[Bioperl-l] Entrez Gene parser questions

Stefan Kirov skirov at utk.edu
Wed Jun 8 16:50:05 EDT 2005

Sure. Thanks for letting me know.
Annie, does it work for you now?

Mingyi Liu wrote:

> Hi,
> Stefan's right in suggesting you turn off -w, which would make your 
> script work.  But thanks for finding this bug.  I just noticed that 
> entrezgene.pm was actually calling the Bio::ASN1::EntrezGene->next_seq 
> incorrectly (probably my documentation was a bit confusing & my module 
> did not follow standard hash-based parameter passing of subroutines).  
> It should be called like ->next_seq(1), but entrezgene.pm called using 
> ->next_seq(-trimopt => 1).  This worked for all of us who do not use 
> -w, as it would fall back to option '1' in my next_seq function 
> (exactly as Stefan's calling function wanted).  Therefore this bug 
> went unnoticed until you turned on -w (I guess we were all spoiled by 
> the easy (and sometimes messy) life of weak datatyping in Perl).
> Stefan would you please change the calling of next_seq to 
> next_seq(1)?  This would fix the error messages Annie was seeing.
> Thanks,
> Mingyi

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