Bio::DB::SwissProt(3) User Contributed Perl DocumentationBio::DB::SwissProt(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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
perl v5.14.1 2011-07-22 Bio::DB::SwissProt(3)
