/ 
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