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This queue is for tickets about the bioperl CPAN distribution.

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The Basics
Id: 54590
Status: resolved
Priority: 0/
Queue: bioperl
People
Owner: Nobody in particular
Requestors: asekhar [...] dow.com
Cc:
AdminCc:
Bug Information
Severity: (no value)
Broken in: (no value)
Fixed in: (no value)
Attachments
parseblast.pl
sequences _public.fasta
xmlresults.xml

History Show all quoted text
  Sat Feb 13 12:24:10 2010 asekhar [...] dow.com - Ticket created
Subject: Bug with XML parser
Date: Sat, 13 Feb 2010 11:35:47 -0500
To: <bug-bioperl [...] rt.cpan.org>
From: "ThirumalaiswamySekhar, Arvind (A)" <asekhar [...] dow.com>
Current BLASTXML(Bioperl 1.6.1) parser does not iterate through different queries when the FASTA file for BLASTing has multiple queries within it. Parsing does occur for Hits and HSPs but all of these are linked to the same QUERY/RESULT which is the very first query in the multi query file. Example files are attached here. <<xmlresults.xml>> <<parseblast.pl>> <<sequences _public.fasta>>

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Download sequences _public.fasta
application/octet-stream 11.5k

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  Mon Jan 31 12:29:29 2011 cjfields [...] uiuc.edu - Correspondence added
On Sat Feb 13 12:24:10 2010, asekhar@dow.com wrote: Show quoted text
> Current BLASTXML(Bioperl 1.6.1) parser does not iterate through > different queries when the FASTA file for BLASTing has multiple queries > within it. Parsing does occur for Hits and HSPs but all of these are > linked to the same QUERY/RESULT which is the very first query in the > multi query file. > > Example files are attached here. > > <<xmlresults.xml>> <<parseblast.pl>> <<sequences _public.fasta>>
You do not want to set 'psiblast' as the blast type parameter, as that assumes the entire report is a PSI-BLAST report; the Iteration tag is logically parsed into Iteration objects based on that assumption. Once this is unset the query parses as expected. I have added a bit of documentation to that effect in the Bio::SearchIO::blastxml docs. If you have any other suggestions on how that could be improved feel free to let us know. http://bit.ly/ekwTde
  Mon Jan 31 12:29:30 2011 The RT System itself - Status changed from 'new' to 'open'
  Mon Jan 31 12:29:30 2011 cjfields [...] uiuc.edu - Status changed from 'open' to 'resolved'