --quiet for less detail and a --log flag for more detail.