Bio::SearchIO::IteratedSearchResultEventBuilder - Event Handler for
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NAME
Bio::SearchIO::IteratedSearchResultEventBuilder - Event Handler for
SearchIO events.
SYNOPSIS
# Do not use this object directly, this object is part of the SearchIO
# event based parsing system.
DESCRIPTION
This object handles Search Events generated by the SearchIO classes
and build appropriate Bio::Search::* objects from them.
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Steve Chervitz
CONTRIBUTORS
Parts of code based on SearchResultEventBuilder by Jason Stajich
jason@bioperl.org
Sendu Bala, bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::SearchIO::IteratedSearchResultEventBuilder->new();
Function: Builds a new Bio::SearchIO::IteratedSearchResultEventBuilder object
Returns : Bio::SearchIO::IteratedSearchResultEventBuilder
Args : -hsp_factory => Bio::Factory::ObjectFactoryI
-hit_factory => Bio::Factory::ObjectFactoryI
-result_factory => Bio::Factory::ObjectFactoryI
-iteration_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 Bio::SearchIO::SearchResultEventBuilder for more information
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
SAX methods
start_result
Title : start_result
Usage : $handler->start_result($resulttype)
Function: Begins a result event cycle
Returns : none
Args : Type of Report
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
start_iteration
Title : start_iteration
Usage : $handler->start_iteration()
Function: Starts an Iteration event cycle
Returns : none
Args : type of event and associated hashref
end_iteration
Title : end_iteration
Usage : $handler->end_iteration()
Function: Ends an Iteration event cycle
Returns : Bio::Search::Iteration object
Args : type of event and associated hashref
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 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.
signif
Synonym for max_significance() (max_significance)
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 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.
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 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.
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 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.
inclusion_threshold
See Bio::SearchIO::blast::inclusion_threshold.
#------------------------------------------------------------------
#
# BioPerl module for Bio::SearchIO::IteratedSearchResultEventBuilder
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Steve Chervitz <sac@bioperl.org> and Jason Stajich <jason@bioperl.org>
#
# Copyright Steve Chervitz
#
# You may distribute this module under the same terms as perl itself
#------------------------------------------------------------------
# POD documentation - main docs before the code
# Let the code begin...
package Bio::SearchIO::IteratedSearchResultEventBuilder;
use vars qw(%KNOWNEVENTS $DEFAULT_INCLUSION_THRESHOLD
$MAX_HSP_OVERLAP
);
use strict;
use Bio::Factory::ObjectFactory;
use base qw(Bio::SearchIO::SearchResultEventBuilder);
# 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;
$MAX_HSP_OVERLAP = 2; # Used when tiling multiple HSPs.
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($hitF, $resultF, $hspF, $iterationF) =
$self->_rearrange([qw(
HIT_FACTORY
RESULT_FACTORY
HSP_FACTORY
ITERATION_FACTORY
)],@args);
$self->_init_parse_params(@args);
# Note that we need to override the setting of result and factories here
# so that we can set different default factories than are set by the super class.
$self->register_factory('result', $resultF ||
Bio::Factory::ObjectFactory->new(
-type => 'Bio::Search::Result::BlastResult',
-interface => 'Bio::Search::Result::ResultI'));
$self->register_factory('hit', $hitF ||
Bio::Factory::ObjectFactory->new(
-type => 'Bio::Search::Hit::BlastHit',
-interface => 'Bio::Search::Hit::HitI'));
$self->register_factory('hsp', $hspF ||
Bio::Factory::ObjectFactory->new(
-type => 'Bio::Search::HSP::GenericHSP',
-interface => 'Bio::Search::HSP::HSPI'));
# TODO: Change this to BlastIteration (maybe)
$self->register_factory('iteration', $iterationF ||
Bio::Factory::ObjectFactory->new(
-type => 'Bio::Search::Iteration::GenericIteration',
-interface => 'Bio::Search::Iteration::IterationI'));
return $self;
}
#Initializes parameters used during parsing of Blast reports.
sub _init_parse_params {
my ($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);
}
sub will_handle{
my ($self,$type) = @_;
# these are the events we recognize
return ( $type eq 'hsp' || $type eq 'hit' || $type eq 'result' || $type eq 'iteration' ||
$type eq 'newhits' || $type eq 'oldhits' );
}
sub start_result {
my $self = shift;
#print STDERR "ISREB: start_result()\n";
$self->SUPER::start_result(@_);
$self->{'_iterations'} = [];
$self->{'_iteration_count'} = 0;
$self->{'_old_hit_names'} = undef;
$self->{'_hit_names_below'} = undef;
return;
}
sub end_result {
my ($self,$type,$data) = @_;
#print STDERR "ISREB: end_result\n";
## How is runid getting set? Purpose?
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);
$args{'-iterations'} = $self->{'_iterations'};
my $result = $self->factory('result')->create_object(%args);
$result->hit_factory($self->factory('hit'));
$self->{'_iterations'} = [];
return $result;
}
# Title : _add_hit (private function for internal use only)
# Purpose : Applies hit filtering and calls _store_hit if it passes filtering.
# Argument: Bio::Search::Hit::HitI object
sub _add_hit {
my ($self, $hit) = @_;
my $hit_name = uc($hit->{-name});
my $hit_signif = $hit->{-significance};
my $ithresh = $self->{'_inclusion_threshold'};
# 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};
$add_hit = 0 unless $hit_bits >= $self->{'_min_bits'};
}
}
$add_hit && $self->_store_hit($hit, $hit_name, $hit_signif);
# Building hit lookup hashes for determining if the hit is old/new and
# above/below threshold.
$self->{'_old_hit_names'}->{$hit_name}++;
$self->{'_hit_names_below'}->{$hit_name}++ if $hit_signif <= $ithresh;
}
# Title : _store_hit (private function for internal use only)
# Purpose : Collects hit objects into defined sets that are useful for
# analyzing PSI-blast results.
# These are ultimately added to the iteration object in end_iteration().
#
# Strategy:
# Primary split = old vs. new
# Secondary split = below vs. above threshold
# 1. Has this hit occurred in a previous iteration?
# 1.1. If yes, was it below threshold?
# 1.1.1. If yes, ---> [oldhits_below]
# 1.1.2. If no, is it now below threshold?
# 1.1.2.1. If yes, ---> [oldhits_newly_below]
# 1.1.2.2. If no, ---> [oldhits_not_below]
# 1.2. If no, is it below threshold?
# 1.2.1. If yes, ---> [newhits_below]
# 1.2.2. If no, ---> [newhits_not_below]
# 1.2.3. If don't know (no inclusion threshold data), ---> [newhits_unclassified]
# Note: As long as there's a default inclusion threshold,
# there won't be an unclassified set.
#
# For the first iteration, it might be nice to detect non-PSI blast reports
# and put the hits in the unclassified set.
# However, it shouldn't matter where the hits get put for the first iteration
# for non-PSI blast reports since they'll get flattened out in the
# result and iteration search objects.
sub _store_hit {
my ($self, $hit, $hit_name, $hit_signif) = @_;
my $ithresh = $self->{'_inclusion_threshold'};
# This is the assumption leading to Bug 1986. The assumption here is that
# the hit name is unique (and thus new), therefore any subsequent encounters
# with a hit containing the same name are filed as old hits. This isn't
# always true (see the bug report for a few examples). Adding an explicit
# check for the presence of iterations, adding to new hits otherwise.
if (exists $self->{'_old_hit_names'}->{$hit_name}
&& scalar @{$self->{_iterations}}) {
if (exists $self->{'_hit_names_below'}->{$hit_name}) {
push @{$self->{'_oldhits_below'}}, $hit;
} elsif ($hit_signif <= $ithresh) {
push @{$self->{'_oldhits_newly_below'}}, $hit;
} else {
push @{$self->{'_oldhits_not_below'}}, $hit;
}
} else {
if ($hit_signif <= $ithresh) {
push @{$self->{'_newhits_below'}}, $hit;
} else {
push @{$self->{'_newhits_not_below'}}, $hit;
}
}
$self->{'_hitcount'}++;
}
sub start_iteration {
my ($self,$type) = @_;
#print STDERR "ISREB: start_iteration()\n";
$self->{'_iteration_count'}++;
# Reset arrays for the various classes of hits.
# $self->{'_newhits_unclassified'} = [];
$self->{'_newhits_below'} = [];
$self->{'_newhits_not_below'} = [];
$self->{'_oldhits_below'} = [];
$self->{'_oldhits_newly_below'} = [];
$self->{'_oldhits_not_below'} = [];
$self->{'_hitcount'} = 0;
return;
}
sub end_iteration {
my ($self,$type,$data) = @_;
# print STDERR "ISREB: end_iteration()\n";
my %args = map { my $v = $data->{$_}; s/ITERATION//; ($_ => $v); }
grep { /^ITERATION/ } keys %{$data};
$args{'-number'} = $self->{'_iteration_count'};
$args{'-oldhits_below'} = $self->{'_oldhits_below'};
$args{'-oldhits_newly_below'} = $self->{'_oldhits_newly_below'};
$args{'-oldhits_not_below'} = $self->{'_oldhits_not_below'};
$args{'-newhits_below'} = $self->{'_newhits_below'};
$args{'-newhits_not_below'} = $self->{'_newhits_not_below'};
$args{'-hit_factory'} = $self->factory('hit');
my $it = $self->factory('iteration')->create_object(%args);
push @{$self->{'_iterations'}}, $it;
return $it;
}
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'};
}
sub signif { shift->max_significance }
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'};
}
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'};
}
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'};
}
sub inclusion_threshold {
my $self = shift;
return $self->{'_inclusion_threshold'} = shift if @_;
return $self->{'_inclusion_threshold'};
}
1;