NAME¶

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

SYNOPSIS¶

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

DESCRIPTION¶

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.

SEE ALSO¶

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

FEEDBACK¶

  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mark A. Jensen¶

Email maj -at- fortinbras -dot- us

CONTRIBUTORS¶

Much inspiration from Bio::SeqIO and family.

APPENDIX¶

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