Provided by: libbio-perl-perl_1.6.924-3_all 
NAME
Bio::DB::HIV::HIVQueryHelper - Routines and packages used by Bio::DB::HIV and
Bio::DB::Query::HIVQuery
SYNOPSIS
Used in Bio::DB::Query::HIVQuery. No need to use directly.
DESCRIPTION
"Bio::DB::HIV::HIVQueryHelper" contains a number of packages for use by
Bio::DB::Query::HIVQuery. Package "HIVSchema" parses the "lanl-schema.xml" file, and
allows access to it in the context of the relational database it represents (see APPENDIX
for excruciating detail). Packages "QRY", "R", and "Q" together create the query string
parser that enables NCBI-like queries to be understood by "Bio::DB::Query::HIVQuery". They
provide objects and operators to perform and simplify logical expressions involving "AND",
"OR", and "()" and return hash structures that can be handled by
"Bio::DB::Query::HIVQuery" routines.
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 contained packages. Internal methods
are usually preceded with a _
HIVSchema - objects/methods to manipulate a version of the LANL HIV DB schema
HIVSchema SYNOPSIS
$schema = new HIVSchema( 'lanl-schema.xml' );
@tables = $schema->tables;
@validFields = $schema->fields;
@validAliases = $schema->aliases;
@query_aliases_for_coreceptor = $schema->aliases( 'SEQ_SAMple.SSAM_second_receptor' );
$pk_for_SequenceEntry = $schema->primarykey('SequenceEntry'); # returns 'SequenceEntry.SE_id'
$fk_for_SEQ_SAMple_to_SequenceEntry =
$schema->foreignkey('SEQ_SAMple', 'SequenceEntry'); # returns 'SEQ_SAMple.SSAM_SE_id'
$table = $schema->tablepart('SEQ_SAMple.SSAM_badseq'); # returns 'SEQ_SAMple'
$column = $schema->columnpart('SEQ_SAMple.SSAM_badseq'); # returns 'SSAM_badseq'
HIVSchema DESCRIPTION
HIVSchema methods are used in Bio::DB::Query::HIVQuery for table, column, primary/foreign
key manipulations based on the observed Los Alamos HIV Sequence Database (LANL DB) naming
conventions for their CGI parameters. The schema is contained in an XML file
("lanl-schema.xml") which is read into an HIVSchema object, in turn a property of the
HIVQuery object. HIVSchema methods are used to build correct cgi queries in a way that
attempts to preserve the context of the relational database the query parameters
represent.
HIVSchema CONSTRUCTOR
HIVSchema::new
Title : new
Usage : $schema = new HIVSchema( "lanl-schema.xml ");
Function:
Example :
Returns : an HIVSchema object
Args : XML filename
HIVSchema INSTANCE METHODS
HIVSchema tables
Title : tables
Usage : $schema->tables()
Function: get all table names in schema
Example :
Returns : array of table names
Args : none
HIVSchema columns
Title : columns
Usage : $schema->columns( [$tablename] );
Function: return array of columns for specified table, or all columns in
schema, if called w/o args
Example :
Returns :
Args : tablename or fieldname string
HIVSchema fields
Title : fields
Usage : $schema->fields();
Function: return array of all fields in schema, in format "table.column"
Example :
Returns : array of all fields
Args : none
HIVSchema options
Title : options
Usage : $schema->options(@fieldnames)
Function: get array of options (i.e., valid match data strings) available
to specified field
Example :
Returns : array of match data strings
Args : [array of] fieldname string[s] in "table.column" format
HIVSchema aliases
Title : aliases
Usage : $schema->aliases(@fieldnames)
Function: get array of aliases to specified field[s]
Example :
Returns : array of valid query aliases for fields as spec'd in XML file
Args : [an array of] fieldname[s] in "table.column" format
HIVSchema ankh
Title : ankh (annotation key hash)
Usage : $schema->ankh(@fieldnames)
Function: return a hash translating fields to annotation keys for the
spec'd fields.
(Annotation keys are used for parsing the tab-delimited response
to Bio::DB::Query::HIVQuery::_do_lanl_request.)
Example :
Returns : hash ref
Args : [an array of] fieldname[s] in "table.column" format
HIVSchema tablepart
Title : tablepart (alias: tbl)
Usage : $schema->tbl(@fieldnames)
Function: return the portion of the fieldname[s] that refer to the
db table
Example : $schema->tbl('SequenceEntry.SE_id'); # returns 'SequenceEntry'
Returns : table name as string
Args : [an array of] fieldname[s] in "table.column" format
HIVSchema columnpart
Title : columnpart (alias: col)
Usage : $schema->col(@fieldnames)
Function: return the portion of the fieldname[s] that refer to the
db column
Example : $schema->col('SequenceEntry.SE_id'); # returns 'SE_id'
Returns : column name as string
Args : [an array of] fieldname[s] in "table.column" format
HIVSchema primarykey
Title : primarykey [alias: pk]
Usage : $schema->pk(@tablenames);
Function: return the primary key of the specified table[s], as judged by
the syntax of the table's[s'] fieldnames
Example : $schema->pk('SequenceEntry') # returns 'SequenceEntry.SE_id'
Returns : primary key fieldname[s] in "table.column" format, or null if
no pk exists
Args : [an array of] table name[s] (fieldnames are ok, table part used)
HIVSchema foreignkey
Title : foreignkey [alias: fk]
Usage : $schema->fk($intable [, $totable])
Function: return foreign key fieldname in table $intable referring to
table $totable, or all foreign keys in $intable if $totable
unspec'd
Example : $schema->fk('AUthor', 'SequenceEntry'); # returns 'AUthor_AU_SE_id'
Returns : foreign key fieldname[s] in "table.column" format
Args : tablename [, optional foreign table name] (fieldnames are ok,
table part used)
HIVSchema foreigntable
Title : foreigntable [alias ftbl]
Usage : $schema->ftbl( @foreign_key_fieldnames );
Function: return tablename of table that foreign keys points to
Example : $schema->ftbl( 'AUthor.AU_SE_id' ); # returns 'SequenceEntry'
Returns : tablename
Args : [an array of] fieldname[s] in "table.column" format
HIVSchema find_join
Title : find_join
Usage : $sch->find_join('Table1', 'Table2')
Function: Retrieves a set of foreign and primary keys (in table.column
format) that represents a join path from Table1 to Table2
Example :
Returns : an array of keys (as table.column strings) -or- an empty
array if Table1 == Table2 -or- undef if no path exists
Args : two table names as strings
HIVSchema _find_join_guts
Title : _find_join_guts
Usage : $sch->_find_join_guts($table1, $table2, $stackref, \$found, $reverse)
(call with $stackref = [], $found=0)
Function: recursive guts of find_join
Example :
Returns : if a path is found, $found==1 and @$stackref contains the keys
in table.column format representing the path; if a path is not
found, $found == 0 and @$stackref contains garbage
Args : $table1, $table2 : table names as strings
$stackref : an arrayref to an empty array
\$found : a scalar ref to the value 0
$rev : if $rev==1, the arrays of table names will be reversed;
this can give a shorter path if cycles exist in the
schema graph
HIVSchema loadSchema
Title : loadHIVSchema [alias: loadSchema]
Usage : $schema->loadSchema( $XMLfilename )
Function: read (LANL DB) schema spec from XML
Example : $schema->loadSchema('lanl-schema.xml');
Returns : hashref to schema data
Keys are fieldnames in "table.column" format.
Each value is a hashref with the following properties:
{name} : HIVWEB 'table.column' format fieldname,
can be used directly in the cgi query
{aliases} : ref to array containing valid aliases/shortcuts for
{name}; can be used in routines creating the HTML query
{options} : ref to array containing valid matchdata for this field
can be used directly in the HTML query
{ankey} : contains the annotation key for this field used with
Bioperl annotation objects
{..attr..}: ..value_of_attr.. for this field (app-specific metadata)
Args :
HIVSchema _sfieldh
Title : _sfieldh
Usage : $schema->_sfieldh($fieldname)
Function: get hashref to the specified field hash
Example :
Returns : hashref
Args : fieldname in "table.column" format
Class QRY - a query algebra for HIVQuery
QRY SYNOPSIS
$Q = new QRY(
new R(
new Q('coreceptor', 'CXCR4'),
new Q('country', 'ZA')
)
);
QRY::Eq(QRY::And($Q, $Q), $Q); # returns 1
QRY::Eq(QRY::Or($Q, $Q), $Q); # returns 1
$Q2 = $Q1->clone;
$Q2 = new QRY(
new R(
new Q( 'coreceptor', 'CCR5' ),
new Q( 'country', 'ZA')
)
);
(QRY::And($Q, $Q2))->isnull; # returns 1
$Q3 = QRY::Or($Q, $Q2);
print $Q3->A; # prints '(CCR5 CXCR4)[coreceptor] (ZA)[country]'
QRY DESCRIPTION
The QRY package provides a query parser for Bio::DB::Query::HIVQuery. Currently, the
parser supports AND, OR, and () operations. The structure of the LANL cgi makes it tricky
to perform NOTs, though this could be implemented if the desire were great.
Two class methods do the work. "QRY::_parse_q" does a first-pass parse of the query
string. "QRY::_make_q" interprets the parse tree as returned by "QRY::_parse_q" and
produces an array of hash structures that can be used directly by
"Bio::DB::Query::HIVQuery" query execution methods. Validation of query fields and options
is performed at the "Bio::DB::Query::HIVQuery" level, not here.
"QRY" objects are collections of "R" (or request) objects, which are in turn collections
of "Q" (or atomic query) objects. "Q" objects represent a query on a single field, with
match data options "OR"ed together, e.g. "(A B)[subtype]". "R" objects collect "Q" objects
that could be processed in a single HTTP request; i.e., a set of atomic queries each
having different fields "AND"ed together, such as
(A B)[subtype] AND ('CCR5')[coreceptor] AND (US CA)[country]
The "QRY" object collects "R"s that cannot be reduced (through logical operations) to a
single HTTP request, e.g.
((C)[subtype] AND (SI)[phenotype]) OR ( (D)[subtype] AND (NSI)[phenotype] ),
which cannot be got in one go through the current LANL cgi implementation (as far as I can
tell). The parser will simplify something like
((C)[subtype] AND (SI)[phenotype]) OR ((C)[subtype] AND (NSI)[phenotype])
to the single request
(C)[subtype] AND (NSI SI)[phenotype]
however.
The operators "&" and "|" are overloaded to "QRY::And" and "QRY::Or", to get Perl
precedence and grouping for free. "bool" is overloaded to get symbolic tests such as "if
($QRY) {stuff}". "==" is overloaded with "QRY::Eq" for convenience. No overloading is done
for "R" or "Q".
QRY _make_q
Title : _make_q
Usage : QRY::_make_q($parsetree)
Function: creates hash structures suitable for HIVQuery from parse tree
returned by QRY::_parse_q
Example :
Returns : array of hashrefs of query specs
Args : a hashref
QRY _make_q_guts
Title : _make_q_guts (Internal class method)
Usage : _make_q_guts($ptree, $q_expr, $qarry, $anarry)
Function: traverses the parse tree returned from QRY::_parse_q, checking
syntax and creating HIVQuery-compliant query structures
Example :
Returns :
Args : $parse_tree (hashref), $query_expression (scalar string ref),
$query_array (array ref : stack for returning query structures),
$annotation_array (array ref : stack for returning annotation
fields)
QRY _parse_q
Title : _parse_q
Usage : QRY::_parse_q($query_string)
Function: perform first pass parse of a query string with some syntax
checking, return a parse tree suitable for QRY::_make_q
Example : QRY::_parse_q(" to[be] OR (not to)[be] ");
Returns : hashref
Args : query string
QRY CONSTRUCTOR
QRY Constructor
Title : QRY constructor
Usage : $QRY = new QRY()
Function:
Example :
Returns :
Args : array of R objects, optional
QRY INSTANCE METHODS
QRY requests
Title : requests
Usage : $QRY->requests
Function: get/set array of requests comprising this QRY object
Example :
Returns :
Args : array of class R objects
QRY put_requests
Title : put_requests
Usage : $QRY->put_request(@R)
Function: add object of class R to $QRY
Example :
Returns :
Args : [an array of] of class R object[s]
QRY isnull
Title : isnull
Usage : $QRY->isnull
Function: test if QRY object is null
Example :
Returns : 1 if null, 0 otherwise
Args :
QRY A
Title : A
Usage : print $QRY->A
Function: get a string representation of QRY object
Example :
Returns : string scalar
Args :
QRY len
Title : len
Usage : $QRY->len
Function: get number of class R objects contained by QRY object
Example :
Returns : scalar
Args :
QRY clone
Title : clone
Usage : $QRY2 = $QRY1->clone;
Function: create and return a clone of the object
Example :
Returns : object of class QRY
Args :
QRY CLASS METHODS
QRY Or
Title : Or
Usage : $QRY3 = QRY::Or($QRY1, $QRY2)
Function: logical OR for QRY objects
Example :
Returns : a QRY object
Args : two class QRY objects
QRY And
Title : And
Usage : $QRY3 = QRY::And($QRY1, $QRY2)
Function: logical AND for QRY objects
Example :
Returns : a QRY object
Args : two class QRY objects
QRY Bool
Title : Bool
Usage : QRY::Bool($QRY1)
Function: allows symbolic testing of QRY object when bool overloaded
Example : do {stuff} if $QRY1 *same as* do {stuff} if !$QRY1->isnull
Returns :
Args : a class QRY object
QRY Eq
Title : Eq
Usage : QRY::Eq($QRY1, $QRY2)
Function: test if R objects in two QRY objects are the same
(irrespective of order)
Example :
Returns : 1 if equal, 0 otherwise
Args : two class QRY objects
Class R - request objects for QRY algebra
R SYNOPSIS
$R = new R( $q1, $q2 );
$R->put_atoms($q3);
$R->del_atoms('coreceptor', 'phenotype');
return $R->clone;
$R1 = new R( new Q('subtype', 'B') );
$R2 = new R( new Q('subtype', 'B C'),
new Q('country', 'US') );
R::Eq( (R::And($R1, $R2))[0],
new R( new Q('subtype', 'B' ),
new Q('country', 'US') )); # returns 1
QRY::Eq( new QRY(R::Or($R1, $R2)), new QRY($R1, $R2) ); # returns 1
R::In( (R::And($R1, $R2))[0], $R1 ); # returns 1
R DESCRIPTION
Class R objects contain a list of atomic queries (class Q objects). Each class R object
represents a single HTTP request to the LANL DB. When converted to a DB query, the class Q
objects contained by an R object are effectively "AND"ed.
R CONSTRUCTOR
R constructor
Title : R constructor
Usage : $R = new R()
Function: create a new R (request) object
Example :
Returns : class R (request) object
Args : optional, array of class Q objects
R INSTANCE METHODS
R len
Title : len
Usage : $R->len
Function: get number of class Q objects contained in R object
Example :
Returns : scalar
Args :
R atoms
Title : atoms
Usage : $R->atoms( [optional $field])
Function: get array of class Q (atomic query) objects in class R object
Example : $R->atoms(); $R->atoms('coreceptor')
Returns : array of class Q objects (all Qs or those corresponding to $field
if present)
Args : optional, scalar string
R fields
Title : fields
Usage : $R->fields
Function: get array of fields of all Q objects contained in $R
Example :
Returns : array of scalars
Args :
R put_atoms
Title : put_atoms
Usage : $R->put_atoms( @q )
Function: AND an atomic query (class Q object) to the class R object's list
Example :
Returns : void
Args : an [array of] class Q object[s]
R del_atoms
Title : del_atoms
Usage : $R->del_atoms( @qfields )
Function: removes class Q objects from R object's list according to the
field names given in arguments
Example :
Returns : the class Q objects deleted
Args : scalar array of field names
R isnull
Title : isnull
Usage : $R->isnull
Function: test if class R object is null
Example :
Returns : 1 if null, 0 otherwise
Args :
R A
Title : A
Usage : print $R->A
Function: get a string representation of class R object
Example :
Returns : string scalar
Args :
R clone
Title : clone
Usage : $R2 = $R1->clone;
Function: create and return a clone of the object
Example :
Returns : object of class R
Args :
R CLASS METHODS
R In
Title : In
Usage : R::In($R1, $R2)
Function: tests whether the query represented by $R1 would return a subset
of items returned by the query represented by $R2
Example : print "R2 gets those and more" if R::In($R1, $R2);
Returns : 1 if R1 is subset of R2, 0 otherwise
Args : two class R objects
R And
Title : And
Usage : @Rresult = R::And($R1, $R2)
Function: logical AND for R objects
Example :
Returns : an array containing class R objects
Args : two class R objects
R Or
Title : Or
Usage : @Rresult = R::Or($R1, $R2)
Function: logical OR for R objects
Example :
Returns : an array containing class R objects
Args : two class R objects
R Eq
Title : Eq
Usage : R::Eq($R1, $R2)
Function: test if class Q objects in two R objects are the same
(irrespective of order)
Example :
Returns : 1 if equal, 0 otherwise
Args : two class R objects
Class Q - atomic query objects for QRY algebra
Q SYNOPSIS
$q = new Q('coreceptor', 'CXCR4 CCR5');
$u = new Q('coreceptor', 'CXCR4');
$q->fld; # returns 'coreceptor'
$q->dta; # returns 'CXCR4 CCR5'
print $q->A; # prints '(CXCR4 CCR5)[coreceptor]
Q::qeq($q, $u); # returns 0
Q::qeq( Q::qor($q, $q), $q ); # returns 1
Q::qin($u, $q) # returns 1
Q::qeq(Q::qand($u, $q), $u ); # returns 1
Q DESCRIPTION
Class Q objects represent atomic queries, that can be described by a single LANL cgi
parameter=value pair. Class R objects (requests) are built from class Qs. The logical
operations at the higher levels ("QRY, R") ultimately depend on the lower level operations
on Qs: "qeq, qin, qand, qor".
Q CONSTRUCTOR
Q constructor
Title : Q constructor
Usage : $q = new Q($field, $data)
Function: create a new Q (atomic query) object
Example :
Returns : class Q object
Args : optional $field, $data strings
Q INSTANCE METHODS
Q isnull
Title : isnull
Usage : $q->isnull
Function: test if class Q object is null
Example :
Returns : 1 if null, 0 otherwise
Args :
Q fld
Title : fld
Usage : $q->fld($field)
Function: get/set fld (field name) property
Example :
Returns : scalar
Args : scalar
Q dta
Title : dta
Usage : $q->dta($data)
Function: get/set dta (whsp-separated data string) property
Example :
Returns : scalar
Args : scalar
Q A
Title : A
Usage : print $q->A
Function: get a string representation of class Q object
Example :
Returns : string scalar
Args :
Q clone
Title : clone
Usage : $q2 = $q1->clone;
Function: create and return a clone of the object
Example :
Returns : object of class Q
Args :
Q CLASS METHODS
Q qin
Title : qin
Usage : Q::qin($q1, $q2)
Function: tests whether the query represented by $q1 would return a subset
of items returned by the query represented by $q2
Example : print "q2 gets those and more" if Q::qin($q1, $q2);
Returns : 1 if q1 is subset of q2, 0 otherwise
Args : two class Q objects
Q qeq
Title : qeq
Usage : Q::qeq($q1, $q2)
Function: test if fld and dta properties in two class Q objects are the same
(irrespective of order)
Example :
Returns : 1 if equal, 0 otherwise
Args : two class Q objects
Q qor
Title : qor
Usage : @qresult = Q::qor($q1, $q2)
Function: logical OR for Q objects
Example :
Returns : an array of class Q objects
Args : two class Q objects
Q qand
Title : qand
Usage : @qresult = Q::And($q1, $q2)
Function: logical AND for R objects
Example :
Returns : an array of class Q objects
Args : two class Q objects
Q INTERNALS
Q unique
Title : unique
Usage : @ua = unique(@a)
Function: return contents of @a with duplicates removed
Example :
Returns :
Args : an array
Additional tools for Bio::AnnotationCollectionI
Bio::AnnotationCollectionI SYNOPSIS (additional methods)
$seq->annotation->put_value('patient_id', 1401)
$seq->annotation->get_value('patient_ids') # returns 1401
$seq->annotation->put_value('patient_group', 'MassGenH')
$seq->annotation->put_value(['clinical', 'cd4count'], 503);
$seq->annotation->put_value(['clinical', 'virus_load'], 150805);
foreach ( qw( cd4count virus_load ) ) {
$blood_readings{$_} = $seq->annonation->get_value(['clinical', $_]);
}
Bio::AnnotationCollectionI DESCRIPTION (additional methods)
"get_value()" and "put_value" allow easy creation of and access to an annotation
collection tree with nodes of Bio::Annotation::SimpleValue. These methods obiviate direct
accession of the SimpleValue objects.
get_value
Title : get_value
Usage : $ac->get_value($tagname) -or-
$ac->get_value( $tag_level1, $tag_level2,... )
Function: access the annotation value assocated with the given tags
Example :
Returns : a scalar
Args : an array of tagnames that descend into the annotation tree
put_value
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 )
Note : 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'.
get_keys
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]