/ 
BioPerl-Run-1.007003
River stage one • 2 direct dependents • 2 total dependents
/ Bio::DB::SoapEUtilities::FetchAdaptor::seq

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 _