[Bioperl-l] Entrez Gene parser

Brian Osborne brian_osborne at cognia.com
Thu Apr 7 14:26:56 EDT 2005


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.
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