[BioPython] EMBL parsing in Biopython 1.43
Peter
biopython at maubp.freeserve.co.uk
Sun Apr 29 22:11:07 UTC 2007
Peter wrote:
> Michiel de Hoon wrote:
>> Do you have an idea as to what may be going wrong here?
>
> Yes - I wrote and EMBL parser using the latest file format, while I
> suspect your file from the Pasteur Institute uses an older format -
> specifically one where the first list (the ID line) has a different
> number of fields.
The file you tried seems to use the pre 2006 style ID line. I found
another example like this on the BioPerl webpage. See also:
http://www.ebi.ac.uk/embl/Documentation/archivedchanges.html
> I hope to have a fix in CVS today/tomorrow.
I have updated Bio/GenBank/Scanner.py to cope with these old EMBL ID
lines and added another EMBL test case to test_SeqIO.py
Your example now parses fine, giving a single SeqRecord as expected. I
have not checked the annotation or features...
Peter
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