Bio::DB BioFetch
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Summary
Bio::DB::BioFetch - Database object interface to BioFetch retrieval
Package variables
No package variables defined.
Included modules
HTTP::Request::Common ' POST '
Inherit
Bio::DB::WebDBSeqI Bio::Root::Root
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.
Methods
BEGIN Code
newDescriptionCode
new_from_registryDescriptionCode
get_Seq_by_versionDescriptionCode
get_requestDescriptionCode
default_formatDescriptionCode
default_dbDescriptionCode
dbDescriptionCode
_namespace
No description
Code
postprocess_dataDescriptionCode
request_formatDescriptionCode
get_Stream_by_accDescriptionCode
_check_idDescriptionCode
Methods description
newcode    nextTop
 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_registrycodeprevnextTop
 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_versioncodeprevnextTop
 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_requestcodeprevnextTop
 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_formatcodeprevnextTop
 Title   : default_format
Usage : $format = $self->default_format
Function: return the default format
Returns : a string
Args :
default_dbcodeprevnextTop
 Title   : default_db
Usage : $db = $self->default_db
Function: return the default database
Returns : a string
Args :
dbcodeprevnextTop
 Title   : db
Usage : $db = $self->db([$db])
Function: get/set the database
Returns : a string
Args : new database
postprocess_datacodeprevnextTop
 Title   : postprocess_data
Usage : $self->postprocess_data ( 'type' => 'string',
'location' => \$datastr);
Function: process downloaded data before loading into a Bio::SeqIO
Returns : void
Args : hash with two keys - 'type' can be 'string' or 'file'
- 'location' either file location or string
reference containing data
request_formatcodeprevnextTop
 Title   : request_format
Usage : my ($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
get_Stream_by_acccodeprevnextTop
  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_idcodeprevnextTop
  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
Methods code
BEGINTop
BEGIN {
    
    %FORMATMAP = (
	'embl' => {
	    default   => 'embl',  # default BioFetch format/SeqIOmodule pair
embl => 'embl', # alternative BioFetch format/module pair
fasta => 'fasta', # alternative BioFetch format/module pair
namespace => 'embl', }, 'swissprot' => { default => 'swiss', swissprot => 'swiss', fasta => 'fasta', namespace => 'uniprot', }, 'refseq' => { default => 'genbank', genbank => 'genbank', fasta => 'fasta', namespace => 'RefSeq', }, 'swall' => { default => 'swiss', swissprot => 'swiss', fasta => 'fasta', namespace => 'uniprot', }, 'uniprot' => { default => 'swiss', swissprot => 'swiss', fasta => 'fasta', namespace => 'uniprot', }, 'genbank' => { default => 'genbank', genbank => 'genbank', namespace => 'genbank', }, 'genpep' => { default => 'genbank', genbank => 'genbank', namespace => 'genpep', }, 'unisave' => { default => 'swiss', swissprot => 'swiss', fasta => 'fasta', namespace => 'unisave', } );
}
newdescriptionprevnextTop
sub new {
  my ($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  my ($db) = $self->_rearrange([qw(DB)],@args);
  $db    ||= $self->default_db;
  $self->db($db);
  $self->url_base_address(DEFAULT_LOCATION) unless $self->url_base_address;
  $self;
}
new_from_registrydescriptionprevnextTop
sub new_from_registry {
    my ($class,%config)=@_;

    my $self = $class->SUPER::new(
				  -BASEADDRESS=>$config{'location'}
				  );
    $self->db($config{'dbname'}) if $config{dbname};
    return $self;
}

# from Bio::DB::RandomAccessI
}
get_Seq_by_versiondescriptionprevnextTop
sub get_Seq_by_version {
   my ($self,$seqid) = @_;
   return $self->get_Seq_by_acc($seqid);
}
get_requestdescriptionprevnextTop
sub get_request {
    my ($self, @qualifiers) = @_;
    my ($uids, $format) = $self->_rearrange([qw(UIDS FORMAT)],
					    @qualifiers);
    my $db     = $self->db;
    my $namespace = $self->_namespace;

    $self->throw("Must specify a value for UIDs to fetch")
	unless defined $uids;
    my $tmp;
    my $format_string = '';

    $format ||= $self->default_format;
    ($format, $tmp) = $self->request_format($format);

    my $base = $self->url_base_address;
    my $uid = join('+',ref $uids ? @$uids : $uids);
    $self->debug("\n$base$format_string&id=$uid\n");
    return POST($base,
		[ db     => $namespace,
		  id     => join('+',ref $uids ? @$uids : $uids),
		  format => $format,
		  style  => 'raw'
	     ]);
}
default_formatdescriptionprevnextTop
sub default_format {
     return 'default';
}
default_dbdescriptionprevnextTop
sub default_db {
 'embl'
}
dbdescriptionprevnextTop
sub db {
  my $self = shift;

  if (@_) {

      my $db = lc shift;
      my $base = $self->url_base_address;
      $FORMATMAP{$db} or $self->throw("invalid db [$db] at [$base], must be one of [".
				     join(' ',keys %FORMATMAP).  "]");
      $self->{_db} = $db;
  }
  return $self->{_db} || $self->default_db ;
}
_namespacedescriptionprevnextTop
sub _namespace {
  my $self = shift;
  my $db = $self->db;
  return $FORMATMAP{$db}{namespace} or $db;
}
postprocess_datadescriptionprevnextTop
sub postprocess_data {
  my ($self,%args) = @_;

  # check for errors in the stream
if ($args{'type'} eq 'string') { my $stringref = $args{'location'}; if ($$stringref =~ /^ERROR (\d+) (.+)/m) { $self->throw("BioFetch Error $1: $2"); } } elsif ($args{'type'} eq 'file') { open (F,$args{'location'}) or $self->throw("Couldn't open $args{location}: $!"); # this is dumb, but the error may be anywhere on the first three lines because the
# CGI headers are sometimes printed out by the server...
my @data = grep {defined $_} (scalar <F>,scalar <F>,scalar <F>); if (join('',@data) =~ /^ERROR (\d+) (.+)/m) { $self->throw("BioFetch Error $1: $2"); } close F; } else { $self->throw("Don't know how to postprocess data of type $args{'type'}"); }
}
request_formatdescriptionprevnextTop
sub request_format {
    my ($self, $value) = @_;
    if ( defined $value ) { 
	my $db = $self->db;
	my $namespace = $self->_namespace;
	my $format = lc $value;
	print "format:", $format, " module:", $FORMATMAP{$db}->{$format}, " ($namespace)\n" 
	    if $self->verbose > 0; 
	$self->throw("Invalid format [$format], must be one of [".
		     join(' ',keys %{$FORMATMAP{$db}}). "]")
	    unless  $format eq 'default' || $FORMATMAP{$db}->{$format};

	$self->{'_format'} = [ $format, $FORMATMAP{$db}->{$format}];
    }
    return @{$self->{'_format'}};
}
get_Stream_by_accdescriptionprevnextTop
sub get_Stream_by_acc {
    my ($self, $ids ) = @_;
    $self->_check_id($ids);
    return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single');
}
_check_iddescriptionprevnextTop
sub _check_id {
    my ($self, $id) = @_;

    # 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 $id =~ /NT_/; # Asking for a RefSeq from EMBL/GenBank
if ($id =~ /N._/ && $self->db ne 'refseq') { $self->warn("[$id] is not a normal sequence entry but a RefSeq entry.". " Redirecting the request.\n") if $self->verbose >= 0; $self->db('RefSeq'); } } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 SteinTop
Email Lincoln Stein <lstein@cshl.org<
Also thanks to Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> for the
BioFetch server and interface specification.
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
get_Seq_by_idTop
 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_accTop
 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_giTop
 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_Stream_by_idTop
  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_giTop
  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_batchTop
  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 useTop
Bio::DB::WebDBSeqI methodsTop
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.