[Bioperl-l] Entrez Gene ASN.1 solution

Colin Erdman cerdman2 at du.edu
Wed Apr 13 15:16:45 EDT 2005

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'removed' and withdrawn genes in the file so there are more than the 370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!
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) 
    *cvs -d :pserver:cvs at cvs.open-bio.org
:/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
:/home/repository/bioperl checkout 
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


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