[Bioperl-l] Bio::SearchIO broken in bioperl-live by missing Iteration/GenericIteration module

[Jason Stajich]

did you do
% cvs update -dP
?
On Fri, 25 Apr 2003, Matthew Vaughn wrote:

> I just updated to the latest bioperl-live yesterday to address another
> issue I had been having. Today, I tried to run a simple BLAST parser
> script I'd written that was compatible with earlier versions of
> BioPerl. Unfortunately, it's dying upon trying to call next_result. I
> tried updating to today's bioperl-live on the chance that this was just
> a gremlin, but no joy. Interestingly, on both my machines running the
> latest bioperl, there's no such animal as
> Bio::Search::Iteration::GenericIteration, which is probably the core
> problem. Iteration/GenericIteration is in the CVS tree, but is not
> coming through in the cvs update.
>
> On the off chance there's more to this than a missing module, here's
> the error message and a code snippet:
>
> gruyere{vaughn}8% perl sirna6.pl smallRNAs-112502.blast.txt
>
> -------------------- WARNING ---------------------
> MSG: Cannot find module Bio::Search::Iteration::GenericIteration,
> unable to set type
> ---------------------------------------------------
>
> ------------- EXCEPTION  -------------
> MSG: Passed in a Bio::Root::Root as a Iteration which is not a
> Bio::Search::IterationI.
> STACK Bio::Search::Result::BlastResult::add_iteration
> /Library/Perl/Bio/Search/Result/BlastResult.pm:235
> STACK Bio::Search::Result::BlastResult::new
> /Library/Perl/Bio/Search/Result/BlastResult.pm:124
> STACK Bio::Factory::GenericObjectFactory::create
> /Library/Perl/Bio/Factory/GenericObjectFactory.pm:125
> STACK Bio::SearchIO::IteratedSearchResultEventBuilder::end_result
> /Library/Perl/Bio/SearchIO/IteratedSearchResultEventBuilder.pm:240
> STACK Bio::SearchIO::blast::end_element
> /Library/Perl/Bio/SearchIO/blast.pm:960
> STACK Bio::SearchIO::blast::next_result
> /Library/Perl/Bio/SearchIO/blast.pm:323
> STACK toplevel sirna6.pl:70
>
> --------------------------------------
>
> and here's the relevant code
>
> use Bio::SearchIO;
> $filename = $ARGV[0];
> # blah blah
> my $searchio = new Bio::SearchIO( -format => 'blast',
> 					        -file   => $filename);
> # This next line is where the script is dying...
> while ( my $result = $searchio->next_result() ) {
>
> 	# do stuff with $result, its hits, and corresponding hsp's
> }
>
> --
> Matthew W. Vaughn, Ph.D.
> Cold Spring Harbor Laboratory
> Delbruck Laboratory / Martienssen Group
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
>
> phone: (516) 422-4128
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu