[Biopython-dev] [Bug 3069] More robust feature parser for GenBank/EMBL records

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3069


laserson at mit.edu changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
Attachment #1492 is|0                           |1
           obsolete|                            |




------- Comment #9 from laserson at mit.edu  2010-04-30 11:23 EST -------
Created an attachment (id=1497)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1497&action=view)
New IMGT parser object

This patch changes four files.  Most of it is in Bio/GenBank/Scanner.py, and
then there are a few extra additions to integrate it into SeqIO (for parse()
and index()).

I still have not been able to run through the whole IMGT database with this
parser but this is because of actual errors in the IMGT records (which I will
report back to the IMGT curators), or because of other bugs that I have
discovered in the EMBL parser (from which the IMGT parser is derived; e.g., Bug
#3071).  However, it does breeze through most of the IMGT records without a
problem, and handles both the EMBL-indented, and the IMGT-over-indented
records.


-- 
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.