NAME

Bio::DB::BioFetch - Database object interface to BioFetch retrieval

SYNOPSIS

use Bio::DB::BioFetch;

$bf = Bio::DB::BioFetch->new();

$seq = $bf->get_Seq_by_id('BUM');  # EMBL or SWALL ID

# change formats, storage procedures
$bf = Bio::DB::BioFetch->new(-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 $@;

DESCRIPTION

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/Tools/dbfetch/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.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Lincoln Stein

Email Lincoln Stein <lstein@cshl.org<

Also thanks to Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> for the BioFetch server and interface specification.

APPENDIX

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/Tools/dbfetch/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.

The remainder of these methods are for internal use

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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq