[Biopython-dev] [Biopython - Bug #3009] (New) Check the FASTA m10 alignment parser works with FASTA36

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Issue #3009 has been updated by Peter Cock.

Category changed from Unit Tests to Main Distribution
Status changed from Closed to New
% Done changed from 100 to 0

Reopening bug, found some examples with multiple HSPs for the same query and match, separated by new line ">--".

I will add an example to the test suite, but the parser will need revising (something I was looking at doing anyway for other reasons).
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Bug #3009: Check the FASTA m10 alignment parser works with FASTA36
https://redmine.open-bio.org/issues/3009

Author: Peter Cock
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: Not Applicable
URL: 


Bill Pearson has just announced the release of FASTA36:
http://faculty.virginia.edu/wrpearson/fasta/fasta36/

>From his email,
> This version is a major update from FASTA version 35.
> It's main new feature is the ability to report all
> statistically significant alignments between a query
> and library sequence (equivalent to BLAST's multiple
> HSPs).  All previous versions of the FASTA program
> reported only the best alignment between the query
> and library sequence, a serious shortcoming when
> comparing a query protein to a multi-exon gene or
> multi-domain protein.

We need to check the FASTA36 -m 10 output, add this to
our unit tests, and update our parser as required.


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