[Biopython-dev] [Bug 2131] SProt.py fails to parse the current Swiss-Prot version 51.0

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2131





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2006-11-02 13:07 -------
Created an attachment (id=491)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=491&action=view)
First four records from uniprot_sprot.dat.gz release 51

I was hoping for a smaller test case, uniprot_sprot.dat.gz is 185MB compressed,
and 836MB as plain text!  Anyway, I have extracted and attached a file with the
just the first four records in it for anyone interested in testing.

I would guess from your stack trace that this recent change to the ID line that
has caused the trouble:

http://ca.expasy.org/sprot/relnotes/sp_news.html#rel9.0

Old (with MoleculeType):
ID   EntryName DataClass; MoleculeType; SequenceLength.

New (without MoleculeType):
ID   EntryName DataClass; SequenceLength.

e.g.
ID   CYC_PIG                 Reviewed;         104 AA.
ID   Q3ASY8_CHLCH            Unreviewed;     36805 AA.

This shouldn't be too hard to fix...


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