[Bioperl-l] pb with remote method in Bio::Tools::Blast

[Elia Stupka]

> # use local program golden from N. Joly to fetch a sequence locally my
> $Seq_in = Bio::SeqIO->new (-file => 'golden sp:TAUD_ECOLI | ', -format
> => 'swiss');

It sounds to me like your local program is returning html, and thus it
cannot be parsed, you are telling it parse swissprote format, but the file
you are giving it is not in swissprot format. The format parameter is not
to be confused with a database parameter, it merely describes the sequence
format used. I think in this case you want your golden script to take away
all the rest and just give back the fasta sequence, and then change the
-format paramter to "fasta".

Elia

> -------------------- EXCEPTION -------------------- MSG: Blast file
> TAUD_ECOLI.blastp2.swissprot.temp.html is incomplete: can't find
> program name. Possibly an unrecognized report format. STACK
> Bio::Tools::Blast::Run::Webblast::_blast
> /local/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast/Run/Webblast.pm:1175
> STACK Bio::Tools::Blast::Run::Webblast::blast_remote
> /local/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast/Run/Webblast.pm:580
> STACK Bio::Tools::Blast::_run_remote
> /local/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast.pm:1234 STACK
> Bio::Tools::Blast::run
> /local/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast.pm:1169 STACK
> Bio::Tools::SeqAnal::_initialize
> /local/lib/perl5/site_perl/5.6.0/Bio/Tools/SeqAnal.pm:279 STACK
> Bio::Root::Object::new
> /local/lib/perl5/site_perl/5.6.0/Bio/Root/Object.pm:474 STACK toplevel
> /local/private/sis/letondal/TMP/b.pl:18
> -------------------------------------------
> 

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