[Biopython-dev] [Bug 2477] SeqIO.parse does not handle embl files

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2477





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2008-03-27 06:49 EST -------
Thanks for the clarification.  I can reproduce the problem here.

It looks like they may have tweaked their file format slightly.  Biopython will
be ignoring the apparently new PA line, which isn't described here:
http://www.ebi.ac.uk/webin-align/fflink2.html

You can also fetch the first problem record from their webpage, choose "Save",
"ASCII text/table", "complete entries"
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:AAA03323]+-newId

As a minor point, personally I find the following style simpler:

from Bio import SeqIO
fName = 'twoEmblRecords.embl'
f = file(fName)
s = SeqIO.parse(f, 'embl')
for rec in s :
    print rec.description
    print rec.annotations['taxonomy']
f.close()

(you may of course have good reason for using the .next() method explicitly)

I'll take a look at this bug now...


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