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.\" ========================================================================
.\"
.IX Title "Bio::DB::SwissProt 3pm"
.TH Bio::DB::SwissProt 3pm "2020-01-01" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::DB::SwissProt \- Database object interface to SwissProt retrieval
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    use Bio::DB::SwissProt;
\&
\&    $sp = Bio::DB::SwissProt\->new();
\&
\&    $seq = $sp\->get_Seq_by_id(\*(AqKPY1_ECOLI\*(Aq); # SwissProt ID
\&    # <4\-letter\-identifier>_<species 5\-letter code>
\&    # or ...
\&    $seq = $sp\->get_Seq_by_acc(\*(AqP43780\*(Aq); # 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(\*(Aq\-servertype\*(Aq => \*(Aqexpasy\*(Aq,
\&                                 \*(Aq\-hostlocation\*(Aq => \*(Aqus\*(Aq);
\&
\&    $seq = $sp\->get_Seq_by_id(\*(AqBOLA_HAEIN\*(Aq); # SwissProtID
.Ve
.SH "DESCRIPTION"
.IX Header "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/.
.PP
Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the
SwissProt database via an Expasy retrieval.
.PP
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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email Jason Stajich  <jason@bioperl.org <
.PP
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.
.PP
Also thanks to Heikki Lehvaslaiho <heikki\-at\-bioperl\-dot\-org>
for help with adding \s-1EBI\s0 swall server.
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "Routines from Bio::DB::RandomAccessI"
.IX Subsection "Routines from Bio::DB::RandomAccessI"
.SS "get_Seq_by_id"
.IX Subsection "get_Seq_by_id"
.Vb 6
\& Title   : get_Seq_by_id
\& Usage   : $seq = $db\->get_Seq_by_id(\*(AqROA1_HUMAN\*(Aq)
\& 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
.Ve
.SS "get_Seq_by_acc"
.IX Subsection "get_Seq_by_acc"
.Vb 6
\& Title   : get_Seq_by_acc
\& Usage   : $seq = $db\->get_Seq_by_acc(\*(AqX77802\*(Aq);
\& 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
.Ve
.SS "get_Stream_by_id"
.IX Subsection "get_Stream_by_id"
.Vb 6
\&  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
.Ve
.SS "get_Stream_by_acc"
.IX Subsection "get_Stream_by_acc"
.Vb 7
\&  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()
.Ve
.SS "get_Stream_by_batch"
.IX Subsection "get_Stream_by_batch"
.Vb 10
\&  Title   : get_Stream_by_batch
\&  Usage   : $seq = $db\->get_Stream_by_batch($ref);
\&  Function: Retrieves Seq objects from SwissProt \*(Aqen masse\*(Aq, 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.
.Ve
.PP
\&\s-1NOTE:\s0 deprecated \s-1API.\s0  Use \fBget_Stream_by_id()\fR instead.
.SS "Implemented Routines from Bio::DB::WebDBSeqI interface"
.IX Subsection "Implemented Routines from Bio::DB::WebDBSeqI interface"
.SS "get_request"
.IX Subsection "get_request"
.Vb 5
\& 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)
.Ve
.SS "postprocess_data"
.IX Subsection "postprocess_data"
.Vb 8
\& Title   : postprocess_data
\& Usage   : $self\->postprocess_data ( \*(Aqtype\*(Aq => \*(Aqstring\*(Aq,
\&                                     \*(Aqlocation\*(Aq => \e$datastr);
\& Function: process downloaded data before loading into a Bio::SeqIO
\& Returns : void
\& Args    : hash with two keys \- \*(Aqtype\*(Aq can be \*(Aqstring\*(Aq or \*(Aqfile\*(Aq
\&                              \- \*(Aqlocation\*(Aq either file location or string
\&                                           reference containing data
.Ve
.SS "default_format"
.IX Subsection "default_format"
.Vb 5
\& Title   : default_format
\& Usage   : my $format = $self\->default_format
\& Function: Returns default sequence format for this module
\& Returns : string
\& Args    : none
.Ve
.SS "Bio::DB::SwissProt specific routines"
.IX Subsection "Bio::DB::SwissProt specific routines"
.SS "servertype"
.IX Subsection "servertype"
.Vb 6
\& Title   : servertype
\& Usage   : my $servertype = $self\->servertype
\&           $self\->servertype($servertype);
\& Function: Get/Set server type
\& Returns : string
\& Args    : server type string [optional]
.Ve
.SS "hostlocation"
.IX Subsection "hostlocation"
.Vb 6
\& Title   : hostlocation
\& Usage   : my $location = $self\->hostlocation()
\&          $self\->hostlocation($location)
\& Function: Set/Get Hostlocation
\& Returns : string representing hostlocation
\& Args    : string specifying hostlocation [optional]
.Ve
.SS "location_url"
.IX Subsection "location_url"
.Vb 5
\& Title   : location
\& Usage   : my $url = $self\->location_url()
\& Function: Get host url
\& Returns : string representing url
\& Args    : none
.Ve
.SS "request_format"
.IX Subsection "request_format"
.Vb 10
\& Title   : request_format
\& Usage   : my ($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    : $format = sequence format
.Ve
.SS "idtracker"
.IX Subsection "idtracker"
.Vb 5
\& Title   : idtracker
\& Usage   : my ($newid) = $self\->idtracker($oldid);
\& Function: Retrieve new ID using old ID.
\& Returns : single ID if one is found
\& Args    : ID to look for
.Ve
.SS "id_mapper"
.IX Subsection "id_mapper"
.Vb 11
\& Title   : id_tracker
\& Usage   : my $map = $self\->id_mapper( \-from => \*(Aq\*(Aq,
\&                                       \-to   => \*(Aq\*(Aq,
\&                                       \-ids  => \e@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
.Ve