[Bioperl-l] Write features in a gbk

[Hilmar Lapp]

Bio::SeqIO->new() creates a Bio::SeqIO object, not a Bio::Seq object.
Bio::SeqIO is for writing (or reading) sequence objects to/from a file.

If you want to add a feature object to a sequence object, create the
sequence object.

  -hilmar


On Wed, Mar 5, 2014 at 8:36 PM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:

> Hi,
>
> I want to write some features to generate a new gbk file. I try like this:
> #!/usr/bin/perl
>
>
>
> use Bio::Seq;
> use Bio::SeqIO;
> use Bio::SeqFeature::Generic;
>
>
> $feat = new Bio::SeqFeature::Generic(-start   => 40,
>                                        -end     => 80,
>                                        -strand  => 1,
>                                        -primary => 'exon',
>                                        -source  => 'internal' );
>
> $seqobj = Bio::SeqIO->new(-file => '>test.gbk', -format => 'genbank');
> $seqobj->add_SeqFeature($feat); # Add the SeqFeature to the Seq object
>
> But I got this error:
> Can't locate object method "add_SeqFeature" via package
> "Bio::SeqIO::genbank" at ./annotation.pl line 17.
>
> Thank!
>
>
>
>
>
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-- 
Hilmar Lapp -:- lappland.io