/ 
bioperl-1.0.2
/ Bio::DB::RefSeq

NAME

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

SYNOPSIS use Bio::DB::RefSeq;

 $db = new Bio::DB::RefSeq;

 # 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 bandwith
 # and request Fasta sequence
 $db = new Bio::DB::RefSeq(-retrievaltype => 'tempfile' ,
			       -format => 'fasta');
 my $seqio = $db->get_Stream_by_batch(['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 database using the dbfetch script at EBI: http://www.ebi.ac.uk/cgi-bin/dbfetch.

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 retrives 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://bio.perl.org/MailList.html             - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHOR - Heikki Lehvaslaiho

Email Heikki Lehvaslaiho <Heikki@ebi.ac.uk>

APPENDIX

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