[Bioperl-l] Blast with GI's

[James Gilbert]

This is failing where it tries to work out what
flavour of blast you have run (BLASTN, BLASTX
etc...).  What does the top of your file look
like?

You may get more mileage from Bio::Tools::BPlite

On Mon, 17 Dec 2001, Ross Gibbs wrote:

> Does bioperl parse blast reports when NCBI GI numbers are included?
> 
> I'm running reports using "BLAST with client-server support" which creates
> an HTML report.
> 
> When a try to parse a non_html version of the report I get the output
> below.
> 
> Suggestions?
> Ross
> 
> 
> 
> 
> MSG: Unexpected error during read: -------------------- EXCEPTION
> -------------------- MSG: Can't determine program type from BLAST report.
> STACK Bio::Tools::Blast::_parse_header
> /usr/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast.pm:1928 STACK
> Bio::Tools::Blast::__ANON__
> /usr/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast.pm:1761 STACK (eval)
> /usr/lib/perl5/site_perl/5.6.0/Bio/Root/IOManager.pm:752 STACK
> Bio::Root::IOManager::read
> /usr/lib/perl5/site_perl/5.6.0/Bio/Root/IOManager.pm:736 STACK
> Bio::Root::Object::read
> /usr/lib/perl5/site_perl/5.6.0/Bio/Root/Object.pm:1511 STACK
> Bio::Tools::Blast::_parse_blast_stream
> /usr/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast.pm:1615 STACK
> Bio::Tools::Blast::parse
> /usr/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast.pm:1465 STACK
> Bio::Tools::SeqAnal::_initialize
> /usr/lib/perl5/site_perl/5.6.0/Bio/Tools/SeqAnal.pm:281 STACK
> Bio::Root::Object::new
> /usr/lib/perl5/site_perl/5.6.0/Bio/Root/Object.pm:474 STACK toplevel
> ./bioperl.pl:19 ------------------------------------------- STACK
> Bio::Root::IOManager::read
> /usr/lib/perl5/site_perl/5.6.0/Bio/Root/IOManager.pm:763 STACK
> Bio::Root::Object::read
> /usr/lib/perl5/site_perl/5.6.0/Bio/Root/Object.pm:1511 STACK
> Bio::Tools::Blast::_parse_blast_stream
> /usr/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast.pm:1615 STACK
> Bio::Tools::Blast::parse
> /usr/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast.pm:1465 STACK
> Bio::Tools::SeqAnal::_initialize
> /usr/lib/perl5/site_perl/5.6.0/Bio/Tools/SeqAnal.pm:281 STACK
> Bio::Root::Object::new
> /usr/lib/perl5/site_perl/5.6.0/Bio/Root/Object.pm:474 STACK toplevel
> ./bioperl.pl:19 -------------------------------------------
> 
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
James G.R. Gilbert            The Wellcome Trust Sanger Institute
Fax: +44 (0)1223 494919              Wellcome Trust Genome Campus
Tel: +44 (0)1223 494906              Hinxton, Cambridge, CB10 1SA