Bio::DB::BioFetch(3pm)

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('HSFOS');  # 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(['HSFOS','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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 - Lincoln Stein

Email Lincoln Stein <[email protected]<

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