[Biopython-dev] [Biopython - Bug #3335] (New) NameError: global name 'StringIO' is not defined

[redmine at redmine.open-bio.org]

Issue #3335 has been reported by John Comeau.

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Bug #3335: NameError: global name 'StringIO' is not defined
https://redmine.open-bio.org/issues/3335

Author: John Comeau
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


Bio.ParserSupport method parse_str uses StringIO but the module does not import it. I don't have a proper patch, just added the

import StringIO

on line 37 to fix. The modified file:

bash-3.2$ grep -n StringIO /data1/igm3/sw/packages/python-2.7/lib/python2.7/site-packages/biopython-1.59-py2.7-linux-x86_64.egg/Bio/ParserSupport.py
37:import StringIO
57:        return self.parse(StringIO.StringIO(string))

I realize maintaining the legacy parsers is not a high priority for the BioPython team, but I need this to work, or write my own parser, or switch to BioPerl, and the latter two options are not happy ones for me.


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