Christopher Fields > BioPerl-Run > Bio::DB::SoapEUtilities::FetchAdaptor::seq

Download:
BioPerl-Run-1.006900.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  2
Open  1
View/Report Bugs
Source  

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 _

syntax highlighting: