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Manual Reference Pages  -  BIO::DB::SWISSPROT (3)

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NAME

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

CONTENTS

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://github.com/bioperl/bioperl-live/issues



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



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