[Bioperl-l] not getting all exons back when using Bio::DB::GFF

[Lincoln Stein]

Hi Niels,

I just tried WS150 myself and I'm getting five exons when I run your example. 
Are you using bioperl 1.51 or an earlier version?

Lincoln


On Thursday 09 March 2006 10:23, Niels Klitgord wrote:
> Hello,
>   Perhaps this is because I'm not using Bio::DB::GFF correctly.  Perhaps
> I missed a previous post on this, if so I apologize.  But on occasion
> when I try to get all the exons of an orf from a segment I wind up
> missing 1.  I am using  wormbase  WS150 release GFF, and am using
> GFF.pm,v 1.102 perl modual (maybe  I need to upgrade?).
> This is the code I was using:
>
> #!/usr/local/bin/perl -w
> use strict;
> use Bio::DB::GFF;
>
> my $GFFdb = new Bio::DB::GFF(-adaptor=>'dbi::mysqlopt',
>               -dsn=>'dbi:mysql:gff150;host=dome',
>               -user=>'niels')or die("can't open gffDB");
>
> my $gene = 'C08C3.3';
>
> my @seg = $GFFdb->segment(-name=>$gene,  -class=>'CDS');
>
> print "$gene CDS: ", $seg[0]->abs_start, "\t", $seg[0]->abs_stop, "\n";
>
> my @all_exons = $seg[0]->features( 'exon:curated' );
> foreach my $k (sort { $a->start <=> $b->start} @all_exons) {
>     print "feature: ", $k->class, "\t", $k->type, "\t", $k->name, "\t",
> $k->abs_start, "\t",  $k->abs_stop, "\n"
> }
>
> and get:
> C08C3.3 CDS: 7783311    7777192
> feature: CDS    exon:curated    C08C3.3 7782898 7782816
> feature: CDS    exon:curated    C08C3.3 7782130 7782027
> feature: CDS    exon:curated    C08C3.3 7778462 7778314
> feature: CDS    exon:curated    C08C3.3 7777314 7777192
>
> However in the raw gff file we see  (and also in the mysql ):
> CHROMOSOME_III  curated exon    7777192 7777314 .   -   .   CDS
> "C08C3.3"  <found>
> CHROMOSOME_III  curated exon    7778314 7778462 .   -   .   CDS
> "C08C3.3" <found>
> CHROMOSOME_III  curated exon    7782027 7782130 .   -   .   CDS
> "C08C3.3" <found>
> CHROMOSOME_III  curated exon    7782816 7782898 .   -   .   CDS
> "C08C3.3" <found>
>
> CHROMOSOME_III  curated exon    7783168 7783311 .   -   .   CDS
> "C08C3.3" <not found!!>
>
> Am I just using this wrong, or should the last entry be returned as well?
> Much thanks in advance,
>   Niels
>
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
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