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BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::DB::SwissProt

NAME

Bio::DB::SwissProt - Database object interface to SwissProt retrieval

SYNOPSIS

    use Bio::DB::SwissProt;

    $sp = Bio::DB::SwissProt->new();

    $seq = $sp->get_Seq_by_id('KPY1_ECOLI'); # SwissProt ID
    # <4-letter-identifier>_<species 5-letter code>
    # 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.

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:

https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

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.

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Routines from Bio::DB::RandomAccessI

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_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_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
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: 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.

Implemented Routines from Bio::DB::WebDBSeqI interface

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)

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

default_format

Title   : default_format
Usage   : my $format = $self->default_format
Function: Returns default sequence format for this module
Returns : string
Args    : none

Bio::DB::SwissProt specific routines

servertype

Title   : servertype
Usage   : my $servertype = $self->servertype
          $self->servertype($servertype);
Function: Get/Set server type
Returns : string
Args    : server type string [optional]

hostlocation

Title   : hostlocation
Usage   : my $location = $self->hostlocation() 
         $self->hostlocation($location) 
Function: Set/Get Hostlocation 
Returns : string representing hostlocation
Args    : string specifying hostlocation [optional]

location_url

Title   : location
Usage   : my $url = $self->location_url()
Function: Get host url
Returns : string representing url
Args    : none

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

idtracker

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_mapper

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