best N hits

[tyleraland]

New argument --best N keeps only the best N hits for each query sequence, as ranked by absolute number of mismatches from the query.

I've been comparing the before and after (with and without --best 2) for a particular data set generated by the capture pipeline (classifying individual query sequences) and the results appear pretty promising. You can compare the before and after classifications here:

/mnt/disk2/molmicro/working/tland9/2016-02-25_bioy_slashname_filtering/classifications-nobest /mnt/disk2/molmicro/working/tland9/2016-02-25_bioy_slashname_filtering/classifications-best2

Potential Feedback:

• Suggestions for a more descriptive argument name?
• Note the requirement on the "mismatches" field means blast results need to look a little different
• Some of my lines may be a little long. Is there a strict 80 character style limit?

[nhoffman]

Can we name the argument --best-n-hits ?

[crosenth]

Don't forget to update the CHANGLOG.rst