[Bioperl-l] parsing entrezgene file (lost data)

[Smithies, Russell]

Bio::ASN1::EntrezGene is not the easiest to work with but you can access everything if you try hard enough.
I used it last year from transforming ASN.1 gene records from NCBI into fully annotated Wiki pages and it was very successful though I got sick of typing so many curly brackets ;-)


--Russell


> -----Original Message-----
> From: carandraug at gmail.com [mailto:carandraug at gmail.com] On Behalf Of
> Carnë Draug
> Sent: Wednesday, 6 July 2011 10:16 a.m.
> To: Smithies, Russell
> Cc: bioperl mailing list
> Subject: Re: [Bioperl-l] parsing entrezgene file (lost data)
> 
> On 5 July 2011 22:55, Smithies, Russell
> <Russell.Smithies at agresearch.co.nz> wrote:
> > It is in there, just takes a bit of getting at.
> > Frequent use of Data::Dumper to work out where you are helps.
> >
> >
> >
> > use warnings;
> > use strict;
> > use Bio::ASN1::EntrezGene;
> > use Data::Dumper;
> >
> > my $parser = Bio::ASN1::EntrezGene->new('file' => "entrezgene.asn");
> > while(my $result = $parser->next_seq){
> >    $result = $result->[0] if(ref($result) eq 'ARRAY');
> >    foreach my $l (@{$result->{locus}}){
> >        foreach my $p (@{$l->{products}}){
> >
> >          my $nuc_gi = $p->{seqs}->[0]->{whole}->[0]->{gi};
> >          my $nuc_acc = $p->{accession};
> >
> >          my $prot_gi = $p->{products}->[0]->{seqs}->[0]->{whole}-
> >[0]->{gi};
> >          my $prot_acc = $p->{products}->[0]->{accession};
> >
> >          print "$nuc_gi, $nuc_acc\t$prot_gi, $prot_acc \n";
> >        }
> >    }
> > }
> >
> 
> Hmm.. I see it now but it's still not there when using the Bio::SeqIO
> module (I just tried with Bio::ASN1::EntrezGene as in your example and
> I can see it now). I thought that using the specific module was not
> recommended.
> 
> I just cloned the bioperl repo but the modules code is too much for
> me. It seems that Bio::SeqIO uses the Bio::SeqIO::entrezgene module
> instead of Bio::ASN1::EntrezGene . But then Bio::SeqIO::entrezgene
> does use Bio::ASN1::EntrezGene on the initializing method (this is the
> line from the module code)
> 
>     $self->{_parser} = Bio::ASN1::EntrezGene->new( file => $param{-
> file} );
> 
> So I have no idea what's wrong. Still, it's nice to have a workaround
> for now. Thank you,
> 
> Carnë
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