[Bioperl-l] Problem with spliced_seq in BioPerl 1.5.2

[Chris Fields]

Can you file a bug on this?  Attach the script and maybe detail what  
data is loaded into your local MySQL database (if possible).

chris

On May 1, 2007, at 6:10 PM, Gathman, Allen wrote:

> Hi, all --
>
> I've been using BioPerl 1.4 for a while; recently I installed  
> 1.5.2, and
> found that scripts that had been using spliced_seq are now broken.   
> Any
> thoughts on what might be going on?
>
> Here's a sample script:
>
> *********************************************
>
> #!/usr/bin/perl -w
>
> use strict;
> use Bio::DB::GFF;
>
> my $db  = Bio::DB::GFF-> new ( - adaptor => 'dbi::mysql',
>                                -dsn        =>
> 'dbi:mysql:database=cc;host=localhost',
>                                -fasta      => '/gbrowse/databases/cc'
>                                );
> $db->add_aggregator('transcript{CDS/mRNA}');
> my $seg=$db->segment('ccin_Contig120');
> my @genes=$seg->features(-types=>('transcript:GLEAN_alt'));
>
> for my $gene (@genes) {
>     my $gid = $gene->display_id;
>
>     print STDERR "Gene is $gid\n";
>     my $splgene = $gene->spliced_seq();
> }
>
> ********************************************
> The line with "spliced_seq" in it crashes the program.  Here's the
> STDERR output:
>
> Gene is Jan06m400_GLEAN_11487
>
> -------------------- WARNING ---------------------
>
> MSG: Calling spliced_seq with a Bio::Das::SegmentI which does have
> absolute set to 1 -- be warned you may not be getting things on the
> correct strand
>
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
>
> MSG: seq doesn't validate, mismatch is
> ::,(0,88211,0),::,(0,8821170),::,(0,8821260),::,(0,8821308),::, 
> (0,881935
> ,),::,(0,881,468),::,(0,881,4,4),::,(0,8818,0),::,(0,8819098)
>
> ---------------------------------------------------
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
>
> MSG: Attempting to set the sequence to
> [Bio::PrimarySeq=HASH(0x88211d0)Bio::PrimarySeq=HASH(0x8821170) 
> Bio::Prim
> arySeq=HASH(0x8821260)Bio::PrimarySeq=HASH(0x8821308) 
> Bio::PrimarySeq=HAS
> H(0x881935c)Bio::PrimarySeq=HASH(0x881f468)Bio::PrimarySeq=HASH 
> (0x881f4a
> 4)Bio::PrimarySeq=HASH(0x8818ff0)Bio::PrimarySeq=HASH(0x8819098)]  
> which
> does not look healthy
>
> STACK: Error::throw
>
> STACK: Bio::Root::Root::throw
> /usr/lib/perl5/site_perl/5.8.6/Bio/Root/Root.pm:359
>
> STACK: Bio::PrimarySeq::seq
> /usr/lib/perl5/site_perl/5.8.6/Bio/PrimarySeq.pm:258
>
> STACK: Bio::PrimarySeq::new
> /usr/lib/perl5/site_perl/5.8.6/Bio/PrimarySeq.pm:210
>
> STACK: Bio::Seq::new /usr/lib/perl5/site_perl/5.8.6/Bio/Seq.pm:484
>
> STACK: Bio::SeqFeatureI::spliced_seq
> /usr/lib/perl5/site_perl/5.8.6/Bio/SeqFeatureI.pm:498
>
> STACK: /transfer/testsplice.pl:20
>
> -----------------------------------------------------------
>
> Allen Gathman
>
> http://cstl-csm.semo.edu/gathman
>
>
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign