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lib/Bio/DB/SoapEUtilities.pm  view on Meta::CPAN

Here is a rundown of the different adaptor flavors:

=over

=item * C<efetch>, Fetch Adaptors, and BioPerl object iterators

The C<FetchAdaptor> creates bona fide BioPerl objects. Currently,
there are FetchAdaptor subclasses for sequence data (both Genbank and
FASTA rettypes) and taxonomy data. The choice of FetchAdaptor is based
on information in the result message, and should be transparent to the
user.

 $seqio = $fac->efetch( -db =>'nucleotide',
                        -id => \@ids,
                        -rettype => 'gb' )->run( -auto_adapt => 1 );
 while (my $seq = $seqio->next_seq) {
    my $taxio = $fac->efetch( 
	-db => 'taxonomy', 
	-id => $seq->species->ncbi_taxid )->run(-auto_adapt => 1);
    my $tax = $taxio->next_species;