Bio::DB::HIV(3) User Contributed Perl Documentation Bio::DB::HIV(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::DB::HIV(3)
