#
# BioPerl module for Bio::SearchIO::SearchResultEventBuilder
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SearchIO::SearchResultEventBuilder - Event Handler for SearchIO events.
=head1 SYNOPSIS
# Do not use this object directly, this object is part of the SearchIO
# event based parsing system.
=head1 DESCRIPTION
This object handles Search Events generated by the SearchIO classes
and build appropriate Bio::Search::* objects from them.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 CONTRIBUTORS
Sendu Bala, bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SearchIO::SearchResultEventBuilder;
use strict;
use Bio::Factory::ObjectFactory;
use base qw(Bio::Root::Root Bio::SearchIO::EventHandlerI);
use vars qw($DEFAULT_INCLUSION_THRESHOLD
$MAX_HSP_OVERLAP
);
# e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp)
# NOTE: Executing `blastpgp -` incorrectly reports that the default is 0.005.
# (version 2.2.2 [Jan-08-2002])
$DEFAULT_INCLUSION_THRESHOLD = 0.001;
$MAX_HSP_OVERLAP = 2; # Used when tiling multiple HSPs.
=head2 new
Title : new
Usage : my $obj = Bio::SearchIO::SearchResultEventBuilder->new();
Function: Builds a new Bio::SearchIO::SearchResultEventBuilder object
Returns : Bio::SearchIO::SearchResultEventBuilder
Args : -hsp_factory => Bio::Factory::ObjectFactoryI
-hit_factory => Bio::Factory::ObjectFactoryI
-result_factory => Bio::Factory::ObjectFactoryI
-inclusion_threshold => e-value threshold for inclusion in the
PSI-BLAST score matrix model (blastpgp)
-signif => float or scientific notation number to be used
as a P- or Expect value cutoff
-score => integer or scientific notation number to be used
as a blast score value cutoff
-bits => integer or scientific notation number to be used
as a bit score value cutoff
-hit_filter => reference to a function to be used for
filtering hits based on arbitrary criteria.
See L<Bio::Factory::ObjectFactoryI> for more information
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($resultF, $hitF, $hspF) =
$self->_rearrange([qw(RESULT_FACTORY
HIT_FACTORY
HSP_FACTORY)],@args);
$self->_init_parse_params(@args);
$self->register_factory('result', $resultF ||
Bio::Factory::ObjectFactory->new(
-type => 'Bio::Search::Result::GenericResult',
-interface => 'Bio::Search::Result::ResultI'));
$self->register_factory('hit', $hitF ||
Bio::Factory::ObjectFactory->new(
-type => 'Bio::Search::Hit::GenericHit',
-interface => 'Bio::Search::Hit::HitI'));
$self->register_factory('hsp', $hspF ||
Bio::Factory::ObjectFactory->new(
-type => 'Bio::Search::HSP::GenericHSP',
-interface => 'Bio::Search::HSP::HSPI'));
return $self;
}
# Initializes parameters used during parsing of reports.
sub _init_parse_params {
my ($self, @args) = @_;
# -FILT_FUNC has been replaced by -HIT_FILTER.
# Leaving -FILT_FUNC in place for backward compatibility
my($ithresh, $signif, $score, $bits, $hit_filter, $filt_func) =
$self->_rearrange([qw(INCLUSION_THRESHOLD SIGNIF SCORE BITS
HIT_FILTER FILT_FUNC
)], @args);
$self->inclusion_threshold( defined($ithresh) ? $ithresh : $DEFAULT_INCLUSION_THRESHOLD);
my $hit_filt = $hit_filter || $filt_func;
defined $hit_filter && $self->hit_filter($hit_filt);
defined $signif && $self->max_significance($signif);
defined $score && $self->min_score($score);
defined $bits && $self->min_bits($bits);
}
=head2 will_handle
Title : will_handle
Usage : if( $handler->will_handle($event_type) ) { ... }
Function: Tests if this event builder knows how to process a specific event
Returns : boolean
Args : event type name
=cut
sub will_handle{
my ($self,$type) = @_;
# these are the events we recognize
return ( $type eq 'hsp' || $type eq 'hit' || $type eq 'result' );
}
=head2 SAX methods
=cut
=head2 start_result
Title : start_result
Usage : $handler->start_result($resulttype)
Function: Begins a result event cycle
Returns : none
Args : Type of Report
=cut
sub start_result {
my ($self,$type) = @_;
$self->{'_resulttype'} = $type;
$self->{'_hits'} = [];
$self->{'_hsps'} = [];
$self->{'_hitcount'} = 0;
return;
}
=head2 end_result
Title : end_result
Usage : my @results = $parser->end_result
Function: Finishes a result handler cycle
Returns : A Bio::Search::Result::ResultI
Args : none
=cut
# this is overridden by IteratedSearchResultEventBuilder
# so keep that in mind when debugging
sub end_result {
my ($self,$type,$data) = @_;
if( defined $data->{'runid'} &&
$data->{'runid'} !~ /^\s+$/ ) {
if( $data->{'runid'} !~ /^lcl\|/) {
$data->{"RESULT-query_name"} = $data->{'runid'};
} else {
($data->{"RESULT-query_name"},
$data->{"RESULT-query_description"}) =
split(/\s+/,$data->{"RESULT-query_description"},2);
}
if( my @a = split(/\|/,$data->{'RESULT-query_name'}) ) {
my $acc = pop @a ; # this is for accession |1234|gb|AAABB1.1|AAABB1
# this is for |123|gb|ABC1.1|
$acc = pop @a if( ! defined $acc || $acc =~ /^\s+$/);
$data->{"RESULT-query_accession"}= $acc;
}
delete $data->{'runid'};
}
my %args = map { my $v = $data->{$_}; s/RESULT//; ($_ => $v); }
grep { /^RESULT/ } keys %{$data};
$args{'-algorithm'} = uc( $args{'-algorithm_name'}
|| $data->{'RESULT-algorithm_name'}
|| $type);
($self->isa('Bio::SearchIO::IteratedSearchResultEventBuilder')) ?
( $args{'-iterations'} = $self->{'_iterations'} )
: ( $args{'-hits'} = $self->{'_hits'} );
my $result = $self->factory('result')->create_object(%args);
$result->hit_factory($self->factory('hit'));
($self->isa('Bio::SearchIO::IteratedSearchResultEventBuilder')) ?
( $self->{'_iterations'} = [] )
: ( $self->{'_hits'} = [] );
return $result;
}
=head2 start_hsp
Title : start_hsp
Usage : $handler->start_hsp($name,$data)
Function: Begins processing a HSP event
Returns : none
Args : type of element
associated data (hashref)
=cut
sub start_hsp {
my ($self,@args) = @_;
return;
}
=head2 end_hsp
Title : end_hsp
Usage : $handler->end_hsp()
Function: Finish processing a HSP event
Returns : none
Args : type of event and associated hashref
=cut
sub end_hsp {
my ($self,$type,$data) = @_;
if( defined $data->{'runid'} &&
$data->{'runid'} !~ /^\s+$/ ) {
if( $data->{'runid'} !~ /^lcl\|/) {
$data->{"RESULT-query_name"}= $data->{'runid'};
} else {
($data->{"RESULT-query_name"},
$data->{"RESULT-query_description"}) =
split(/\s+/,$data->{"RESULT-query_description"},2);
}
if( my @a = split(/\|/,$data->{'RESULT-query_name'}) ) {
my $acc = pop @a ; # this is for accession |1234|gb|AAABB1.1|AAABB1
# this is for |123|gb|ABC1.1|
$acc = pop @a if( ! defined $acc || $acc =~ /^\s+$/);
$data->{"RESULT-query_accession"}= $acc;
}
delete $data->{'runid'};
}
# this code is to deal with the fact that Blast XML data
# always has start < end and one has to infer strandedness
# from the frame which is a problem for the Search::HSP object
# which expect to be able to infer strand from the order of
# of the begin/end of the query and hit coordinates
if( defined $data->{'HSP-query_frame'} && # this is here to protect from undefs
(( $data->{'HSP-query_frame'} < 0 &&
$data->{'HSP-query_start'} < $data->{'HSP-query_end'} ) ||
$data->{'HSP-query_frame'} > 0 &&
( $data->{'HSP-query_start'} > $data->{'HSP-query_end'} ) )
)
{
# swap
($data->{'HSP-query_start'},
$data->{'HSP-query_end'}) = ($data->{'HSP-query_end'},
$data->{'HSP-query_start'});
}
if( defined $data->{'HSP-hit_frame'} && # this is here to protect from undefs
((defined $data->{'HSP-hit_frame'} && $data->{'HSP-hit_frame'} < 0 &&
$data->{'HSP-hit_start'} < $data->{'HSP-hit_end'} ) ||
defined $data->{'HSP-hit_frame'} && $data->{'HSP-hit_frame'} > 0 &&
( $data->{'HSP-hit_start'} > $data->{'HSP-hit_end'} ) )
)
{
# swap
($data->{'HSP-hit_start'},
$data->{'HSP-hit_end'}) = ($data->{'HSP-hit_end'},
$data->{'HSP-hit_start'});
}
$data->{'HSP-query_frame'} ||= 0;
$data->{'HSP-hit_frame'} ||= 0;
# handle Blast 2.1.2 which did not support data member: hsp_align-len
$data->{'HSP-query_length'} ||= $data->{'RESULT-query_length'};
$data->{'HSP-hit_length'} ||= $data->{'HIT-length'};
# If undefined lengths, calculate from alignment without gaps and separators
if (not defined $data->{'HSP-query_length'}) {
if (my $hsp_qry_seq = $data->{'HSP-query_seq'}) {
$hsp_qry_seq =~ s/[-\.]//g;
$data->{'HSP-query_length'} = length $hsp_qry_seq;
}
else {
$data->{'HSP-query_length'} = 0;
}
}
if (not defined $data->{'HSP-hit_length'}) {
if (my $hsp_hit_seq = $data->{'HSP-hit_seq'}) {
$hsp_hit_seq =~ s/[-\.]//g;
$data->{'HSP-hit_length'} = length $hsp_hit_seq;
}
else {
$data->{'HSP-hit_length'} = 0;
}
}
$data->{'HSP-hsp_length'} ||= length ($data->{'HSP-homology_seq'} || '');
my %args = map { my $v = $data->{$_}; s/HSP//; ($_ => $v) }
grep { /^HSP/ } keys %{$data};
$args{'-algorithm'} = uc( $args{'-algorithm_name'} ||
$data->{'RESULT-algorithm_name'} || $type);
# copy this over from result
$args{'-query_name'} = $data->{'RESULT-query_name'};
$args{'-hit_name'} = $data->{'HIT-name'};
my ($rank) = scalar @{$self->{'_hsps'} || []} + 1;
$args{'-rank'} = $rank;
$args{'-hit_desc'} = $data->{'HIT-description'};
$args{'-query_desc'} = $data->{'RESULT-query_description'};
my $bits = $args{'-bits'};
my $hsp = \%args;
push @{$self->{'_hsps'}}, $hsp;
return $hsp;
}
=head2 start_hit
Title : start_hit
Usage : $handler->start_hit()
Function: Starts a Hit event cycle
Returns : none
Args : type of event and associated hashref
=cut
sub start_hit{
my ($self,$type) = @_;
$self->{'_hsps'} = [];
return;
}
=head2 end_hit
Title : end_hit
Usage : $handler->end_hit()
Function: Ends a Hit event cycle
Returns : Bio::Search::Hit::HitI object
Args : type of event and associated hashref
=cut
sub end_hit{
my ($self,$type,$data) = @_;
# Skip process unless there is HSP data or Hit Significance (e.g. a bl2seq with no similarity
# gives a hit with the subject, but shows a "no hits found" message instead
# of the alignment data and don't have a significance value).
# This way, we avoid false positives
my @hsp_data = grep { /^HSP/ } keys %{$data};
return unless (scalar @hsp_data > 0 or exists $data->{'HIT-significance'});
my %args = map { my $v = $data->{$_}; s/HIT//; ($_ => $v); } grep { /^HIT/ } keys %{$data};
# I hate special cases, but this is here because NCBI BLAST XML
# doesn't play nice and is undergoing mutation -jason
if(exists $args{'-name'} && $args{'-name'} =~ /BL_ORD_ID/ ) {
($args{'-name'}, $args{'-description'}) = split(/\s+/,$args{'-description'},2);
}
$args{'-algorithm'} = uc( $args{'-algorithm_name'} ||
$data->{'RESULT-algorithm_name'} || $type);
$args{'-hsps'} = $self->{'_hsps'};
$args{'-query_len'} = $data->{'RESULT-query_length'};
$args{'-rank'} = $self->{'_hitcount'} + 1;
unless( defined $args{'-significance'} ) {
if( defined $args{'-hsps'} &&
$args{'-hsps'}->[0] ) {
# use pvalue if present (WU-BLAST), otherwise evalue (NCBI BLAST)
$args{'-significance'} = $args{'-hsps'}->[0]->{'-pvalue'} || $args{'-hsps'}->[0]->{'-evalue'};
}
}
my $hit = \%args;
$hit->{'-hsp_factory'} = $self->factory('hsp');
$self->_add_hit($hit);
$self->{'_hsps'} = [];
return $hit;
}
# Title : _add_hit (private function for internal use only)
# Purpose : Applies hit filtering and store it if it passes filtering.
# Argument: Bio::Search::Hit::HitI object
sub _add_hit {
my ($self, $hit) = @_;
my $hit_signif = $hit->{-significance};
# Test significance using custom function (if supplied)
my $add_hit = 1;
my $hit_filter = $self->{'_hit_filter'};
if($hit_filter) {
# since &hit_filter is out of our control and would expect a HitI object,
# we're forced to make one for it
$hit = $self->factory('hit')->create_object(%{$hit});
$add_hit = 0 unless &$hit_filter($hit);
}
else {
if($self->{'_confirm_significance'}) {
$add_hit = 0 unless $hit_signif <= $self->{'_max_significance'};
}
if($self->{'_confirm_score'}) {
my $hit_score = $hit->{-score} || $hit->{-hsps}->[0]->{-score};
$add_hit = 0 unless $hit_score >= $self->{'_min_score'};
}
if($self->{'_confirm_bits'}) {
my $hit_bits = $hit->{-bits} || $hit->{-hsps}->[0]->{-bits} || 0;
$add_hit = 0 unless $hit_bits >= $self->{'_min_bits'};
}
}
$add_hit && push @{$self->{'_hits'}}, $hit;;
$self->{'_hitcount'} = scalar @{$self->{'_hits'}};
}
=head2 Factory methods
=cut
=head2 register_factory
Title : register_factory
Usage : $handler->register_factory('TYPE',$factory);
Function: Register a specific factory for a object type class
Returns : none
Args : string representing the class and
Bio::Factory::ObjectFactoryI
See L<Bio::Factory::ObjectFactoryI> for more information
=cut
sub register_factory{
my ($self, $type,$f) = @_;
if( ! defined $f || ! ref($f) ||
! $f->isa('Bio::Factory::ObjectFactoryI') ) {
$self->throw("Cannot set factory to value $f".ref($f)."\n");
}
$self->{'_factories'}->{lc($type)} = $f;
}
=head2 factory
Title : factory
Usage : my $f = $handler->factory('TYPE');
Function: Retrieves the associated factory for requested 'TYPE'
Returns : a Bio::Factory::ObjectFactoryI
Throws : Bio::Root::BadParameter if none registered for the supplied type
Args : name of factory class to retrieve
See L<Bio::Factory::ObjectFactoryI> for more information
=cut
sub factory{
my ($self,$type) = @_;
return $self->{'_factories'}->{lc($type)} ||
$self->throw(-class=>'Bio::Root::BadParameter',
-text=>"No factory registered for $type");
}
=head2 inclusion_threshold
See L<Bio::SearchIO::blast::inclusion_threshold>.
=cut
sub inclusion_threshold {
my $self = shift;
return $self->{'_inclusion_threshold'} = shift if @_;
return $self->{'_inclusion_threshold'};
}
=head2 max_significance
Usage : $obj->max_significance();
Purpose : Set/Get the P or Expect value used as significance screening cutoff.
This is the value of the -signif parameter supplied to new().
Hits with P or E-value at HIT level above this are skipped.
Returns : Scientific notation number with this format: 1.0e-05.
Argument : Number (sci notation, float, integer) (when setting)
Throws : Bio::Root::BadParameter exception if the supplied argument is
: not a valid number.
Comments : Screening of significant hits uses the data provided on the
: description line. For NCBI BLAST1 and WU-BLAST, this data
: is P-value. for NCBI BLAST2 it is an Expect value.
=cut
sub max_significance {
my $self = shift;
if (@_) {
my $sig = shift;
if( $sig =~ /[^\d.e-]/ or $sig <= 0) {
$self->throw(-class => 'Bio::Root::BadParameter',
-text => "Invalid significance value: $sig\n"
. "Must be a number greater than zero.",
-value => $sig);
}
$self->{'_confirm_significance'} = 1;
$self->{'_max_significance'} = $sig;
}
sprintf "%.1e", $self->{'_max_significance'};
}
=head2 signif
Synonym for L<max_significance()|max_significance>
=cut
sub signif { shift->max_significance }
=head2 min_score
Usage : $obj->min_score();
Purpose : Gets the Blast score used as screening cutoff.
This is the value of the -score parameter supplied to new().
Hits with scores at HIT level below this are skipped.
Returns : Integer (or undef if not set)
Argument : Integer (when setting)
Throws : Bio::Root::BadParameter exception if the supplied argument is
: not a valid number.
Comments : Screening of significant hits uses the data provided on the
: description line.
=cut
sub min_score {
my $self = shift;
if (@_) {
my $score = shift;
if( $score =~ /[^\de+]/ or $score <= 0) {
$self->throw(-class => 'Bio::Root::BadParameter',
-text => "Invalid score value: $score\n"
. "Must be an integer greater than zero.",
-value => $score);
}
$self->{'_confirm_score'} = 1;
$self->{'_min_score'} = $score;
}
return $self->{'_min_score'};
}
=head2 min_bits
Usage : $obj->min_bits();
Purpose : Gets the Blast bit score used as screening cutoff.
This is the value of the -bits parameter supplied to new().
Hits with bits score at HIT level below this are skipped.
Returns : Integer (or undef if not set)
Argument : Integer (when setting)
Throws : Bio::Root::BadParameter exception if the supplied argument is
: not a valid number.
Comments : Screening of significant hits uses the data provided on the
: description line.
=cut
sub min_bits {
my $self = shift;
if (@_) {
my $bits = shift;
if( $bits =~ /[^\de+]/ or $bits <= 0) {
$self->throw(-class => 'Bio::Root::BadParameter',
-text => "Invalid bits value: $bits\n"
. "Must be an integer greater than zero.",
-value => $bits);
}
$self->{'_confirm_bits'} = 1;
$self->{'_min_bits'} = $bits;
}
return $self->{'_min_bits'};
}
=head2 hit_filter
Usage : $obj->hit_filter();
Purpose : Set/Get a function reference used for filtering out hits.
This is the value of the -hit_filter parameter supplied to new().
Hits that fail to pass the filter at HIT level are skipped.
Returns : Function ref (or undef if not set)
Argument : Function ref (when setting)
Throws : Bio::Root::BadParameter exception if the supplied argument is
: not a function reference.
=cut
sub hit_filter {
my $self = shift;
if (@_) {
my $func = shift;
if(not ref $func eq 'CODE') {
$self->throw(-class => 'Bio::Root::BadParameter',
-text => "Not a function reference: $func\n"
. "The -hit_filter parameter must be function reference.",
-value => $func);
}
$self->{'_hit_filter'} = $func;
}
return $self->{'_hit_filter'};
}
1;