Question: Fetch mRNA sequence from mysql database using Bio::DB::SeqFeature::Store
0
gravatar for firoz.imtech
5.4 years ago by
firoz.imtech50
United States
firoz.imtech50 wrote:

I have uploaded genomic fasta sequence and GFF3 file into local mysql database using "bp_seqfeature_load.pl". Now, I want to extract sequence from position 8966215-8966961 on "+" strand of Chromosome I, and print only the mRNA transcript segment between 8966215-8966961. If there are many isoforms found between these position, print each isoform sequences with name and position as fasta format. Could you please tell me what is the best approach to do it for it. My code does not work well. Thanks

 

#!/user/bin/perl
use strict;
use warnings;
use Bio::Seq;
use Bio::SeqIO;
use Bio::SeqFeatureI;
use Bio::DB::SeqFeature::Store;
use Bio::DB::SeqFeature::Segment;

my @features;
my $db = Bio::DB::SeqFeature::Store->
    new(-adaptor=> 'DBI::mysql',
        -dsn=> '..',
        -user=> '..',
        -pass=> '..',
    );


my @foo = $db->features(-seq_id =>'I',-start=>'8966215',-end=>'8966961', -strand =>'+1',
                        -type => 'mRNA',
                            );

for my $f(@foo){

    print ">",$->name,"_",$f->start,"_",$f->end,"\n";
    print $f->dna,"\n";

}

exit;

 

genome sequence assembly gene • 1.7k views
ADD COMMENTlink written 5.4 years ago by firoz.imtech50
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