[Biopython-dev] [Bug 2904] Interface for Novoalign

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2904


chapmanb at 50mail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #2 from chapmanb at 50mail.com  2009-09-16 18:00 EST -------
Osvaldo;
Thanks much for the submission. This is committed and lives in:

Bio/Sequencing/Applications

to create a namespace for future sequencing related commandlines. You can
import with:

from Bio.Sequencing.Applications import NovoalignCommandline

It would be great if you wanted to add a cookbook example of using it
(http://biopython.org/wiki/Category:Cookbook) based on a simple pipeline.
Perhaps something involving downstream parsing of the novoalign format, or
converted to SAM as you suggested in Bug 2905.

Thanks,
Brad


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