Bio::DB::BioFetch - Database object interface to BioFetch retrieval use Bio::DB::BioFetch; $bf = new Bio::DB::BioFetch; $seq = $bf->get_Seq_by_id('BUM'); # EMBL or SWALL ID # change formats, storage procedures $bf = new Bio::DB::BioFetch(-format => 'fasta', -retrievaltype => 'tempfile', -db => 'EMBL'); $stream = $bf->get_Stream_by_id(['BUM','J00231']); while (my $s = $stream->next_seq) { print $s->seq,"\n"; } # get a RefSeq entry $bf->db('refseq'); eval { $seq = $bf->get_Seq_by_version('NM_006732.1'); # RefSeq VERSION }; print "accession is ", $seq->accession_number, "\n" unless $@; Bio::DB::BioFetch is a guaranteed best effort sequence entry fetching method. It goes to the Web-based dbfetch server located at the EBI (http://www.ebi.ac.uk/cgi-bin/dbfetch) to retrieve sequences in the EMBL or GenBank sequence repositories. This module implements all the Bio::DB::RandomAccessI interface, plus the get_Stream_by_id() and get_Stream_by_acc() methods that are found in the Bio::DB::SwissProt interface.

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://bugzilla.bioperl.org/ Email Lincoln Stein <lstein@cshl.org< Also thanks to Heikki Lehvaslaiho <heikki@ebi.ac.uk> for the BioFetch server and interface specification. The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : $bf = Bio::DB::BioFetch->new(@args) Function: Construct a new Bio::DB::BioFetch object Returns : a Bio::DB::BioFetch object Args : see below Throws : @args are standard -name=>value options as listed in the following table. If you do not provide any options, the module assumes reasonable defaults. Option Value Default ------ ----- ------- -baseaddress location of dbfetch server http://www.ebi.ac.uk/cgi-bin/dbfetch -retrievaltype "tempfile" or "io_string" io_string -format "embl", "fasta", "swissprot", embl or "genbank" -db "embl", "genbank" or "swissprot" embl

new_from_registry
Title : new_from_registry Usage : $biofetch = $db->new_from_registry(%config) Function: Creates a BioFetch object from the registry config hash Returns : itself Args : A configuration hash (see Registry.pm) Throws :

get_Seq_by_id
Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception

get_Seq_by_acc
Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception

get_Seq_by_gi
Title : get_Seq_by_gi Usage : $seq = $db->get_Seq_by_gi('405830'); Function: Gets a Bio::Seq object by gi number Returns : A Bio::Seq object Args : gi number (as a string) Throws : "gi does not exist" exception

get_Seq_by_version
Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_version('X77802.1'); Function: Gets a Bio::Seq object by sequence version Returns : A Bio::Seq object Args : accession.version (as a string) Throws : "acc.version does not exist" exception

get_Stream_by_id
Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] ); Function: Gets a series of Seq objects by unique identifiers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of unique identifiers for the desired sequence entries

get_Stream_by_gi
Title : get_Stream_by_gi Usage : $seq = $db->get_Seq_by_gi([$gi1, $gi2]); Function: Gets a series of Seq objects by gi numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of gi numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id()

get_Stream_by_batch
Title : get_Stream_by_batch Usage : $seq = $db->get_Stream_by_batch($ref); Function: Get a series of Seq objects by their IDs Example : Returns : a Bio::SeqIO stream object Args : $ref : an array reference containing a list of unique ids/accession numbers. In some of the Bio::DB::* moduels, get_Stream_by_id() is called get_Stream_by_batch(). Since there seems to be no consensus, this is provided as an alias.

get_request
Title : get_request Usage : my $url = $self->get_request Function: returns a HTTP::Request object Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc)

default_format
Title : default_format Usage : $format = $self->default_format Function: return the default format Returns : a string Args :

default_db
Title : default_db Usage : $db = $self->default_db Function: return the default database Returns : a string Args :

db
Title : db Usage : $db = $self->db([$db]) Function: get/set the database Returns : a string Args : new database

postprocess_data
Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data

request_format
Title : request_format Usage : my ($req_format, $ioformat) = $self->request_format; $self->request_format("genbank"); $self->request_format("fasta"); Function: Get/Set sequence format retrieval. The get-form will normally not be used outside of this and derived modules. Returns : Array of two strings, the first representing the format for retrieval, and the second specifying the corresponding SeqIO format. Args : $format = sequence format

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 Bio::DB::RefSeq.

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

_check_id
Title : _check_id Usage : Function: Throw on whole chromosome NCBI sequences not in sequence databases and redirect RefSeq accession requests sent to EMBL. Returns : Args : $id(s), $string Throws : if accessionn number indicates whole chromosome NCBI sequence