[Bioperl-l] Bio::DB::GFF with additional information

Jason Stajich jason at bioperl.org
Wed Feb 18 06:26:16 UTC 2009

Alper -

When you have a feature you can get (or set) the tags for this type of  

# note, list context because this method returns a list
my ($height) = $f->get_tag_values('Peak_Height');

# or you can set it, and then use a Bio::DB::GFF store method to  
update the data in the database

There are also some Bio::DB::GFF specific method for getting and  
setting tags, forgetting what they are off the top of my head, but I  
encourage you to read the Bio::DB::GFF documentation, (perldoc  
Bio::DB::GFF) or link to the wiki page for this module and see the  
links to CPAN and our Pdoc generated HTML.  Lincoln as usual provides  
extensive documentation for his contributed modules.

Eventually you may want to take a look at Bio::DB::SeqFeature::Store  
which more properly implements GFF3, but for many purposes  
Bio::DB::GFF will be speedy and and just what you need.

On Feb 17, 2009, at 10:06 PM, Alper Yilmaz wrote:

> Hi Jason,
> Thanks for quick reply. I modified the ninth column but couldn't  
> figure out
> how to extract that information. If I have Peak_Height information  
> in 9th
> column for gene locations gff file, how do I get that particular  
> peak height
> after I select the segment by:
> my $segment=$db->segment('gene1');
> Same goes for the score column, if I had utilized it, how do I  
> retrieve the
> data in that column?
> thanks,
> Alper Yilmaz
> Post-doctoral Researcher
> Plant Biotechnology Center
> The Ohio State University
> 1060 Carmack Rd
> Columbus, OH 43210
> (614)688-4954
> On Wed, Feb 18, 2009 at 12:24 AM, Jason Stajich <jason at bioperl.org>  
> wrote:
>> if it is a single data point you want to include you can use the  
>> score
>> column for GFF, if you want to store more complicated data you can  
>> just add
>> that to the ninth column, like (if using GFF3 - slightly different  
>> format if
>> you are using GFF2)
>> ID 
>> =Probe_ax102242;ArrayProbeVersion=2;Experiment1=0.30;Experiment2=0.40
>> The Gbrowse tutorial at GMOD site should give you some better  
>> examples.
>> -jason
>> On Feb 17, 2009, at 8:42 PM, Alper Yilmaz wrote:
>> Hi,
>>> I am using Bio::DB::GFF so that I can overlay data from different  
>>> sources.
>>> Currently, I'm uploading a GFF file to database whenever I want to  
>>> add new
>>> data. I was wondering is there a way to keep not only start-end  
>>> location
>>> of
>>> features but also their "level" data (such as expression level, e- 
>>> value,
>>> peak heght). In other words, can I integrate a non-GFF formatted  
>>> data with
>>> an existing database created by Bio::DB::GFF?
>>> thanks,
>>> alper
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> Jason Stajich
>> jason at bioperl.org

Jason Stajich
jason at bioperl.org

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