Bio::DB RefSeq
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Summary
Bio::DB::RefSeq - Database object interface for RefSeq retrieval
Package variables
No package variables defined.
Inherit
Bio::DB::DBFetch
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.
Methods
BEGIN Code
new
No description
Code
get_seq_stream
No description
Code
Methods description
None available.
Methods code
BEGINTop
BEGIN {
    # you can add your own here theoretically.
%HOSTS = ( 'dbfetch' => { baseurl => 'http://%s/Tools/dbfetch/dbfetch?db=refseq&style=raw', hosts => { 'ebi' => 'www.ebi.ac.uk' } } ); %FORMATMAP = ( 'embl' => 'embl', 'genbank' => 'genbank', 'fasta' => 'fasta' ); $DEFAULTFORMAT = 'genbank';
}
newdescriptionprevnextTop
sub new {
    my ($class, @args ) = @_;
    my $self = $class->SUPER::new(@args);

    $self->{ '_hosts' } = {};
    $self->{ '_formatmap' } = {};

    $self->hosts(\%HOSTS);
    $self->formatmap(\%FORMATMAP);
    $self->{'_default_format'} = $DEFAULTFORMAT;

    return $self;
}
get_seq_streamdescriptionprevnextTop
sub get_seq_stream {
   my ($self,%qualifiers) = @_;
   if( exists $qualifiers{'-uids'} ) {
       if( ref($qualifiers{'-uids'}) =~ /ARRAY/i ) {
	   foreach my $u ( @{$qualifiers{'-uids'}} ) {
	       $u =~ s/^(\S+)\|//;
	   }
       } else { 
	   $qualifiers{'-uids'} =~ s/^(\S+)\|//;
       }
   }
   $self->SUPER::get_seq_stream(%qualifiers);
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki LehvaslaihoTop
Email Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _