[Bioperl-l] Entrez Gene parser questions
mingyi.liu at gpc-biotech.com
Thu Jun 2 12:59:28 EDT 2005
Stefan's more familiar with the requirements of entrezgene.pm. Based on
my experience installing entrezgene.pm for bioperl 1.5 (I don't have
1.4) there's no need for a util.pm. I suspect the reason why you
mentioned a util.pm was that previously my Bio::ASN1::EntrezGene needed
a util.pm, but that was eliminated since V1.02 or so and before
Bio::ASN1 space was created on CPAN. Maybe Stefan had not updated the
documentation to reflect this change?
You do need to install Bio::ASN1::EntrezGene first, then copy both the
entrezgene.pm and the latest Bio::Annotation::DBLink from bioperl CVS
since entrezgene.pm uses the url() in DBLink, which is not present in
even bioperl 1.5. For me, I also had to do a force install
Grapha::Directed, but that might not be a problem for you if your system
already has it (my bioperl installation was old and incomplete before).
Law, Annie wrote:
>I would appreciate help with the following. First of all, I would like to say it's great that a Entrez gene parser was written. I just have some questions to get me started.
>A) I already have bioperl 1.4 installed. I would like to know if I can install the Entrez gene parser and
>Stefan Kirov's entrezgene.pm with out reinstalling bioperl. If this is not advised then I would reinstall bioperl.
>I was going to 1. install the Bio::ASN1::EntrezGene module (perl Makefile.PL, make, make test, make install, etc...)
> 2. just take only the entrezgene.pm and util.pm file and put it in the appropriate directory
> (which util.pm shold I use?? I searched CPAN and got many results for util.pm
> is it Biblio::Util, Boulder::Util, or something else??)
>B) For each Entrez gene id how do I access the associated Unigene id, accession numbers, gene symbol, gene name,
>And GO IDs.
>Also, I have been looking at the code and the POD within it. Are there some other places that I can look for documentation?
>Thanks so much!!
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