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

Carnë Draug carandraug+dev at gmail.com
Wed Jun 29 20:53:42 UTC 2011


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.

Thanks in advance,
Carnë




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