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

[Matthew Vaughn]

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