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.\" ========================================================================
.\"
.IX Title "Bio::DB::RefSeq 3pm"
.TH Bio::DB::RefSeq 3pm "2019-12-30" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::DB::RefSeq \- Database object interface for RefSeq retrieval
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::DB::RefSeq;
\&
\&  $db = Bio::DB::RefSeq\->new();
\&
\&  # most of the time RefSeq_ID eq RefSeq acc
\&  $seq = $db\->get_Seq_by_id(\*(AqNM_006732\*(Aq); # RefSeq ID
\&  print "accession is ", $seq\->accession_number, "\en";
\&
\&  # or changeing to accession number and Fasta format ...
\&  $db\->request_format(\*(Aqfasta\*(Aq);
\&  $seq = $db\->get_Seq_by_acc(\*(AqNM_006732\*(Aq); # RefSeq ACC
\&  print "seq is ", $seq\->seq, "\en";
\&
\&  # especially when using versions, you better be prepared
\&  # in not getting what what want
\&  eval {
\&      $seq = $db\->get_Seq_by_version(\*(AqNM_006732.1\*(Aq); # RefSeq VERSION
\&  };
\&  print "accesion is ", $seq\->accession_number, "\en" unless $@;
\&
\&  # or ... best when downloading very large files, prevents
\&  # keeping all of the file in memory
\&
\&  # also don\*(Aqt want features, just sequence so let\*(Aqs save bandwidth
\&  # and request Fasta sequence
\&  $db = Bio::DB::RefSeq\->new(\-retrievaltype => \*(Aqtempfile\*(Aq ,
\&                               \-format => \*(Aqfasta\*(Aq);
\&  my $seqio = $db\->get_Stream_by_id([\*(AqNM_006732\*(Aq, \*(AqNM_005252\*(Aq] );
\&  while( my $seq  =  $seqio\->next_seq ) {
\&        print "seqid is ", $seq\->id, "\en";
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Allows the dynamic retrieval of sequence objects Bio::Seq from the
RefSeq nucleotide database using the dbfetch script at \s-1EBI:\s0
.PP
http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
.PP
At this time the module specifically retrieves nucleotide sequences 
only.
.PP
In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out.  This allows later
additions of more servers in different geographical locations.
.PP
The functionality of this module is inherited from Bio::DB::DBFetch
which implements Bio::DB::WebDBSeqI.
.PP
This module retrieves entries from \s-1EBI\s0 although it
retrieves database entries produced at \s-1NCBI.\s0 When read into bioperl
objects, the parser for GenBank format it used. RefSeq is a
\&\s-1NONSTANDARD\s0 GenBank file so be ready for surprises.
.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 one
of the Bioperl mailing lists.  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
\&\fIbioperl\-l@bioperl.org\fR
.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
the bugs and their resolution.  Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Heikki Lehvaslaiho"
.IX Header "AUTHOR - Heikki Lehvaslaiho"
Email Heikki Lehvaslaiho <heikki\-at\-bioperl\-dot\-org>
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _