[Bioperl-l] Entrez Gene ASN.1 solution

[Stefan Kirov]

Colin,
$seq->(_status} will give you the status of the gene (reviewed, 
withdrawn, etc.) It is not supposed to be accessed like that, but this 
parser is not finished yet, so it may move as a part of the annotation 
(and most probably will).
$seq->desc will give you naturally the description (or summary)
To get the refereneces do:

$ann      = $seqobj->annotation();
foreach my $ref ( $ann->get_Annotations('reference') ) {
	print "Reference ",$ref->pubmed,"\n"; (or  $ref->medline)    
}
To get the accession numbers you will have to get the both the Bio::Seq and Bio::Cluster object. 
In it you will have Bio::Seq objects and you should get the accession_number or the id (accession number is actually the gi).
Next week I will submit some significant changes+more documentation so you may want to wait a bit...
Stefan



Colin Erdman wrote:

>I would very much like to give this a shot. My current project is being held up because of ASN.1 parsing issues. BioPerl is new to me, and an intuitive parsing module would be great. Mark I posted the CVS instructions that I received from Stefan Kirov yesterday (below).
>
> 
>
>Stefan: I have been using your entrezgene parser from bioperl-live and I like it a lot. I am just trying to figure out a few things. 1) How do I select only genes from the entrezgene seq object that are current (have an official symbol, description etc)? I saved that output for all non-pseudogene Homo sapiens Chr21 genes (~370) in ASN format and I need to sift through that file. The only problem is that there seem to be all the ‘removed’ and withdrawn genes in the file so there are more than the 370 ‘current’ actually being parsed etc. 
>
>        2) How do I access the accession number lists and references for the gene objects? Is this just included in the uncaptured data or what Bio::Seq object or annotation object to I use to get to them?
>
> 
>
>Thanks again as always!
>
>Colin
>
> 
>
> 
>
>Stefan Kirov Wrote:
>
>>>>> 
>
>The example below shows how to login to the bioperl repository. To login 
>
>to other repositories simply alter the /home/repository/(project) 
>
>information.
>
> 
>
>    *cvs -d :pserver:cvs at cvs.open-bio.org <http://portal.open-bio.org/mailman/listinfo/bioperl-l>:/home/repository/bioperl login*
>
>    /when prompted, the password is 'cvs'/
>
> 
>
> 
>
>(4) Each project CVS repository can have many different packages 
>
>available for download. You may need to browse the web interface for a 
>
>bit to determine the packages of interest. After a successful login you 
>
>may "checkout" the project package you are interested in.
>
> 
>
>The following command should be executed as one line. The specific 
>
>example shows how to check out the primary bioperl codebase which is 
>
>contained in the "*bioperl-live*" package.
>
> 
>
>* cvs -d :pserver:cvs at cvs.open-bio.org <http://portal.open-bio.org/mailman/listinfo/bioperl-l>:/home/repository/bioperl checkout 
>
>bioperl-live
>
>then perl Makefile.PL and finally make install
>
>In order for this parser to work you need to get GI::Parser::Entrezgene 
>
>from sourceforge. You can get the address for this module from the perl 
>
>doc of entrezgene: perldoc Bio::SeqIO::entrezgene
>
>Stefan
>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
USA
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

"And the wars go on with brainwashed pride
For the love of God and our human rights
And all these things are swept aside"