Raw content of Bio::DB::EMBL # # $Id: EMBL.pm,v 2003/06/25 13:44:18 heikki Exp $ # # BioPerl module for Bio::DB::EMBL # # Cared for by Heikki Lehvaslaiho <Heikki@ebi.ac.uk> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::EMBL - Database object interface for EMBL entry retrieval =head1 SYNOPSIS use Bio::DB::EMBL; $embl = new Bio::DB::EMBL; # remember that EMBL_ID does not equal GenBank_ID! $seq = $embl->get_Seq_by_id('BUM'); # EMBL ID print "cloneid is ", $seq->id, "\n"; # or changeing to accession number and Fasta format ... $embl->request_format('fasta'); $seq = $embl->get_Seq_by_acc('J02231'); # EMBL ACC print "cloneid is ", $seq->id, "\n"; # especially when using versions, you better be prepared # in not getting what what want eval { $seq = $embl->get_Seq_by_version('J02231.1'); # EMBL VERSION }; print "cloneid is ", $seq->id, "\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 $embl = new Bio::DB::EMBL(-retrievaltype => 'tempfile' , -format => 'fasta'); my $seqio = $embl->get_Stream_by_batch(['AC013798', 'AC021953'] ); while( my $clone = $seqio->next_seq ) { print "cloneid is ", $clone->id, "\n"; } =head1 DESCRIPTION Allows the dynamic retrieval of sequence objects L<Bio::Seq> from the EMBL database using the dbfetch script at EBI: L<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 L<Bio::DB::DBFetch> which implements L<Bio::DB::WebDBSeqI>. =head1 FEEDBACK =head2 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 =head2 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://bugzilla.bioperl.org/ =head1 AUTHOR - Heikki Lehvaslaiho Email Heikki Lehvaslaiho E<lt>Heikki@ebi.ac.ukE<gt> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::EMBL; use strict; use vars qw(@ISA $MODVERSION %HOSTS %FORMATMAP $DEFAULTFORMAT); $MODVERSION = '0.2'; use Bio::DB::DBFetch; use Bio::DB::RefSeq; @ISA = qw(Bio::DB::DBFetch); BEGIN { # you can add your own here theoretically. %HOSTS = ( 'dbfetch' => { baseurl => 'http://%s/cgi-bin/dbfetch?db=embl&style=raw', hosts => { 'ebi' => 'www.ebi.ac.uk' } } ); %FORMATMAP = ( 'embl' => 'embl', 'fasta' => 'fasta' ); $DEFAULTFORMAT = 'embl'; } =head2 new Title : new Usage : $gb = Bio::DB::GenBank->new(@options) Function: Creates a new genbank handle Returns : New genbank handle Args : -delay number of seconds to delay between fetches (3s) NOTE: There are other options that are used internally. =cut sub new { my ($class, @args ) = @_; my $self = $class->SUPER::new(@args); $self->{ '_hosts' } = {}; $self->{ '_formatmap' } = {}; $self->hosts(\%HOSTS); $self->formatmap(\%FORMATMAP); $self->{'_default_format'} = $DEFAULTFORMAT; return $self; } =head2 Bio::DB::WebDBSeqI methods Overriding WebDBSeqI method to help newbies to retrieve sequences. EMBL database is all too often passed RefSeq accessions. This redirects those calls. See L<Bio::DB::RefSeq>. =head2 get_Stream_by_acc Title : get_Stream_by_acc Usage : $seq = $db->get_Seq_by_acc([$acc1, $acc2]); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() =cut sub get_Stream_by_acc { my ($self, $ids ) = @_; my $newdb = $self->_check_id($ids); if ($newdb && $newdb->isa('Bio::DB::RefSeq')) { return $newdb->get_seq_stream('-uids' => $ids, '-mode' => 'single'); } else { return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single'); } } =head2 _check_id Title : _check_id Usage : Function: Returns : A Bio::DB::RefSeq reference or throws Args : $id(s), $string =cut sub _check_id { my ($self, $ids) = @_; # NT contigs can not be retrieved $self->throw("NT_ contigs are whole chromosome files which are not part of regular". "database distributions. Go to ftp://ftp.ncbi.nih.gov/genomes/.") if $ids =~ /NT_/; # Asking for a RefSeq from EMBL/GenBank if ($ids =~ /N._/) { $self->warn("[$ids] is not a normal sequence database but a RefSeq entry.". " Redirecting the request.\n") if $self->verbose >= 0; return new Bio::DB::RefSeq(-verbose => $self->verbose); } } 1;