[Biopython-dev] [Biopython - Bug #3363] (New) Blast NCBIXML parser sets HSP gaps varyingly as int or tuple

[redmine at redmine.open-bio.org]

Issue #3363 has been reported by Eric Talevich.

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Bug #3363: Blast NCBIXML parser sets HSP gaps varyingly as int or tuple
https://redmine.open-bio.org/issues/3363

Author: Eric Talevich
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


As described in Bio.Blast.Record, the (obsolete) plain-text Blast parser sets the hsp.gaps attribute as a tuple of (gaps, total aligned), while the NCBIXML parser sets the same attribute as the integer number of gaps when the Hsp_gaps element is parsed. However, the Blast XML report omits this element if there are no gaps in a hit, and so the value of hsps.gaps remains the surprising default value (None, None) instead of an integer.

To avoid breaking the plain-text parser, I would guess the best approach is to set the value of hsp.gaps to 0 initially in the NCBIXML parser.


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