[Bioperl-l] Entrez Gene parser

Hilmar Lapp hlapp at gnf.org
Fri Apr 8 19:50:10 EDT 2005

Cool, thanks for your work Stefan. I'll be sure to check this out. Is 
Mingyi's parser that presumably you're using on CPAN already?


On Apr 7, 2005, at 10:50 AM, Stefan Kirov wrote:

> 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.
> Thanks!
> Stefan
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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