Bio::SearchIO IteratedSearchResultEventBuilder
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Summary
Bio::SearchIO::IteratedSearchResultEventBuilder - Event Handler for
SearchIO events.
Package variables
No package variables defined.
Included modules
Bio::Factory::ObjectFactory
Inherit
Bio::SearchIO::SearchResultEventBuilder
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.
Methods
newDescriptionCode
_init_parse_params
No description
Code
will_handleDescriptionCode
start_resultDescriptionCode
end_resultDescriptionCode
_add_hit
No description
Code
_store_hit
No description
Code
start_iterationDescriptionCode
end_iterationDescriptionCode
max_significanceDescriptionCode
signifDescriptionCode
min_scoreDescriptionCode
min_bitsDescriptionCode
hit_filterDescriptionCode
inclusion_thresholdDescriptionCode
Methods description
newcode    nextTop
 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_handlecodeprevnextTop
 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
start_resultcodeprevnextTop
 Title   : start_result
Usage : $handler->start_result($resulttype)
Function: Begins a result event cycle
Returns : none
Args : Type of Report
end_resultcodeprevnextTop
 Title   : end_result
Usage : my @results = $parser->end_result
Function: Finishes a result handler cycle
Returns : A Bio::Search::Result::ResultI
Args : none
start_iterationcodeprevnextTop
 Title   : start_iteration
Usage : $handler->start_iteration()
Function: Starts an Iteration event cycle
Returns : none
Args : type of event and associated hashref
end_iterationcodeprevnextTop
 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_significancecodeprevnextTop
 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.
signifcodeprevnextTop
Synonym for max_significance()
min_scorecodeprevnextTop
 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_bitscodeprevnextTop
 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_filtercodeprevnextTop
 Usage     : $obj->hit_filter();
Purpose : Set/Get a function reference used for filtering out hits.
This is the value of the -hit_filter parameter supplied to new().
Hits that fail to pass the filter are skipped.
Returns : Function ref (or undef if not set)
Argument : Function ref (when setting)
Throws : Bio::Root::BadParameter exception if the supplied argument is
: not a function reference.
inclusion_thresholdcodeprevnextTop
See Bio::SearchIO::blast::inclusion_threshold.
Methods code
newdescriptionprevnextTop
sub new {
     my ($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 $self; } #Initializes parameters used during parsing of Blast reports.
}
_init_parse_paramsdescriptionprevnextTop
sub _init_parse_params {
    my ($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);
}
will_handledescriptionprevnextTop
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' );
}
start_resultdescriptionprevnextTop
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; $self->{'_hit_names_below'} = undef; return;
}
end_resultdescriptionprevnextTop
sub end_result {
    my ($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 $result; } # Title : _add_hit (private function for internal use only)
# Purpose : Applies hit filtering and calls _store_hit if it passes filtering.
# Argument: Bio::Search::Hit::HitI object
}
_add_hitdescriptionprevnextTop
sub _add_hit {
    my ($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 <= $ithresh; } # Title : _store_hit (private function for internal use only)
# Purpose : Collects hit objects into defined sets that are useful for
# analyzing PSI-blast results.
# These are ultimately added to the iteration object in end_iteration().
#
# Strategy:
# Primary split = old vs. new
# Secondary split = below vs. above threshold
# 1. Has this hit occurred in a previous iteration?
# 1.1. If yes, was it below threshold?
# 1.1.1. If yes, ---> [oldhits_below]
# 1.1.2. If no, is it now below threshold?
# 1.1.2.1. If yes, ---> [oldhits_newly_below]
# 1.1.2.2. If no, ---> [oldhits_not_below]
# 1.2. If no, is it below threshold?
# 1.2.1. If yes, ---> [newhits_below]
# 1.2.2. If no, ---> [newhits_not_below]
# 1.2.3. If don't know (no inclusion threshold data), ---> [newhits_unclassified]
# Note: As long as there's a default inclusion threshold,
# there won't be an unclassified set.
#
# For the first iteration, it might be nice to detect non-PSI blast reports
# and put the hits in the unclassified set.
# However, it shouldn't matter where the hits get put for the first iteration
# for non-PSI blast reports since they'll get flattened out in the
# result and iteration search objects.
}
_store_hitdescriptionprevnextTop
sub _store_hit {
    my ($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; } } $self->{'_hitcount'}++;
}
start_iterationdescriptionprevnextTop
sub start_iteration {
    my ($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'} = []; $self->{'_hitcount'} = 0; return;
}
end_iterationdescriptionprevnextTop
sub end_iteration {
    my ($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;
}
max_significancedescriptionprevnextTop
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'};
}
signifdescriptionprevnextTop
sub signif {
 shift->max_significance
}
min_scoredescriptionprevnextTop
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'};
}
min_bitsdescriptionprevnextTop
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'};
}
hit_filterdescriptionprevnextTop
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'};
}
inclusion_thresholddescriptionprevnextTop
sub inclusion_threshold {
    my $self = shift;
    return $self->{'_inclusion_threshold'} = shift if @_;
    return $self->{'_inclusion_threshold'};
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 ChervitzTop
Email sac-at-bioperl.org
CONTRIBUTORSTop
Parts of code based on SearchResultEventBuilder by Jason Stajich jason@bioperl.org
Sendu Bala, bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
SAX methodsTop