[Biopython-dev] [Bug 2750] EMBL format: reference titles split across lines are not parsed correctly; pmids are not parsed

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2750





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2009-02-06 08:34 EST -------
Regarding the missing PUBMED ID, that is also now fixed in CVS.  Note that this
still ignores DOI and AGRICOLA references (supporting this would require a
change to our reference object, and perhaps our BioSQL bindings to).

You will need to update your Bio/GenBank/Scanner.py file to revision 1.27 which
you will be able to download here:

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/GenBank/Scanner.py?cvsroot=biopython

Rather than manually updating these two files (Bio/GenBank/__init__.py as per
comment 1, and Bio/GenBank/Scanner.py as above), you may find doing a full
installation from CVS simpler.

e.g.

>>> from Bio import SeqIO
>>> record = SeqIO.read(open("long_ref.embl"),"embl")
>>> for ref in record.annotations["references"] : print ref
... 
authors: Lau NC, Lim LP, Weinstein EG, Bartel DP, Lim LP, Lau NC, Weinstein EG;
title: "An abundant class of tiny RNAs with probable regulatory roles in
Caenorhabditis elegans";
journal: Science. 294:858-862(2001).
medline id: 
pubmed id: 11679671
comment: 

Again, please let us know if that solves your problem.


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