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