[Bioperl-l] Problem with Bio::DB::GFF

[Gathman, Allen]

Hello all - 

 

Although this problem arises in the context of Gbrowse, I'm pretty sure it's
more of a straight bioperl question.  

I'm trying to pull specific features out of a database that I'm using to run
Gbrowse, using the tools in Bio::DB::GFF.  Here's a test program:

 

#!/usr/bin/perl

 

use Bio::DB::GFF;

my $db=Bio::DB::GFF->new(-adaptor => 'dbi::mysql',

                         -dsn     =>
'dbi:mysql:database=ccsmall;host=localhost',

                         -fasta   => '/gbrowse/databases/cc'

                        );

$outfile= $ARGV[0];

open (OUT, ">$outfile");

@gfeat=$db->features(-attributes => {-Gene => 'lcc1'});

print OUT "Genes: @gfeat\n";

foreach $feat (@gfeat){

    print OUT "Start is " . $feat->start . "\n";

    }

close OUT; 

 

When I run this script, the output file says:

 

Genes:

 

 

And that's it.  No features are returned.  A gff file loaded into the
ccsmall database using load_gff.pl has this first line:

 

ccin_Contig34     CURATED_PRIVATE   mRNA  64853 68924 .     -     .     Gene
lcc1; Eval 0.0; Lab Kues
 

 

So it would appear that the attribute -Gene => 'lcc1' should pull out
something - but obviously I'm missing something here, because it doesn't.  

 

I wrote another script that uses the get_seq_stream method, and it pulls out
this gene, among others.  I've been able to get at the 'lcc1' by looking at
$f->group for each feature in the stream: 

 

$gefeat=$db->get_seq_stream(-type => ['mRNA:CURATED_PRIVATE']);

while ($f=$gefeat->next_seq) { 

      $group=$f->group;

       if ($group='lcc1') { bla bla bla }

}

 

But this is sort of (well, okay, REALLY) clumsy.

 

So my question is, what am I doing wrong with the "features" method?  I'd
really prefer to be able to get at features by name if possible.  And for
that matter, if I wanted to get at them by Eval or Lab, I'm not sure what
would do that at all. 

 

Thanks for any suggestions you can make --

 

-Allen

 

Allen Gathman

http://cstl-csm.semo.edu/gathman