[Bioperl-l] Entrez Gene parser questions

Brian Osborne brian_osborne at cognia.com
Thu Jun 9 07:53:44 EDT 2005 

Stefan,

Of course you're right. There are no deadlines and your efforts in this
regard are very much appreciated, by all.

Brian O.


On 6/8/05 11:01 PM, "Stefan Kirov" <skirov at utk.edu> wrote:

> Hilmar Lapp 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.
> 
> Agree, but there may be a need for a transitional period. Annie, why do
> you need bioperl 1.4? Is there something that lacks backcompatibility? I
> think in general most modules try to provide such...
> 
>> 
>> 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)
> 
> None taken. But this is not even a developer's release and I believe
> such bugs are usual and normal (as long as they are not there for ever).
> I am creating tests and I will fix the warnings when I commit these, but
> I believe there are no deadlines I am missing. Please correct me if I am
> wrong and I can probably spend some more time fixing the warnings
> produced by entrezgene parser.
> Overall I don't believe it is a bad idea for people to explore
> particular code without strict (provided this does not go into
> production). That's why the term 'unstable'  exists, does it not?
> Stefan
> 
>> 
>>     -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.
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
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> 
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