Bio::DB SwissProt
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::DB::SwissProt - Database object interface to SwissProt retrieval
Package variables
No package variables defined.
Included modules
Bio::DB::WebDBSeqI
HTTP::Request::Common
Inherit
Bio::DB::WebDBSeqI
Synopsis
    use Bio::DB::SwissProt;

    $sp = new Bio::DB::SwissProt;

    $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 = new Bio::DB::SwissProt('-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. This is in contrast to EMBL/GenBank/DDBJ
which are archives of protein information. 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. Perhaps through SRS
later.
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_batchDescriptionCode
get_requestDescriptionCode
postprocess_dataDescriptionCode
default_formatDescriptionCode
servertypeDescriptionCode
hostlocationDescriptionCode
location_urlDescriptionCode
request_formatDescriptionCode
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.
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    : $format = sequence format
Methods code
newdescriptionprevnextTop
sub new {
    my ($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, $ids) = @_;
    return $self->get_Stream_by_id( $ids);
}
get_requestdescriptionprevnextTop
sub get_request {
    my ($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 ) = @_;
    $location = lc $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 '' ) {
	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'}};
}
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://bio.perl.org/MailList.html             - About the mailing lists
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 email
or the web:
  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/
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@ebi.ac.uk> 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