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 / 
bioperl-0.7.0
/ Bio::DB::SwissProt

NAME

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

SYNOPSIS

    use Bio::DB::SwissProt;

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

    $seq = $sp->get_Seq_by_id('P43780'); # SwissProtID
    # or ...
    $seq = $sp->get_Seq_by_acc('P43780'); # SwissProtID
    # can only query on SwissProtID at expasy right now

    # choose a different server to query
    $sp = new Bio::DB::SwissProt('-hostlocation' => 'canada');

    $seq = $sp->get_Seq_by_id('P43780'); # SwissProtID

DESCRIPTION

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.

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://bio.perl.org/MailList.html             - About the mailing lists

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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Jason Stajich

Email Jason Stajich <jason@chg.mc.duke.edu>

APPENDIX

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

Routines from Bio::DB::WebDBSeqI

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