Provided by: libbio-perl-perl_1.6.923-1_all 
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