[Bioperl-l] Fwd: Add sequence feature

Cook, Malcolm MEC at stowers.org
Fri Aug 13 15:56:09 EDT 2010


if you want to show all your code we might not have to guess at what the problem is.....
 


Malcolm Cook
Stowers Institute for Medical Research -  Bioinformatics
Kansas City, Missouri  USA
 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jessica Sun
Sent: Friday, August 13, 2010 2:17 PM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Fwd: Add sequence feature

---------- Forwarded message ----------
From: Jessica Sun <jessica.sun at gmail.com>
Date: Fri, Aug 13, 2010 at 3:16 PM
Subject: Re: [Bioperl-l] Add sequence feature
To: Kevin Brown <Kevin.M.Brown at asu.edu>


yes, I change that, somehow it still did not take the added features in.


On Fri, Aug 13, 2010 at 1:53 PM, Kevin Brown <Kevin.M.Brown at asu.edu> wrote:

> If I'm reading your sample code correctly, then you are mistakenly 
> trying to output the input SeqIO object and not the actual Bio::Seq 
> object that was read in by SeqIO.
>
> My $seqio = Bio::SeqIO->new;
> My $seq = $seqio->next_seq;
>
> #manipulate $seq
>
> My $out = Bio::SeqIO->new;
> $out->write_seq($seq);
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jessica Sun
> Sent: Friday, August 13, 2010 10:07 AM
> To: Roy Chaudhuri
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Add sequence feature
>
> Thanks. I somehow get these error messages.
>
> --------------------- WARNING ---------------------
> MSG:  Bio::SeqIO::genbank=HASH(0xa7ba1c) is not a SeqI compliant module.
> Attempting to dump, but may fail!
> ---------------------------------------------------
> Can't locate object method "seq" via package "Bio::SeqIO::genbank" at 
> /Library/Perl/5.8.8/Bio/SeqIO/genbank.pm line 760, <GEN0> line 447.
>
> by doing this,
>
> my $feat = new Bio::SeqFeature::Generic(-start                 =>20,
>                                        -end         => $40,
>                                        -primary_tag => 'newfeature' );
>                                    $feat->add_tag_value("note","this 
> is notes");  $f->add_SeqFeature($feat); ## f is original feature 
> pointer $io = Bio::SeqIO->new(-format => "genbank", -file => 
> ">$newoutfile" );
>
>    $io->write_seq($seqio_object);
>
> On Fri, Aug 13, 2010 at 11:57 AM, Roy Chaudhuri
> <roy.chaudhuri at gmail.com>wrote:
>
> > Please remember to copy replies to the mailing list.
> >
> > You can loop over the features in your Bio::Seq object:
> > for my $feat ($seq->get_SeqFeatures) { # do something }
> >
> > And once you have found the feature you want to modify, you can add 
> > a
> tag
> > using something like:
> > $feat->add_tag_value('note',"this is a note");
> >
> > When you're finished you can write out the modified sequence object 
> > to
> a
> > new GenBank file.
> >
> >
> > On 13/08/2010 16:40, Jessica Sun wrote:
> >
> >> no i want to load the genbank file with existing features and I 
> >> need
> to
> >> add some new feature tags to the existing ones and then save to a 
> >> new update genbank file for local usage. I just not quite good on 
> >> how to easily merge the two steps you recommended into one in a neat way.
> >>
> >> thx
> >>
> >>
> >> On Fri, Aug 13, 2010 at 11:37 AM, Roy Chaudhuri
> <roy.chaudhuri at gmail.com
> >> <mailto:roy.chaudhuri at gmail.com>> wrote:
> >>
> >>    I'm not sure I understand, do you mean that you want to load just
> >>    the sequence from the GenBank file (ignoring the existing
> >>    annotation), then add your own features? There are instructions on
> >>    how to do that here:
> >>
> http://www.bioperl.org/wiki/HOWTO:SeqIO#Speed.2C_Bio::Seq::SeqBuilder
> >>
> >>
> >>    On 13/08/2010 16:27, Jessica Sun wrote:
> >>
> >>        unfortunately. I want to add the feature to the sequence
> object
> >>        I got
> >>        from the Genbank file, I do not mind to save a new genbank
> file but
> >>        these new genbank file contains the original genbank format
> and
> >>        info I
> >>        got plus the new feature tags I need to added to. Any quick
> >>        solution to
> >>        this?
> >>
> >>        thx
> >>
> >>        Jessica
> >>
> >>
> >>
> >>        On Fri, Aug 13, 2010 at 11:21 AM, Roy Chaudhuri
> >>        <roy.chaudhuri at gmail.com <mailto:roy.chaudhuri at gmail.com>
> >>        <mailto:roy.chaudhuri at gmail.com
> >>        <mailto:roy.chaudhuri at gmail.com>>> wrote:
> >>
> >>            Hi Jessica.
> >>
> >>            You need to use Bio::SeqIO to read in the GenBank file 
> >> to
> a
> >>        BioPerl
> >>            sequence object, and to write your new GenBank file:
> >>        http://www.bioperl.org/wiki/HOWTO:SeqIO
> >>
> >>            To add a new feature follow the instructions here:
> >>
> >>
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Building_Your_Own
> _S
> equences
> >>
> >>            (except that you are adding the feature to the sequence
> >>        object you
> >>            got from the Genbank file, not a new Bio::Seq object).
> >>
> >>            Cheers.
> >>            Roy.
> >>
> >>
> >>            On 13/08/2010 16:06, Jessica Sun wrote:
> >>
> >>                Does anyone knows how to open a genbank file, add new
> >>        feature
> >>                and then save
> >>                a new genbank
> >>                file with new feature added in bioperl ?
> >>
> >>                thx
> >>
> >>
> >>
> >>
> >>
> >>        --
> >>        Jessica Jingping Sun
> >>
> >>
> >>
> >>
> >>
> >> --
> >> Jessica Jingping Sun
> >>
> >
> >
>
>
> --
> Jessica Jingping Sun
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--
Jessica Jingping Sun



-- 
Jessica Jingping Sun
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