[Bioperl-l] getting DNA sequence for exon features from GFF

[Frank Schwach]

Hi Kammani,

While GFF files may contain DNA sequence data, most of them don't, so
you will have to use the location information you get from the GFF
annotation file in conjunction with, e.g., a local FASTA database of the
genomic sequence you are working with or an online resource.


Frank



On Thu, 2010-08-26 at 01:29 -0700, kanmani radha wrote:
> Hi All,
> I would like to get the DNA seq from GFF file. I'm using Bio::Tools::GFF
> module. I could get everything else but not the DNA seq.
> 
> Can anyone help me to find this out, Please. I appreciate your help very
> much.
> thanks,
> Kanmani
> 
> #!/usr/bin/perl
> 
> use strict;
> use warnings;
> use Bio::Tools::GFF;
> 
> my $file = shift;
> 
> my $gffio = Bio::Tools::GFF->new(-file => $file, -gff_version => 3);
> $gffio->features_attached_to_seqs(1);
> 
> while (my $feat = $gffio->next_feature()){
>     my $start = $feat->start;
>     my $end= $feat->end;
>     my $size = $end-$start+1;
>     my $strand = $feat->strand;
>     my $seqid = $feat->seq_id;
>     my $score = $feat->score;
>     my $frame = $feat->frame;
>     my $source = $feat->source_tag;
>     my $type = $feat->primary_tag;
>     my $gffstr = $gffio->gff_string($feat);
>     my @alltags = $feat->all_tags();
>     my @ID_tag_value = $feat->each_tag_value("ID");
> 
>     my  $seq = $feat->seq();
>     print "$seq\n";
> 
>      if($type eq "gene"){     #
>        print "@ID_tag_value\t$size\t$type\t$start\t$end\n";
>     }
> }
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