[Bioperl-l] Entrez Gene parser

Stefan Kirov skirov at utk.edu
Fri Apr 8 20:08:58 EDT 2005

Thanks Hilmar. I think it's not (I think). It is on Sourceforge though. 
The link is in the entrezgene.pm doc. Mingyi, could you put it in CPAN? 
By the way there are 'fake' Entrez Gene records that do break the 
parser. They are designed, as far as I know, to hold GRIF data and I 
don't think they should be parsed at all. Maybe I will include a filter 
to look for those.
I will work on the parser after Tuesday, I need to work on my 
immigration stuff and it is not fun at all :-( .

Hilmar Lapp wrote:

> 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?
>     -hilmar
> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list