[Bioperl-l] SearchIO Parse Errors

Chris Fields cjfields at uiuc.edu
Fri Mar 23 11:17:15 EDT 2007

You can send the archive directly to me (not the group!) or file this  
as a bug in Bugzilla and attach the archive to the report.  It's an  
odd bug but it's hard to say what's going on w/o looking at your code  
and BLAST reports.  I did notice that (when going through the  
StandAloneBlast code) that bl2seq expects a Bio::Tools::BPbl2seq  
object which has been deprecated for a while now and is no longer  


On Mar 23, 2007, at 1:46 AM, Brandon Barker wrote:

> Hi,
> I'm using Bioperl to run BLAST and parse the results of many pairs of
> sequences.  Some of these pairs work fine, but for some of the others
> my script outputs errors of the following form:
> Bio::SearchIO::blast=HASH(0x1a18040)parse error on F18G5.3 / CBG16182
> Bio::SearchIO::blast=HASH(0x19ff2cc)parse error on Y73E7A.3 / CBG22266
> Bio::SearchIO::blast=HASH(0x1a0cbe4)parse error on T23F1.6 / CBG24659
> Bio::SearchIO::blast=HASH(0x19fcca8)parse error on Y71G10AR.4 /  
> CBG13872
> The last two words on the lines above are the sequences that are
> trying to be being aligned.  I'm using the following code to construct
> the searchio objects:
>   my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>   $factory->outfile('blast.out');
>   my $report = $factory->bl2seq($input, $input2);
>   try {
>   my $result = $report->next_result;
>    .....
>   }
> If it would be helpful, I would be more than happy to make an archive
> of the two sequence files and the bioperl script.  I searched the
> bioperl core codebase briefly but didn't see anything that looked
> familiar to this problem.
> Thanks in advance,
> -- 
> Brandon Barker
> Phone: (859) 948-5335
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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