[Biopython-dev] [Bug 2225] Do something with the PROJECT line in GenBank files

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2225


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

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




------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2008-11-09 10:04 EST -------
You've got a minor bug in there Brad...

def dblink(self, content):
    """Store DBLINK cross references as dbxrefs in our record object.
    """
    dblinks = [l for l in content.split() if l]
    self.data.dbxrefs.extend(projects)

Should be: self.data.dbxrefs.extend(dblinks)

However, based on the example DBLINK line, we shouldn't be splitting on spaces
at all - for example this transition example for when the PROJECT line and
DBLINK lines are present:

LOCUS       CP000964             5641239 bp    DNA     circular BCT 24-SEP-2008
DEFINITION  Klebsiella pneumoniae 342, complete genome.
ACCESSION   CP000964
VERSION     CP000964.1  GI:206564770
PROJECT     GenomeProject:28471
DBLINK      Project:28471
            Trace Assembly Archive:123456
....

Note that "Trace Assembly Archive:123456" should be a single cross reference. 
I'll attach a patch for CVS in a moment.


-- 
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.