[Biopython-dev] [Biopython - Bug #3315] Bio.SwissProt fails parsing .dat dumps

[redmine at redmine.open-bio.org]

Issue #3315 has been updated by Leszek Pryszcz.


Simple replacing
<pre>
            assert len(x) == 2, "I don't understand RX line %s" % value
            key, value = x[0], x[1].rstrip(";")
            reference.references.append((key, value))
</pre>
by
<pre>
            #assert len(x) == 2, "I don't understand RX line %s" % value
            if len(x) != 2:
              print " Warning: I don't understand RX line %s" % value
            else:
              key, value = x[0], x[1].rstrip(";")
              reference.references.append((key, value))
</pre>

would do the job.
----------------------------------------
Bug #3315: Bio.SwissProt fails parsing .dat dumps
https://redmine.open-bio.org/issues/3315

Author: Leszek Pryszcz
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


SwissProt module fails when parsing .dat dump of Uniprot_trembl vesion 201111.
The error is due to corrupted RX lines in .dat for Aureococcus anophagefferens (i.e. C6KIH8_AURAN):
> RX   DOI=DOI; 10.1111/j.1529-8817.2010.00841.x;

I have reported the problem. The thing is, that it happened before. Previously, I have reported similar issue in releases 201010, 201011, 201012...
> RX   DOI=10.1098/rspb= .2010.1301;

Will it be possible to alter error catching mechanisms in Bio.SwissProt._read_rx, so the module warns about corrupted entry instead of failing the parser?


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