.\" -*- mode: troff; coding: utf-8 -*-
.\" Automatically generated by Pod::Man 5.01 (Pod::Simple 3.43)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" \*(C` and \*(C' are quotes in nroff, nothing in troff, for use with C<>.
.ie n \{\
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\" ========================================================================
.\"
.IX Title "Bio::DB::SoapEUtilities::FetchAdaptor::seq 3pm"
.TH Bio::DB::SoapEUtilities::FetchAdaptor::seq 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH NAME
Bio::DB::SoapEUtilities::FetchAdaptor::seq \- Fetch adaptor for 'seq'
efetch SOAP messages
.SH SYNOPSIS
.IX Header "SYNOPSIS"
Imported by Bio::DB::SoapEUtilities::FetchAdaptor as required.
.SH DESCRIPTION
.IX Header "DESCRIPTION"
Returns an iterator over Bio::Seq or Bio::Seq::RichSeq objects,
depending on the the return type of the \f(CW\*(C`efetch\*(C'\fR. A standard
\&\f(CW\*(C`efetch\*(C'\fR to a sequence database will return a GenBank SOAP result;
this will be parsed into rich sequence objects:
.PP
.Vb 4
\& my $fac = Bio::DB::SoapEUtilities\->new;
\& my $seqio = $fac\->efetch(\-db => \*(Aqprotein\*(Aq, \-id => 730439)\->run(\-auto_adapt=>1);
\& my $seq = $seqio\->next_seq;
\& $seq\->species\->binomial; # returns \*(AqBacillus caldolyticus\*(Aq
.Ve
.PP
An \f(CW\*(C`efetch\*(C'\fR with \f(CW\*(C`\-rettype =\*(C'\fR 'fasta'> will be parsed into
Bio::Seq objects (VERY much faster):
.PP
.Vb 4
\& $seqio = $fac\->efetch( \-rettype => \*(Aqfasta\*(Aq )\->run(\-auto_adapt=>1);
\& $seq = $seqio\->next_seq;
\& $seq\->species; # undef
\& $seq\->desc; # kitchen sink
.Ve
.PP
To find out the object type returned:
.PP
.Vb 1
\& $class = $seqio\->obj_class;
.Ve
.PP
as for all Bio::DB::SoapEUtilities::FetchAdaptor objects.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::DB::SoapEUtilities, Bio::DB::SoapEUtilities::FetchAdaptor
.SH FEEDBACK
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS Support
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
bioperl\-l@bioperl.org
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Mark A. Jensen"
.IX Header "AUTHOR - Mark A. Jensen"
Email maj \-at\- fortinbras \-dot\- us
.SH CONTRIBUTORS
.IX Header "CONTRIBUTORS"
Much inspiration from Bio::SeqIO and family.
.SH APPENDIX
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _