[Bioperl-l] Entrez Gene parser questions

[Sean Davis]

Just for reference, I am using CVS bioperl-live, Bio::ASN1::entrezgene 
1.09 without any difficulty.

Sean

On Jun 8, 2005, at 11:52 AM, Stefan Kirov wrote:

> Annie,
> Can you just disable use strict for now and tell me again what you see?
> Stefan
>
> Law, Annie wrote:
>
>> Hi,
>> I went to bioperl-live and copied the newest entrezgene.pm and 
>> Bio::AnnotatableI, Bio::SeqFeatureI modules and
>> I got the following output (same output with entrezgene.pm saved on 
>> May 11 as well).  The complaint about the module Generic.pm is gone 
>> now.
>> I am using EntrezGene V 1.09 picked up from CPAN.
>>
>> I'm not sure what is wrong.  I guess I could delete the Bio/ASN1 
>> directory and install EntrezGene V.1.07 but that is not supposed to 
>> make a difference?
>> Here's a wild stab but are the additional messages related to a 
>> statement I read somewhere about the first record being empty?
>>
>> Is my next alternative to install Bioperl 1.5 and try again? If so, 
>> am I correct in thinking that to 'uninstall' there is no such
>> Uninstall command but I would just delete the 
>> /usr/lib/perl5/site_perl/5.8.0/Bio  ie. The Bio directory and then
>> Use CPAN to install bioperl 1.5
>>
>> Thanks so much,
>> Annie.
>>
>>
>> Argument "-trimopt" isn't numeric in numeric eq (==) at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/ASN1/EntrezGene.pm line 450.
>> Pseudo-hashes are deprecated at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 416.
>> Use of uninitialized value in string eq at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 543.
>> Use of uninitialized value in string eq at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 554.
>> Use of uninitialized value in substitution (s///) at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 555.
>> Use of uninitialized value in string eq at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 554.
>> Use of uninitialized value in substitution (s///) at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 555.
>> Pseudo-hashes are deprecated at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 416.
>> Use of uninitialized value in string eq at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 604.
>> Use of uninitialized value in string eq at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 604.
>> Use of uninitialized value in string eq at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 604.
>> Use of uninitialized value in string eq at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 295.
>> Use of uninitialized value in string eq at 
>> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 323.
>>
>>
>> -----Original Message-----
>> From: Stefan Kirov [mailto:skirov at utk.edu] Sent: Tuesday, June 07, 
>> 2005 8:39 PM
>> To: Mingyi Liu
>> Cc: Law, Annie; Bioperl list
>> Subject: Re: [Bioperl-l] Entrez Gene parser questions
>>
>>
>> I am pretty sure it is the old Bio::SeqFeature::Generic that breaks 
>> the code (actually the underlying modules I mentioned...).
>> Thanks for the -file option... There are also some leftover commenst 
>> :-) . I need to clean the code a bit...
>> Stefan