|Bio::DB::SoapEUtilities::FetchAdaptor::seq(3pm)||User Contributed Perl Documentation||Bio::DB::SoapEUtilities::FetchAdaptor::seq(3pm)|
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.
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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
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 _