[Bioperl-l] Entrez Gene parser

Stefan Kirov skirov at utk.edu
Thu Apr 7 14:57:25 EDT 2005

No. That was also Hilmar's concern. So I followed his advice to use 
wantarray, so if you do

$so = $eg->next_seq; 
you get get only one Bio::Seq object,
but if you do 
my ($gene,$gstruct,$uncapt)=$eg->next_seq;

you get everything. Actually this is in the documentation, though it is 
pretty sketchy right now.

Brian Osborne wrote:

>I'm concerned about people using next_seq() in the standard way:
>$so = $eg->next_seq;
>They'll be expecting a Seq object but getting that "uncaptured" information,
>Brian O.
>-----Original Message-----
>From: bioperl-l-bounces at portal.open-bio.org
>[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Stefan Kirov
>Sent: Thursday, April 07, 2005 1:51 PM
>To: Bioperl
>Subject: [Bioperl-l] Entrez Gene parser
>I commited the entrez gene parser code so people can start playing with
>it if they like and send me any notes, requests and bugs. I know that
>sometimes specie description can break the code and I am checking if
>this is due to the GI::Parser::EntrezGene or it is my fault.
>Things that are still on my To do list (in this order):
>1. convert the seq record to allow back compatibility with the previous
>locuslink parser. The tags entrezgene uses are different from those ll
>had, so some renaming needs to be done.
>2. STS Markers are not in the record yet
>3. Optimize the code to speed it up where possible
>4. Check the specie bug
>5. Fix the cycle reference in Transcript and remove the undef
>$transcript->{parent} from the parser code
>Please let me know if you have any notes or requests!
>Negative comments appreciated as well.
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
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"

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