[Bioperl-l] Entrez Gene parser questions
mingyi.liu at gpc-biotech.com
Wed Jun 8 16:44:30 EDT 2005
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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