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Bio::DB::HIV.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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