[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.


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

All tests pass for me.
Bug #3317: Parsing Stockholm files fails with some sequence IDs

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

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


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:

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