[Bioperl-l] Entrez Gene parser questions
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:
> 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.
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