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 bandwith
# 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
database using the dbfetch script at EBI:
http://www.ebi.ac.uk/Tools/dbfetch/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://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 _