[Biopython-dev] [Biopython - Bug #3317] Parsing Stockholm files fails with some sequence IDs

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Wed Jan 18 17:32:35 EST 2012


Issue #3317 has been updated by Connor McCoy.


Sure: I added an example of the previously failing sequence to the existing `Tests/Stockholm/funny.sth` file.

https://github.com/cmccoy/biopython/commit/7e9f697c38f0132952b50482fddfea77ce800536

If there's a better place, please let me know.

All tests pass for me.
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Bug #3317: Parsing Stockholm files fails with some sequence IDs
https://redmine.open-bio.org/issues/3317

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


I ended up with a stockholm file where some sequence IDs end with "/MN1-00", e.g.

363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00

This can't be parsed by the BioPython AlignIO module - it fails attempting to convert "MN1" to an integer.

I wrote a quick patch, which just returns the default value if the type conversion fails:
https://github.com/cmccoy/biopython/commit/77f97b5d7184a077ca6e2e90d90ca0110b5766c3


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