oracular (3) Bio::DB::SoapEUtilities::FetchAdaptor::seq.3pm.gz

Provided by: libbio-perl-run-perl_1.7.3-11_all bug

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
   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments
       and suggestions preferably to the Bioperl mailing list.  Your participation is much appreciated.

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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look
       at the problem and quickly address it. Please include a thorough description of the problem with code and
       data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution.
       Bug reports can be submitted via the web:

         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 _