[Bioperl-l] Bio::DB::GFF::Segment trouble

[Rhazes Spell]

I am having trouble getting a list of features from a segment in my 
database.  I can pull out all of the features, but I can not limit the 
features returned to a specific range.  Following is a code excerpt and 
output.  Any assistance that you can provide would be great!

CODE:
my @segment = $db->segment(-name => 'amata',
			   -start => 1,
			   -end => 40000);
	
foreach my $segment (@segment) {
     my($start,$end) = ($segment->start,$segment->end);

#Some debug info cuz I don't get it yet

     print "\n*** Segment= ",$segment->asString();
     print " Seg Source= ",$segment->sourceseq,"\t";
     print "Reference= ",$segment->ref,"\t";
     print "Abs Start= ",$segment->abs_start," :: ";
     print "Abs End= ", $segment->abs_end,"\n";

#Change the coordinate system to absolute if necessary
     $segment->absolute(1) if (!($segment->sourceseq eq $segment->ref));
     my @f = $segment->features(-types => ['similarity:blastn'],
			      -rangetype => 'contained_in');

     foreach my $feat (@f) {
	print "\n\t",$feat->gff_string(),"\n";
	print "-Target == ";
	foreach ($feat->get_tag_values("Target")) {
	    print $_;
	}
	print "\n-description == ";
	foreach ($feat->get_tag_values("description")) {
	    print $_,"\n";
	}
     }
}

OUTPUT:: (## = Added comment)

*** Segment= amata:1,40000 Seg Source= amata    Reference= amata        
Abs Start= 1 :: Abs End= 40000
##This is the main segment and it should not have any blast 
similarities.

*** Segment= amata:1,40000 Seg Source= amatalpha        Reference= 
amata        Abs Start= 14584 :: Abs End= 54583
## These are blast hits that have a hit on my segment.  I only want the 
hits that occur between 1 and 40000 on
##  the segment, amata
##  I have 2 questions:
## 1: Why are there any hits included with 'Target "Sequence:amata" 
start stop' where start or start is > 40000?
## 2: Why can't I access the members of the Target attribute tag as I 
can the description tag.
## Output follows


         amatalpha       blastn  similarity      14584   14713   
0.832061        +       .       Target "Sequence:a
mata" 41056 41186 ; description "upstream of CAP1 - downstream of CAP1"
-Target ==
-description == upstream of CAP1 - downstream of CAP1

         amatalpha       blastn  similarity      18722   18774   
0.907407        +       .       Target "Sequence:a
mata" 33568 33621 ; description "downstream of SPO14 - downstream of 
SPO14"
-Target ==
-description == downstream of SPO14 - downstream of SPO14

         amatalpha       blastn  similarity      19199   19283   
0.905882        +       .       Target "Sequence:a
mata" 34087 34171 ; description "downstream of SPO14 - downstream of 
SPO14"
-Target ==
-description == downstream of SPO14 - downstream of SPO14

         amatalpha       blastn  similarity      24823   24922   0.83    
+       .       Target "Sequence:amata" 39
695 39794 ; description "upstream of RPL22 - downstream of CAP1"
-Target ==
-description == upstream of RPL22 - downstream of CAP1

         amatalpha       blastn  similarity      25099   25150   
0.923077        +       .       Target "Sequence:a
mata" 39971 40022 ; description "upstream of RPL22 - downstream of CAP1"
-Target ==
-description == upstream of RPL22 - downstream of CAP1



Thanks,
Rhazes

**************************************
Duke University
Department of Biomedical Engineering
Duke University Medical Center,
  Center for Genome Technology

919.684.2720 (lab)
***************************************