[Bioperl-l] Entrez Gene parser questions

Stefan Kirov skirov at utk.edu
Wed Jun 8 23:01:11 EDT 2005 

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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