[Biopython-dev] [Bug 1946] Parsing GenBank Files - unknown line type PROJECT

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1946


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

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




------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2007-03-08 13:46 EST -------
You can download the example here, which the reporter saved as 'bug.gb':

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=NC_001416

Using CVS, the original sample script now runs fine:

from Bio import GenBank
feature_parser = GenBank.FeatureParser()
gb_record = feature_parser.parse(open('bug.gb','r'))

As does something similar using Bio.SeqIO, e.g.

from Bio import SeqIO
records = list(SeqIO.parse(open('bug.gb','rU'),"genbank"))
assert len(records) == 1
gb_record = records[0]

In both cases, the new GenBankScanner class in Bio/GenBank/Scanner.py will
silently ignore the "PROJECT" line, unless run in debug mode.

I have filed Bug 2225 to cover doing something useful with the project data.


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