[Bioperl-guts-l] [BioPerl - Bug #3154] SearchIO:blastxml does not return correct query name for blastp (2.2.24)

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Tue Aug 9 16:20:05 EDT 2011


Issue #3154 has been updated by Chris Fields.


I recalled this had been reported elsewhere for biopython; found "the original report":http://lists.open-bio.org/pipermail/open-bio-l/2011-May/000798.html.  As a sidenote, this may very well be a bug on NCBI's end with the latest BLAST+; still awaiting word back on whether this has been confirmed or not.
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Bug #3154: SearchIO:blastxml does not return correct query name for blastp (2.2.24)
https://redmine.open-bio.org/issues/3154

Author: Kris McGary
Status: In Progress
Priority: Normal
Assignee: Bioperl Guts
Category: Bio::Search/Bio::SearchIO
Target version: unspecified
URL: 


Bio:SearchIO will return the expected query_name when parsing Blast xml output from Blast version 2.2.22 and earlier.  However, it returns 'Query_1' for xml output from blastp (2.2.24), instead of the expected (for my search) '86959'. Looking at the xml code reveals that the xml field that contains the correct name is unchanged, e.g. "<Iteration_query-def>86959</Iteration_query-def>".  However, a related xml field has changed and now seems to be providing the data:
2.2.24 says, "<Iteration_query-ID>Query_1</Iteration_query-ID>"
2.2.22 says, "<Iteration_query-ID>lcl|1_0</Iteration_query-ID>"


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