Christopher Fields
and 1 contributors


Bio::DB::SoapEUtilities::FetchAdaptor::seq - Fetch adaptor for 'seq' efetch SOAP messages


Imported by Bio::DB::SoapEUtilities::FetchAdaptor as required.


Returns an iterator over Bio::Seq or Bio::Seq::RichSeq objects, depending on the the return type of the efetch. A standard efetch to a sequence database will return a GenBank SOAP result; this will be parsed into rich sequence objects:

 my $fac = Bio::DB::SoapEUtilities->new;
 my $seqio = $fac->efetch(-db => 'protein', -id => 730439)->run(-auto_adapt=>1);
 my $seq = $seqio->next_seq;
 $seq->species->binomial; # returns 'Bacillus caldolyticus'

An efetch with -rettype = 'fasta'> will be parsed into Bio::Seq objects (VERY much faster):

 $seqio = $fac->efetch( -rettype => 'fasta' )->run(-auto_adapt=>1);
 $seq = $seqio->next_seq;
 $seq->species; # undef
 $seq->desc; # kitchen sink

To find out the object type returned:

 $class = $seqio->obj_class;

as for all Bio::DB::SoapEUtilities::FetchAdaptor objects.


Bio::DB::SoapEUtilities, Bio::DB::SoapEUtilities::FetchAdaptor


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AUTHOR - Mark A. Jensen

Email maj -at- fortinbras -dot- us


Much inspiration from Bio::SeqIO and family.


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _