[Bioperl-l] Problem with spliced_seq in BioPerl 1.5.2

[Gathman, Allen]

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