Bio::DB::HIV(3) 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. 

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Mark A. Jensen

Email [email protected]

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

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