Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::DB::HIV - Database object interface to the Los Alamos HIV Sequence Database

SYNOPSIS

           $db = new Bio::DB::HIV;

           $seq = $db->get_Seq_by_id('94284');                                 # LANL sequence id
           $seq = $db->get_Seq_by_acc('EF432710');                             # GenBank accession

           $q = new Bio::DB::Query::HIVQuery( " (C D)[subtype] SI[phenotype] (symptomatic AIDS)[patient_health] " );

           $seqio = $db->get_Stream_by_query($q);
           $seq = $seqio->next_seq();
           ($seq->annotation->get_Annotations('Virus'))[0]->{subtype}          # returns 'D'
           ($seq->annotation->get_Annotations('Patient'))[0]->{patient_health} # returns 'AIDS'
           ($seq->annotation->get_Annotations('accession'))[0]->{value}        # returns 'K03454'

DESCRIPTION

       Bio::DB::HIV, along with Bio::DB::Query::HIVQuery, provides an interface for obtaining
       annotated HIV and SIV sequences from the Los Alamos National Laboratory (LANL) HIV
       Sequence Database ( <http://www.hiv.lanl.gov/content/sequence/HIV/mainpage.html> ).
       Unannotated sequences can be retrieved directly from the database object, using either
       LANL ids or GenBank accessions. Annotations are obtained via a query object, and are
       attached to the correct "Bio::Seq" objects when the query is handled by
       "Bio::DB::HIV::get_Seq_by_query" or "Bio::DB::HIV::get_Stream_by_query".

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 the Bioperl mailing list.  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 of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mark A. Jensen

       Email maj@fortinbras.us

CONTRIBUTORS

       Mark A. Jensen

APPENDIX

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

Constructor

   new
        Title   : new
        Usage   : my $obj = new Bio::DB::HIV();
        Function: Builds a new Bio::DB::HIV object
        Returns : an instance of Bio::DB::HIV
        Args    :

WebDBSeqI compliance

   get_request
        Title   : get_request
        Usage   : my $url = $self->get_request
        Function: returns a HTTP::Request object
        Returns :
        Args    : %qualifiers = a hash of qualifiers with keys in
                   (-ids, -format, -mode, -query)
        Note    : Several layers of requests are performed to get to the sequence;
                  see Bio::DB::Query::HIVQuery.

   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

WebDBSeqI overrides

   get_seq_stream
        Title   : get_seq_stream
        Usage   : my $seqio = $self->get_seq_stream(%qualifiers)
        Function: builds a url and queries a web db
        Returns : a Bio::SeqIO stream capable of producing sequence
        Args    : %qualifiers = a hash qualifiers that the implementing class
                  will process to make a url suitable for web querying
        Note    : Some tightening up of the baseclass version

   get_Stream_by_acc
         Title   : get_Stream_by_acc
         Usage   : $seq = $db->get_Stream_by_acc([$acc1, $acc2]);
         Function: Gets a series of Seq objects by GenBank accession numbers
         Returns : a Bio::SeqIO stream object
         Args    : an arrayref of accession numbers for
                   the desired sequence entries
         Note    : For LANL DB, alternative to LANL seqids

   get_Stream_by_query
         Title   : get_Stream_by_query
         Usage   : $stream = $db->get_Stream_by_query($query);
         Function: Gets a series of Seq objects by way of a query string or oject
         Returns : a Bio::SeqIO stream object
         Args    : $query : Currently, only a Bio::DB::Query::HIVQuery object.
                   It's a good idea to create the query object first and interrogate
                   it for the entry count before you fetch a potentially large stream.

Internals

   lanl_base
        Title   : lanl_base
        Usage   : $obj->lanl_base($newval)
        Function: get/set the base url of the LANL HIV database
        Example :
        Returns : value of lanl_base (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   map_db
        Title   : map_db
        Usage   : $obj->map_db($newval)
        Function: get/set the cgi filename for map_db ("Database Map")
        Example :
        Returns : value of map_db (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   make_search_if
        Title   : make_search_if
        Usage   : $obj->make_search_if($newval)
        Function: get/set the cgi filename for make_search_if ("Make Search Interface")
        Example :
        Returns : value of make_search_if (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   search_
        Title   : search_
        Usage   : $obj->search_($newval)
        Function: get/set the cgi filename for the search query page
                  ("Search Database")
        Example :
        Returns : value of search_ (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   _map_db_uri
        Title   : _map_db_uri
        Usage   :
        Function: return the full map_db uri ("Database Map")
        Example :
        Returns : scalar string
        Args    : none

   _make_search_if_uri
        Title   : _make_search_if_uri
        Usage   :
        Function: return the full make_search_if uri ("Make Search Interface")
        Example :
        Returns : scalar string
        Args    : none

   _search_uri
        Title   : _search_uri
        Usage   :
        Function: return the full search cgi uri ("Search Database")
        Example :
        Returns : scalar string
        Args    : none

   _session_id
        Title   : _session_id
        Usage   : $obj->_session_id($newval)
        Function: Contains HIV db session id (initialized in _do_lanl_request)
        Example :
        Returns : value of _session_id (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   _response
        Title   : _response
        Usage   : $obj->_response($newval)
        Function: hold the response to search post
        Example :
        Returns : value of _response (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   Dude, sorry
        Title   : _sorry
        Usage   : $hiv->_sorry
        Function: Throws an exception for unsupported option or parameter
        Example :
        Returns :
        Args    : scalar string