[Biopython-dev] [Bug 3004] PSL alignment format parsing

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3004


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |biopython-
                   |                            |bugzilla at maubp.freeserve.co.
                   |                            |uk
            Summary|PSL alignment format parsing|PSL alignment format parsing
                   |in Bio.AlignIO              |




------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2010-02-01 06:17 EST -------
(In reply to comment #2)
> Now on github:
> 
> http://github.com/vforget/PyBLATPSL
> 
> Vince
> 

Thanks for the link.

I don't see how this connects to sequence alignments for Bio.AlignIO as
suggested in your original comment (bug title edited accordingly). I see
you are parsing tabular output into an object, with addition methods for
scores etc. This looks fairly useful, but is not appropriate for the
Bio.AlignIO module. Maybe it can go under a new namespace instead, maybe
Bio.BLAT?

Peter


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.