[Biopython-dev] [Biopython (old issues only) - Bug #3004] (Resolved) PSL alignment format parsing

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Wed Nov 9 10:09:16 UTC 2016

Issue #3004 has been updated by Peter Cock.

Description updated
Status changed from New to Resolved
% Done changed from 0 to 100

Agreed, relatively new module Bio.SearchIO handles BLAT-PSL files, so I think this has been resolved. e.g.

from Bio import SearchIO
query = SearchIO.read('test.psl','blat-psl')

Hopefully that works for Vince's use case - further enhancements welcomed.

Marking issue as resolved, thank you all.

Bug #3004: PSL alignment format parsing

* Author: Vince Forgetta
* Status: Resolved
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
Hi Bio-pythonistas,

I am interested in contributing code to biopython. I have developed a class to represent PSL output from the BLAT alignment program. I would like to contribute it to the AlignIO module. I have read through and agree to the guidelines stipulated on http://biopython.org/wiki/Contributing. I have never written unit tests before, but I am willing to learn.



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