oracular (3) Bio::DB::RefSeq.3pm.gz

NAME

       Bio::DB::RefSeq - Database object interface for RefSeq retrieval

SYNOPSIS

         use Bio::DB::RefSeq;

         $db = Bio::DB::RefSeq->new();

         # most of the time RefSeq_ID eq RefSeq acc
         $seq = $db->get_Seq_by_id('NM_006732'); # RefSeq ID
         print "accession is ", $seq->accession_number, "\n";

         # or changeing to accession number and Fasta format ...
         $db->request_format('fasta');
         $seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq ACC
         print "seq is ", $seq->seq, "\n";

         # especially when using versions, you better be prepared
         # in not getting what what want
         eval {
             $seq = $db->get_Seq_by_version('NM_006732.1'); # RefSeq VERSION
         };
         print "accesion is ", $seq->accession_number, "\n" unless $@;

         # or ... best when downloading very large files, prevents
         # keeping all of the file in memory

         # also don't want features, just sequence so let's save bandwidth
         # and request Fasta sequence
         $db = Bio::DB::RefSeq->new(-retrievaltype => 'tempfile' ,
                                      -format => 'fasta');
         my $seqio = $db->get_Stream_by_id(['NM_006732', 'NM_005252'] );
         while( my $seq  =  $seqio->next_seq ) {
               print "seqid is ", $seq->id, "\n";
         }

DESCRIPTION

       Allows the dynamic retrieval of sequence objects Bio::Seq from the RefSeq nucleotide database using the
       dbfetch script at EBI:

       http://www.ebi.ac.uk/Tools/dbfetch/dbfetch

       At this time the module specifically retrieves nucleotide sequences only.

       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.

       The functionality of this module is inherited from Bio::DB::DBFetch which implements Bio::DB::WebDBSeqI.

       This module retrieves entries from EBI although it retrieves database entries produced at NCBI. When read
       into bioperl objects, the parser for GenBank format it used. RefSeq is a NONSTANDARD GenBank file so be
       ready for surprises.

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 one of the Bioperl mailing lists.  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 the bugs and their resolution.  Bug
       reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki Lehvaslaiho

       Email Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded
       with a _