| Bio::DB::HIV(3pm) | User Contributed Perl Documentation | Bio::DB::HIV(3pm) |
Bio::DB::HIV - Database object interface to the Los Alamos HIV Sequence Database
$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'
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".
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Mark A. Jensen
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 :
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.
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
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
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
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.
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)
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)
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)
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)
Title : _map_db_uri
Usage :
Function: return the full map_db uri ("Database Map")
Example :
Returns : scalar string
Args : none
Title : _make_search_if_uri
Usage :
Function: return the full make_search_if uri ("Make Search Interface")
Example :
Returns : scalar string
Args : none
Title : _search_uri
Usage :
Function: return the full search cgi uri ("Search Database")
Example :
Returns : scalar string
Args : none
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)
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)
Title : _sorry Usage : $hiv->_sorry Function: Throws an exception for unsupported option or parameter Example : Returns : Args : scalar string
| 2018-10-27 | perl v5.26.2 |