[Bioperl-l] Get a partial GenBank of a circular DNA

[Roy Chaudhuri]

Hi Roi,

You need the trunc_with_features and cat methods in Bio::SeqUtils 
(haven't tested this code but I think it should work):

use Bio::SeqIO;
use Bio::SeqUtils;
my $seq=Bio::SeqIO->new(-file=>$ARGV[0], -format=>'genbank')->next_seq;
my $first=Bio::SeqUtils->trunc_with_features($seq, 800000, 1000000);
my $second=Bio::SeqUtils->trunc_with_features($seq, 1, 100000);
Bio::SeqUtils->cat($first, $second);
Bio::SeqIO->new(-format=>'genbank')->write_seq($first);

Cheers.
Roy.

On 16/06/2010 08:10, Roi Brodo wrote:
>
> Hello,
>
>
>
> Suppose I have some circular DNA RefSeq in a Genbank format. I would
> like to create a new (smaller) Genbank file (both features and sequence)
>   containing only a range of nucleotides from the original file, but a
> range tha overlaps the "end". For example, if my original Genbank spans
> 1,000,000 base (1-1,000,000) I would like to get join(800,000-1,000,000,
>   1-100,000), so the new Genbank file will actually contain 300,000 bp
> from the circular DNA.
>
>
>
> How can I do that? Again, my input is a Genbank file and output should
> also be a Gebnank file.
>
>
>
> Thanks!
>
> - Roi
>
>
>
>
>
>
>
>
>
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