[Bioperl-l] Add sequence feature

Cook, Malcolm MEC at stowers.org
Fri Aug 13 13:37:50 EDT 2010


Jessica,

Show more code!

In particular, where did $f get set?

--Malcolm

 

-----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 12:07 PM
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_Ow
>> n_Sequences
>>
>>            (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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