[Bioperl-l] Entrez Gene parser questions
Law, Annie
Annie.Law at nrc-cnrc.gc.ca
Wed Jun 8 12:01:52 EDT 2005
Hi Stefan,
I commented out the use strict and I think I got the same output.
Here's what I got.
Thanks,
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: Wednesday, June 08, 2005 11:53 AM
To: Law, Annie
Cc: Mingyi Liu; Bioperl list
Subject: Re: [Bioperl-l] Entrez Gene parser questions
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
>
>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.
>>>>
>>>>
>>>
>>>
>>
>>
--
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
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For the love of God and our human rights
And all these things are swept aside"
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