[Bioperl-l] Error while parsing a BLAST Report

deepak shingan deep_ans at yahoo.com
Thu Aug 17 08:03:28 EDT 2006


Hi all, 
  I am getting the following exception while parsing a blast report using SearchIO algorithm.
   
  ------------- EXCEPTION: Bio::Root::Exception -------------
  MSG: Undefined sub-sequence (400,401). Valid range = 285 - 401
  STACK: Error::throw
  STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.5/Bio/Root/Root.pm:328
  STACK: Bio::Search::HSP::HSPI::matches /usr/lib/perl5/site_perl/5.8.5/Bio/Search/HSP/HSPI.pm:711
  STACK: Bio::Search::SearchUtils::_adjust_contigs /usr/lib/perl5/site_perl/5.8.5/Bio/Search/SearchUtils.pm:365
  STACK: Bio::Search::SearchUtils::tile_hsps /usr/lib/perl5/site_perl/5.8.5/Bio/Search/SearchUtils.pm:176
  STACK: Bio::Search::Hit::GenericHit::matches /usr/lib/perl5/site_perl/5.8.5/Bio/Search/Hit/GenericHit.pm:830
    STACK: parserMethod.pl:62

   
  I am using bio-perl version 1.5.1.
  The same parserMethod works fine with all other blast reoprt files but tblastx output files are not getting parsed correctly.
   
  If anybody knows something about this, Please reply .
   
  Regards...
  Deepak
   
  [Note : I am sending source code and the sample blast report file in which the exception is occuring as an attachment with this mail]
   

 		
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