[Bioperl-l] Entrez Gene parser questions

Stefan Kirov skirov at utk.edu
Thu Jun 9 08:02:26 EDT 2005 

Brian,
I also agree on that, but I don't think there is a formal release coming 
soon, is there? Really, when is the next relase due?
Stefan

Brian Osborne wrote:

>Bioperl,
>
>  
>
>>Stefan and Mingyi should fix whatever is needed to silence those
>>warnings. (No offense please)
>>    
>>
>
>Yes, I should support Hilmar here. When we are working through the full test
>suite before a formal release our goal has always been to eliminate all
>errors *and* warnings, not just  errors.
>
>Brian O.
>
>
>On 6/8/05 10:28 PM, "Hilmar Lapp" <hlapp at gmx.net> wrote:
>
>  
>
>>Quite frankly, mixing versions in bioperl has never worked really well
>>and nobody really has time to support this, so I don't think it's good
>>advice to people to suggest plugging in single modules from a recent
>>version into an older one. Just update to current cvs and you should be
>>at a state where at least you're not totally on your own.
>>
>>As for the output, these are obviously warnings, and instead of asking
>>you to turn off -w (L.Wall: Known bugs: -w is not on by default.)
>>Stefan and Mingyi should fix whatever is needed to silence those
>>warnings. (No offense please)
>>
>>-hilmar
>>
>>On Jun 8, 2005, at 11:40 PM, 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
>>>
>>>Mingyi Liu wrote:
>>>
>>>      
>>>
>>>>Hi, Annie
>>>>
>>>>Annie must've been using the Bio::ASN1::EntrezGene V1.09, which worked
>>>>fine with your entrezgene.pm in bioperl-live at least a couple days
>>>>ago, when I replied to Annie.  V1.09 also did not have any significant
>>>>changes in parser code vs. 1.07.
>>>>
>>>>I guess it has something to do with V1.4 since the sample script you
>>>>used below runs perfectly fine on my Bioperl 1.5 + entrezgene.pm.  The
>>>>procedure you used was also correct (there's no need to 'use
>>>>Bio::ASN1::EntrezGene;' though).  Try follow Stefan's suggestion first
>>>>(although I don't quite understand why Bio::ASN1::EntrezGene
>>>>complained about non numerica operon, which can only result from
>>>>incorrect calling of the function.  But Stefan's entrezgene was using
>>>>correct calling and it runs perfectly for me.  I was using
>>>>entrezgene.pm CVS version 1.9.
>>>>
>>>>Keep us posted on your progress.
>>>>
>>>>BTW, Stefan, you could call Bio::ASN1::EntrezGene with either '-file'
>>>>(bioperl style) or 'file' (I allowed both when I implemented this
>>>>switch I think. I usually just use file, which might explain your note
>>>>in the comment in your script.  I just noticed the comment.
>>>>
>>>>Mingyi
>>>>
>>>>Stefan Kirov wrote:
>>>>
>>>>        
>>>>
>>>>>Hi Annie,
>>>>>Few more things to update:
>>>>>Bio::AnnotatableI and Bio::SeqFeatureI.  I believe this is the reason
>>>>>your script does not work. Update also Bio::SeqIO::entrezegene- I
>>>>>added some fixed so you will not see those nasty warning when using
>>>>>strict (nothing critical though).
>>>>>I am not sure we have the same versions for Bio::ASN1::EntrezGene. I
>>>>>have 1.0.7. Where did you get it from (maybe mine is older)?
>>>>>Stefan
>>>>>
>>>>>Law, Annie wrote:
>>>>>
>>>>>          
>>>>>
>>>>>>Hi,
>>>>>>
>>>>>>Thanks for all of the replies.
>>>>>>I am using bioperl 1.4 and I have done the following:
>>>>>>1. installed  Bio::ASN1::EnztrezGene (using perl Makefile.PL, make,
>>>>>>make test, make install)
>>>>>>2. got a copy of the entrezgene.pm from bioperl-live and put it in
>>>>>>the Bio/SeqIO directory
>>>>>>3. copied the Bio::Annotation::DBLink DBLink.pm file and put them in
>>>>>>the corresponding directory
>>>>>>4. the Bio::Cluster::SequenceFamily file was already up to date
>>>>>>5. also have all the most recent bioperl-live Bio::SeqFeature::Gene
>>>>>>modules
>>>>>>
>>>>>>I grabbed the ASN file from
>>>>>>ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN/Mammalia/
>>>>>>
>>>>>>I then wrote a simple perl script which includes:
>>>>>>
>>>>>>#!/usr/bin/perl -w
>>>>>>
>>>>>>use strict;
>>>>>>use Bio::ASN1::EntrezGene;
>>>>>>use Bio::SeqIO;
>>>>>>use Bio::Annotation::DBLink;
>>>>>>use Bio::Cluster::SequenceFamily;
>>>>>>
>>>>>>my $file = '/var/lib/mysql/Homo_sapiens';
>>>>>>
>>>>>>my $seqio = Bio::SeqIO->new(-format => 'entrezgene',
>>>>>>                              -file => $file,
>>>>>>                              -debug => 'on');
>>>>>>
>>>>>>my ($gene,$genestructure,$uncaptured) = $seqio->next_seq;
>>>>>>
>>>>>>After I run this script I get the following errors:
>>>>>>
>>>>>>Useless use of hash element in void context at
>>>>>>/usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 317.
>>>>>>
>>>>>>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 148.
>>>>>>
>>>>>>Use of uninitialized value in string ne at
>>>>>>/usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 150.
>>>>>>
>>>>>>Pseudo-hashes are deprecated at
>>>>>>/usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/entrezgene.pm line 416.
>>>>>>
>>>>>>Can't locate object method "add_tag_value" via package
>>>>>>"Bio::SeqFeature::Generic" at
>>>>>>/usr/lib/perl5/site_perl/5.8.0/Bio/SeqFeature/Generic.pm line 234.
>>>>>>
>>>>>>I'm not sure what I am missing?
>>>>>>
>>>>>>Thanks so much,
>>>>>>Annie.
>>>>>>            
>>>>>>
>>>>>          
>>>>>
>>>>        
>>>>
>>>_______________________________________________
>>>Bioperl-l mailing list
>>>Bioperl-l at portal.open-bio.org
>>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>      
>>>
>
>
>  
>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
USA
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

"And the wars go on with brainwashed pride
For the love of God and our human rights
And all these things are swept aside"

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