[Bioperl-l] Entrez Gene parser questions

Mingyi Liu 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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