[Bioperl-l] How (from where) to retrieve FieldInfo objects?

[Smithies, Russell]

How about just returning ASN.1 then parsing that?
There's far more data in that format than any of the others.

my $factory = Bio::DB::EUtilities->new(-eutil      => 'esearch',
                                       -term       => 'h2afx[sym] AND human[organism]',
                                       -db         => 'gene',
						   -usehistory => 'y');


my $hist  = $factory->next_History || die "No history data returned";
 
$factory->set_parameters(-eutil   => 'efetch',-history => $hist);

print Dumper $factory->get_Response;


--Russell


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Carnë Draug
> Sent: Thursday, 30 June 2011 10:13 a.m.
> To: Brian Osborne
> Cc: bioperl mailing list
> Subject: Re: [Bioperl-l] How (from where) to retrieve FieldInfo
> objects?
> 
> > On Jun 29, 2011, at 4:53 PM, Carnë Draug wrote:
> >
> > Hi
> >
> > By using the einfo script that comes with bioperl I get a list of
> > fields of info that I want to access
> >
> > $ einfo --database=gene
> >
> > If I understood correctly the man page of the script, this returns
> the
> > list of info I should be able to obtain when searching the 'gene'
> > database. As such, I tried to use EUtilities esearch to access this
> > info.
> >
> > Using the deobfuscator, I understood that I should create a
> > Bio::Tools::EUtilities::Query EUtitlities object with
> > Bio::DB::EUtilities esearch. With this object I could use the
> > get_FieldInfo method to obtain an array of FieldInfo objects or the
> > next_FieldInfo method to obtain one of them. However, I'm failing
> > miserably at this. My search returns no FieldInfo objects whatsoever.
> >
> > my $factory = Bio::DB::EUtilities->new(
> >                                       -eutil  => 'esearch',
> >                                       -db     => 'gene',
> >                                       -term   => 'h2afx[sym] AND
> > human[organism]',
> >                                       -retmax => 5,
> >                                       );
> >
> > ## this returns nothing
> > my @fields = $factory->get_FieldInfos;
> >
> > ## it also never gets into this loop
> > while (my $field = $factory->next_FieldInfo) {
> >  say "hello";
> > }
> >
> > My question is how to I access the info fields mentioned when I use
> > the einfo script. I can't find any info on this.
> 
> 2011/6/29 Brian Osborne <bosborne11 at verizon.net>:
> > Carne, something like:
> >
> > #!/usr/bin/perl
> > use Bio::DB::EUtilities;
> > # Get all the fields for a db:
> > #
> > my $factory = Bio::DB::EUtilities->new(-eutil => 'einfo',
> >                                         -db => 'genomeprj', );
> > $factory->print_all;
> 
> Hi Brian
> 
> thank for you answer. Maybe I'm just misunderstanding the point of the
> FieldInfo objects. The script you sent gives me a list of the Field
> Infos, which if I understood correctly is the list of infos I can
> obtain for a specific database (genomeprj in your case). But when I
> search that specific database, how do I get that info?
> 
> For example, running the code you mentioned, one of the Field Info has
> the name 'Sequencing Center' and the code CEN. So when I search the
> genomeprj database with a query, how do I get that value from the
> results?
> 
> Thanks
> Carnë
> 
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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