[Bioperl-l] Genbank files

[Smithies, Russell]

Something like this:

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
                        $feat_object->add_tag_value('color','blue');
                    }
                }
            }
        }
    }
}
#write the new annotations
my $io = Bio::SeqIO->new(-format => "genbank", -file => ">new.gb" );
$io->write_seq($seq_object);

Take another look at http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Building_Your_Own_Sequences

--Russell




> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of BForde
> Sent: Tuesday, 13 December 2011 6:21 a.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Genbank files
> 
> 
> 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
> >> --
> >> View this message in context:
> >> http://old.nabble.com/Genbank-files-tp32941955p32941955.html
> >> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Jason Stajich
> > jason.stajich at gmail.com
> > jason at bioperl.org
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> 
> --
> View this message in context: http://old.nabble.com/Genbank-files-
> tp32941955p32959999.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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