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

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Mon Dec 12 12:47:31 UTC 2011

Issue #3315 has been reported by Leszek Pryszcz.

Bug #3315: Bio.SwissProt fails parsing .dat dumps

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

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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