[Bioperl-l] Entrez Gene parser questions
skirov at utk.edu
Tue Jun 7 20:38:53 EDT 2005
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...
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.
> 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)?
>> Law, Annie wrote:
>>> 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
>>> I grabbed the ASN file from
>>> 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,
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