Bio::DB SwissProt
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Summary
Bio::DB::SwissProt - Database object interface to SwissProt retrieval
Package variables
No package variables defined.
Included modules
HTTP::Request::Common
Inherit
Bio::DB::WebDBSeqI
Synopsis
    use Bio::DB::SwissProt;
$sp = Bio::DB::SwissProt->new(); $seq = $sp->get_Seq_by_id('KPY1_ECOLI'); # SwissProt ID # <4-letter-identifier>_ # or ... $seq = $sp->get_Seq_by_acc('P43780'); # SwissProt AC # [OPQ]xxxxx # In fact in this implementation # these methods call the same webscript so you can use # then interchangeably # choose a different server to query $sp = Bio::DB::SwissProt->new('-servertype' => 'expasy', '-hostlocation' => 'us'); $seq = $sp->get_Seq_by_id('BOLA_HAEIN'); # SwissProtID
Description
SwissProt is a curated database of proteins managed by the Swiss
Bioinformatics Institute. Additional tools for
parsing and manipulating swissprot files can be found at
ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/.
Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the
SwissProt database via an Expasy retrieval.
In order to make changes transparent we have host type (currently only
expasy) and location (default to Switzerland) separated out. This
allows the user to pick the closest Expasy mirror for running their
queries.
Methods
new
No description
Code
get_Stream_by_batch (reference)DescriptionCode
get_requestDescriptionCode
postprocess_dataDescriptionCode
default_formatDescriptionCode
servertypeDescriptionCode
hostlocationDescriptionCode
location_urlDescriptionCode
request_formatDescriptionCode
idtrackerDescriptionCode
id_mapperDescriptionCode
Methods description
get_Stream_by_batchcode    nextTop
  Title   : get_Stream_by_batch
Usage : $seq = $db->get_Stream_by_batch($ref);
Function: Retrieves Seq objects from SwissProt 'en masse', rather than one
at a time. This is implemented the same way as get_Stream_by_id,
but is provided here in keeping with access methods of NCBI
modules.
Example :
Returns : a Bio::SeqIO stream object
Args : $ref : either an array reference, a filename, or a filehandle
from which to get the list of unique ids/accession numbers.
NOTE: deprecated API. Use get_Stream_by_id() instead.
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)
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
default_formatcodeprevnextTop
 Title   : default_format
Usage : my $format = $self->default_format
Function: Returns default sequence format for this module
Returns : string
Args : none
servertypecodeprevnextTop
 Title   : servertype
Usage : my $servertype = $self->servertype
$self->servertype($servertype);
Function: Get/Set server type
Returns : string
Args : server type string [optional]
hostlocationcodeprevnextTop
 Title   : hostlocation
Usage : my $location = $self->hostlocation()
$self->hostlocation($location)
Function: Set/Get Hostlocation
Returns : string representing hostlocation
Args : string specifying hostlocation [optional]
location_urlcodeprevnextTop
 Title   : location
Usage : my $url = $self->location_url()
Function: Get host url
Returns : string representing url
Args : none
request_formatcodeprevnextTop
 Title   : request_format
Usage : my ($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 : $format = sequence format
idtrackercodeprevnextTop
 Title   : idtracker
Usage : my ($newid) = $self->idtracker($oldid);
Function: Retrieve new ID using old ID.
Returns : single ID if one is found
Args : ID to look for
id_mappercodeprevnextTop
 Title   : id_tracker
Usage : my $map = $self->id_mapper( -from => '',
-to => '',
-ids => \@ids);
Function: Retrieve new ID using old ID.
Returns : hash reference of successfully mapped IDs
Args : -from : database mapping from
-to : database mapped to
-ids : a single ID or array ref of IDs to map
Note : For a list of valid database IDs, see:
http://www.uniprot.org/faq/28#id_mapping_examples
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    my ($format, $hostlocation,$servertype) =
	$self->_rearrange([qw(FORMAT HOSTLOCATION SERVERTYPE)],
			  @args);

    if( $format && $format !~ /(swiss)|(fasta)/i ) {
	$self->warn("Requested Format $format is ignored because only SwissProt and Fasta formats are currently supported");
	$format = $self->default_format;
    }
    $servertype = $DEFAULTSERVERTYPE unless $servertype;
    $servertype = lc $servertype;
    $self->servertype($servertype);
    if (  $hostlocation ) {
	$self->hostlocation(lc $hostlocation);
    }

    $self->request_format($format); # let's always override the format, as it must be swiss or fasta
return $self;
}
get_Stream_by_batchdescriptionprevnextTop
sub get_Stream_by_batch {
   my $self = shift;
   $self->deprecated('get_Stream_by_batch() is deprecated; use get_Stream_by_id() instead');
   $self->get_Stream_by_id(@_)
};
}
get_requestdescriptionprevnextTop
sub get_request {
    my ($self, @qualifiers) = @_;
    my ($uids, $format) = $self->_rearrange([qw(UIDS FORMAT)],
					    @qualifiers);

    if( !defined $uids ) {
	$self->throw("Must specify a value for uids to query");
    }
    my ($f,undef) = $self->request_format($format);

    my %vars = (
		 @{$HOSTS{$self->servertype}->{'basevars'}},
		 ( 'format' => $f )
		 );

    my $url = $self->location_url;

    my $uid;
    my $jointype = $HOSTS{$self->servertype}->{'jointype'} || ' ';
    my $idvar = $HOSTS{$self->servertype}->{'idvar'} || 'id';

    if( ref($uids) =~ /ARRAY/i ) {
	# HTTP::Request automagically converts the ' ' to %20
$uid = join($jointype, @$uids); } else { $uid = $uids; } $vars{$idvar} = $uid; return POST $url,\% vars;
}
postprocess_datadescriptionprevnextTop
sub postprocess_data {
    my ($self, %args) = @_;
    return;
}
default_formatdescriptionprevnextTop
sub default_format {
    return $DEFAULTFORMAT;
}
servertypedescriptionprevnextTop
sub servertype {
    my ($self, $servertype) = @_;
    if( defined $servertype && $servertype ne '') {
	$self->throw("You gave an invalid server type ($servertype)".
			 " - available types are ".
			 keys %HOSTS) unless( $HOSTS{$servertype} );
	$self->{'_servertype'} = $servertype;
	$self->{'_hostlocation'} = $HOSTS{$servertype}->{'default'};

	# make sure format is reset properly in that different
# servers have different syntaxes
my ($existingformat,$seqioformat) = $self->request_format; $self->request_format($existingformat); } return $self->{'_servertype'} || $DEFAULTSERVERTYPE;
}
hostlocationdescriptionprevnextTop
sub hostlocation {
    my ($self, $location ) = @_;
    my $servertype = $self->servertype;
    $self->throw("Must have a valid servertype defined not $servertype")
	unless defined $servertype;
    my %hosts = %{$HOSTS{$servertype}->{'hosts'}};
    if( defined $location && $location ne '' ) {
    $location = lc $location;
	if( ! $hosts{$location} ) {
	    $self->throw("Must specify a known host, not $location,".
			 " possible values (".
			 join(",", sort keys %hosts ). ")");
	}
	$self->{'_hostlocation'} = $location;
    }
    return $self->{'_hostlocation'};
}
location_urldescriptionprevnextTop
sub location_url {
    my ($self) = @_;
    my $servertype = $self->servertype();
    my $location = $self->hostlocation();

    if( ! defined $location || !defined $servertype )  {
	$self->throw("must have a valid hostlocation and servertype set before calling location_url");
    }
    return sprintf($HOSTS{$servertype}->{'baseurl'},
		   $HOSTS{$servertype}->{'hosts'}->{$location});
}
request_formatdescriptionprevnextTop
sub request_format {
    my ($self, $value) = @_;
    if( defined $value ) {
	if( $self->servertype =~ /expasy/ ) {
	    if( $value =~ /sprot/ || $value =~ /swiss/ ) {
		$self->{'_format'} = [ 'sprot', 'swiss'];
	    } elsif( $value =~ /^fa/ ) {
		$self->{'_format'} = [ 'fasta', 'fasta'];
	    } else {
		$self->warn("Unrecognized format $value requested");
		$self->{'_format'} = [ 'fasta', 'fasta'];
	    }
	} elsif( $self->servertype =~ /ebi/ ) {
	    if( $value =~ /sprot/ || $value =~ /swiss/ ) {
		$self->{'_format'} = [ 'swissprot', 'swiss' ];
	    } elsif( $value =~ /^fa/ ) {
		$self->{'_format'} = [ 'fasta', 'fasta'];
	    } else {
		$self->warn("Unrecognized format $value requested");
		$self->{'_format'} = [ 'swissprot', 'swiss'];
	    }
	}
    }
    return @{$self->{'_format'}};
}
idtrackerdescriptionprevnextTop
sub idtracker {
    my ($self, $id) = @_;
    $self->deprecated(
         -message => 'The SwissProt IDTracker service is no longer available, '.
                     'use id_mapper() instead',
         -warn_version    => 1.006, # warn if $VERSION is >= this version
-throw_version => 1.007 # throw if $VERSION is >= this version
);
}
id_mapperdescriptionprevnextTop
sub id_mapper {
    my $self = shift;
    my ($from, $to, $ids) = $self->_rearrange([qw(FROM TO IDS)], @_);
    for ($from, $to) {
        $self->throw("$_ is not a recognized database") if !exists $ID_MAPPING_DATABASES{$_};
    }
    my @ids = ref $ids ? @$ids : $ids;
    my $params = {
        from => $from,
        to => $to,
        format => 'tab',
        query => join(' ',@ids)
    };
    my $ua = $self->ua;
    push @{ $ua->requests_redirectable }, 'POST';
    my $response = $ua->post("http://www.uniprot.org/mapping/", $params);
    while (my $wait = $response->header('Retry-After')) {
        $self->debug("Waiting...\n");
        $self->_sleep;
        $response = $ua->get($response->base);
    }

    my %map;
    if ($response->is_success) {
        for my $line (split("\n", $response->content)) {
            my ($id_from, $id_to) = split(/\s+/, $line, 2);
            next if $id_from eq 'From';
            push @{$map{$id_from}}, $id_to;
        }
    } else {
        $self->throw("Error: ".$response->status_line."\n");
    }\%
    map;
}

1;

__END__
}
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
SupportTop
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 - Jason StajichTop
Email Jason Stajich <jason@bioperl.org <
Thanks go to Alexandre Gattiker <gattiker@isb-sib.ch> of Swiss
Institute of Bioinformatics for helping point us in the direction of
the correct expasy scripts and for swissknife references.
Also thanks to Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
for help with adding EBI swall server.
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Routines from Bio::DB::RandomAccessITop
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_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_accTop
  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
Note : For GenBank, this just calls the same code for get_Stream_by_id()
Implemented Routines from Bio::DB::WebDBSeqI interfaceTop
Bio::DB::SwissProt specific routinesTop