|Bio::DB::SoapEUtilities::FetchAdaptor::seq(3pm)||User Contributed Perl Documentation||Bio::DB::SoapEUtilities::FetchAdaptor::seq(3pm)|
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
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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 _