Bio::DB::BioFetch.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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/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.

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:
   http://bugzilla.open-bio.org/
 
 

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/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.

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