[Biopython-dev] [Bug 2745] Bio.GenBank.LocationParserError with a GenBank CON file

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Jan 30 16:20:18 UTC 2009


------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2009-01-30 11:20 EST -------
Created an attachment (id=1214)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1214&action=view)
Treat the CONTIG information as a string, not a SeqFeature

As outlined on Bug 2681 comment 8, there are good reasons to simply store the
CONTIG information as a string or perhaps a list of strings.  This will make
our BioSQL bindings consistent with BioPerl.

More generally, I never really liked the idea of storing the CONTIG location as
a SeqFeature.  I could understand in principle using a location-object, but the
current location objects do not deal with joins directly - which is why you
have to use a SeqFeature with subfeatures.

In the long term, a new location object might be a worthwhile change to both
features and the contig.  For now, this patch simply stores the CONTIG
information as one long string.

If we commit this, then Tests/output/test_GenBank will need updating too.

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.

More information about the Biopython-dev mailing list