[Bioperl-l] Genbank files

[BForde]

Than you for the replies.

I am unsure as to how to use the line below with my script. My script so far
reads

use strict;
use Bio::SeqIO;

my @V;
open (LIST1, 'list') ||die;
while (<LIST1>){
    push @V, (split(/\t/, $_))[0];
}
close(LIST1);

my $seqio_object = Bio::SeqIO->new(-file=>"Contig100.gb");
my $seq_object = $seqio_object->next_seq;

for my $feat_object ($seq_object->get_SeqFeatures){
    if ($feat_object->primary_tag eq "CDS"){
        if ($feat_object->has_tag('locus_tag')){
            for my $V3 ($feat_object->get_tag_values('locus_tag')){
                for my $V1 (@V) {
                    if ($V1 eq $V3){
                        ADD NEW FEATURES
                        
                    }    
                }
            }
        }
    }
}
 
The script works down as far as the comparison point where locus_tags in the
genbankfile "Contig100.gb" are compared against a list of locus_tags from a
delimited txt file.
I possbile could you show me how to amend my script so I can add new
features

regards

Brian

Jason Stajich-5 wrote:
> 
> $feature->add_tag_value('color','blue');
> 
> On Dec 9, 2011, at 8:52 AM, BForde wrote:
> 
>> 
>> Hello all,
>> 
>> I am new to Bioperl so I apologise if this is stupid question. 
>> 
>> For CDS features I which to add additional qualifiers e.g. /colour and
>> /note
>> qualifiers. I have looked at the BioPerl wiki but am still unsure as how
>> to
>> do this?
>> 
>> regards
>> 
>> Brian
>> -- 
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>> 
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> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
> 
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