[Bioperl-l] subsection of genbank file
Roy Chaudhuri
roy.chaudhuri at gmail.com
Fri Sep 18 10:43:29 UTC 2009
Hi Liam,
I just discovered your message, which has not yet been replied to. What
you require has been discussed in a recent thread:
http://bioperl.org/pipermail/bioperl-l/2009-August/031071.html
Try using trunc_with_features from Bio::SeqUtils:
my $sub_seqobj=Bio::SeqUtils->trunc_with_features($seqobj, 300, 2000);
Cheers.
Roy.
Liam Elbourne wrote:
> Hi All,
>
> Is there a method or methodology that will produce a fully fledged Seq
> object with all the associated metadata given a start and end
> position? To clarify, I create a sequence object from a genbank file:
>
>
> ****
> my $io = Bio::Seqio->new(as per usual);
>
> my $seqobj = $io->next_seq();
> ****
> I now want:
>
> my $sub_seqobj = $seqobj between 300 and 2000
>
> where $sub_seqobj is a Seq object (which I appreciate is an
> 'aggregate' of objects) too. The "trunc" method only returns a
> PrimarySeq object which lacks all the annotation etc. I've previously
> done this task by iterating through feature by feature and parsing out
> what I needed, but thought there might be a more elegant approach...
>
>
> Regards,
> Liam Elbourne.
--
Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.
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