| Bio::DB::Query::HIVQuery(3pm) | User Contributed Perl Documentation | Bio::DB::Query::HIVQuery(3pm) |
Bio::DB::Query::HIVQuery - Query interface to the Los Alamos HIV Sequence Database
$q = new Bio::DB::Query::HIVQuery(" C[subtype] ZA[country] CXCR4[coreceptor] ");
$q = new Bio::DB::Query::HIVQuery(
-query=>{'subtype'=>'C',
'country'=>'ZA',
'coreceptor'=>'CXCR4'});
$ac = $q->get_annotations_by_id(($q->ids)[0]);
$ac->get_value('Geo', 'country') # returns 'SOUTH AFRICA'
$db = new Bio::DB::HIV();
$seqio = $db->get_Stream_by_query($q); # returns annotated Bio::Seqs
# get subtype C sequences from South Africa and Brazil,
# with associated info on patient health, coreceptor use, and
# infection period:
$q = new Bio::DB::Query::HIVQuery(
-query => {
'query' => {'subtype'=>'C',
'country'=>['ZA', 'BR']},
'annot' => ['patient_health',
'coreceptor',
'days_post_infection']
});
Bio::DB::Query::HIVQuery provides a query-like interface to the cgi-based Los Alamos National Laboratory (LANL) HIV Sequence Database. It uses Bioperl facilities to capture both sequences and annotations in batch in an automated and computable way. Use with Bio::DB::HIV to create "Bio::Seq" objects and annotated "Bio::SeqIO" streams.
The interface implements a simple query language emulation that understands AND, OR, and parenthetical nesting. The basic query unit is
(match1 match2 ...)[fieldname]
Sequences are returned for which "fieldname" equals "match1 OR match2 OR ...". These units can be combined with AND, OR and parentheses. For example:
(B, C)[subtype] AND (2000, 2001, 2002, 2003)[year] AND ((CN)[country] OR (ZA)[country])
which can be shortened to
(B C)[subtype] (2000 2001 2002 2003)[year] (CN ZA)[country]
The user can specify annotation fields, that do not restrict the query, but arrange for the return of the associated field data for each sequence returned. Specify annotation fields between curly braces, as in:
(B C)[subtype] 2000[year] {country cd4_count cd8_count}
Annotations can be accessed off the query using methods described in APPENDIX.
Single query specifications can be made as hash references provided to the "-query" argument of the constructor. There are two forms:
-query => { 'country'=>'BR', 'phenotype'=>'NSI', 'cd4_count'=>'Any' }
equivalent to
-query => [ 'country'=>'BR', 'phenotype'=>'NSI', 'cd4_count'=>'Any' ]
or
-query => { 'query' => {'country'=>'BR', 'phenotype'=>'NSI'},
'annot' => ['cd4_count'] }
In both cases, the CD4 count is included in the annotations returned, but does not restrict the rest of the query.
To 'OR' multiple values of a field, use an anonymous array ref:
-query => { 'country'=>['ZA','BR','NL'], 'subtype'=>['A', 'C', 'D'] }
An attempt was made to make the query field names natural and easy to remember. Aliases are specified in an XML file ("lanl-schema.xml") that is part of the distribution. Custom field aliases can be set up by modifying this file.
An HTML cheatsheet with valid field names, aliases, and match data can be generated from the XML by using "hiv_object->help('help.html')". A query can also be validated locally before it is unleashed on the server; see below.
LANL DB annotations have been organized into a number of natural groupings, tagged "Geo", "Patient", "Virus", and "StdMap". After a successful query, each id is associated with a tree of Bio::Annotation::SimpleValue objects. These can be accessed with methods "get_value" and "put_value" described in APPENDIX.
Accessing the LANL DB involves multiple HTTP requests. The query can be instructed to proceed through all (the default) or only some of them, using the named parameter "RUN_OPTION".
To validate a query locally, use
$q = new Bio::DB::Query::HIVQuery( -query => {...}, -RUN_OPTION=>0 )
which will throw an exception if a field name or option is invalid.
To get a query count only, you can save a server hit by using
$q = new Bio::DB::Query::HIVQuery( -query => {...}, -RUN_OPTION=>1 )
and asking for "$q->count". To finish the query, do
$q->_do_query(2)
which picks up where you left off.
"-RUN_OPTION=>2", the default, runs the full query, returning ids and annotations.
You can clear the query results, retaining the same LANL session and query spec, by doing "$q->_reset". Change the query, and rerun with "$q->_do_query($YOUR_RUN_OPTION)".
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
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.
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
Email maj@fortinbras.us
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 $hiv_query = new Bio::DB::Query::HIVQuery();
Function: Builds a new Bio::DB::Query::HIVQuery object,
running a sequence query against the Los Alamos
HIV sequence database
Returns : an instance of Bio::DB::Query::HIVQuery
Args :
Title : count
Usage : $hiv_query->count($newval)
Function: return number of sequences found
Example :
Returns : value of count (a scalar)
Args : on set, new value (a scalar or undef, optional)
Note : count warns if it is accessed for reading before query
has been executed to at least level 1
Title : ids Usage : $hiv_query->ids($newval) Function: LANL ids of returned sequences Example : Returns : value of ids (an arrayref of sequence accessions/ids) Args : on set, new value (an arrayref or undef, optional)
Title : query Usage : $hiv_query->query Function: Get/set the submitted query hash or string Example : Returns : hashref or string Args : query in hash or string form (see DESCRIPTION)
Title : help
Usage : $hiv_query->help("help.html")
Function: get html-formatted listing of valid fields/aliases/options
based on current schema xml
Example : perl -MBio::DB::Query::HIVQuery -e "new Bio::DB::Query::HIVQuery()->help" | lynx -stdin
Returns : HTML
Args : optional filename; otherwise prints to stdout
Title : get_annotations_by_ids (or ..._by_id) Usage : $ac = $hiv_query->get_annotations_by_ids(@ids) Function: Get the Bio::Annotation::Collection for these sequence ids Example : Returns : A Bio::Annotation::Collection object Args : an array of sequence ids
Title : add_annotations_for_id
Usage : $hiv_query->add_annotations_for_id( $id ) to create a new
empty collection for $id
$hiv_query->add_annotations_for_id( $id, $ac ) to associate
$ac with $id
Function: Associate a Bio::Annotation::Collection with this sequence id
Example :
Returns : a Bio::Annotation::Collection object
Args : sequence id [, Bio::Annotation::Collection object]
Title : remove_annotations_for_ids (or ..._for_id) Usage : $hiv_query->remove_annotations_for_ids( @ids) Function: Remove annotation collection for this sequence id Example : Returns : An array of the previous annotation collections for these ids Args : an array of sequence ids
Title : remove_annotations Usage : $hiv_query->remove_annotations() Function: Remove all annotation collections for this object Example : Returns : The previous annotation collection hash for this object Args : none
Title : get_value
Usage : $ac->get_value($tagname) -or-
$ac->get_value( $tag_level1, $tag_level2,... )
Function: access the annotation value associated with the given tags
Example :
Returns : a scalar
Args : an array of tagnames that descend into the annotation tree
Note : this is a L<Bio::AnnotationCollectionI> method added in
L<Bio::DB::HIV::HIVQueryHelper>
Title : put_value
Usage : $ac->put_value($tagname, $value) -or-
$ac->put_value([$tag_level1, $tag_level2, ...], $value) -or-
$ac->put_value( [$tag_level1, $tag_level2, ...] )
Function: create a node in an annotation tree, and assign a scalar value to it
if a value is specified
Example :
Returns : scalar or a Bio::AnnotationCollection object
Args : $tagname, $value scalars (can be specified as -KEYS=>$tagname,
-VALUE=>$value) -or-
\@tagnames, $value (or as -KEYS=>\@tagnames, -VALUE=>$value )
Notes : This is a L<Bio::AnnotationCollectionI> method added in
L<Bio::DB::HIV::HIVQueryHelper>.
If intervening nodes do not exist, put_value creates them, replacing
existing nodes. So if $ac->put_value('x', 10) was done, then later,
$ac->put_value(['x', 'y'], 20), the original value of 'x' is trashed,
and $ac->get_value('x') will now return the annotation collection
with tagname 'y'.
Title : get_keys
Usage : $ac->get_keys($tagname_level_1, $tagname_level_2,...)
Function: Get an array of tagnames underneath the named tag nodes
Example : # prints the values of the members of Category 1...
print map { $ac->get_value($_) } $ac->get_keys('Category 1') ;
Returns : array of tagnames or empty list if the arguments represent a leaf
Args : [array of] tagname[s]
Title : get_accessions
Usage : $hiv_query->get_accessions()
Function: Return an array of GenBank accessions associated with these
sequences (available only after a query is subjected to a
full run (i.e., when $RUN_OPTION == 2)
Example :
Returns : array of gb accession numbers, or () if none found for this query
Args : none
Title : get_accessions_by_ids (or ..._by_id)
Usage : $hiv_query->get_accessions_by_ids(@ids)
Function: Return an array of GenBank accessions associated with these
LANL ids (available only after a query is subjected to a
full run (i.e., when $RUN_OPTION == 2)
Example :
Returns : array of gb accession numbers, or () if none found for this query
Args : none
Title : _do_query
Usage : $hiv_query->_do_query or $hiv_query->_do_query($run_level)
Function: Execute the query according to argument or $RUN_OPTION
and set _RUN_LEVEL
extent of query reflects the value of argument
0 : validate only (no HTTP action)
1 : return sequence count only
2 : return sequence ids (full query, returns with annotations)
noop if current _RUN_LEVEL of query is >= argument or $RUN_OPTION,
Example :
Returns : actual _RUN_LEVEL (0, 1, or 2) achieved
Args : desired run level (optional, global $RUN_OPTION is default)
Title : _reset
Usage : $hiv_query->_reset
Function: Resets query storage, count, and ids, while retaining session id,
original query string, and db schema
Example :
Returns : void
Args : none
Title : _session_id Usage : $hiv_query->_session_id($newval) Function: Get/set 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 : _run_level Usage : $obj->_run_level($newval) Function: returns the level at which the query has so far been run Example : Returns : value of _run_level (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : _run_option Usage : $hiv_query->_run_option($newval) Function: Get/set HIV db query run option (see _do_query for values) Example : Returns : value of _run_option (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : _ua_hash Usage : $obj->_ua_hash($newval) Function: Example : Returns : value of _ua_hash (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : add_id Usage : $hiv_query->add_id($id) Function: Add new id to ids Example : Returns : the new id Args : a sequence id
Title : map_db Usage : $obj->map_db($newval) Function: 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: 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: 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 : _schema_file Usage : $hiv_query->_schema_file($newval) Function: Example : Returns : value of _schema_file (an XML string or filename) Args : on set, new value (an XML string or filename, or undef, optional)
Title : _schema
Usage : $hiv_query->_schema($newVal)
Function:
Example :
Returns : value of _schema (an HIVSchema object in package
L<Bio::DB::HIV::HIVQueryHelper>)
Args : none (field set directly in new())
Title : _lanl_query
Usage : $hiv_query->_lanl_query(\@query_parms)
Function: pushes \@query_parms onto @{$self->{'_lanl_query'}
Example :
Returns : value of _lanl_query (an arrayref)
Args : on set, new value (an arrayref or undef, optional)
Title : _lanl_response
Usage : $hiv_query->_lanl_response($response)
Function: pushes $response onto @{$hiv_query->{'_lanl_response'}}
Example :
Returns : value of _lanl_response (an arrayref of HTTP::Response objects)
Args : on set, new value (an HTTP::Response object or undef, optional)
Title : _create_lanl_query Usage : $hiv_query->_create_lanl_query() Function: validate query hash or string, prepare for _do_lanl_request Example : Returns : 1 if successful; throws exception on invalid query Args :
Title : _do_lanl_request Usage : $hiv_query->_do_lanl_request() Function: Perform search request on _create_lanl_query-validated query Example : Returns : 1 if successful Args :
Title : _parse_lanl_response
Usage : $hiv_query->_parse_lanl_response()
Function: Parse the tab-separated-value response obtained by _do_lanl_request
for sequence ids, accessions, and annotations
Example :
Returns : 1 if successful
Args :
Title : _parse_query_string
Usage : $hiv_query->_parse_query_string($str)
Function: Parses a query string using query language emulator QRY
: in L<Bio::DB::Query::HIVQueryHelper>
Example :
Returns : arrayref of hash structures suitable for passing to _create_lanl_query
Args : a string scalar
Title : _sorry
Usage : $hiv_query->_sorry("-president=>Powell")
Function: Throws an exception for unsupported option or parameter
Example :
Returns :
Args : scalar string
| 2018-10-27 | perl v5.26.2 |