Bio::EnsEMBL::Analysis::Tools
BasicFilter
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Summary
Bio::EnsEMBL::Analysis::Tools::BasicFilter
Package variables
No package variables defined.
Included modules
Synopsis
my $filter = Bio::EnsEMBL::Analysis::Tools::BasicFilter
->new(
-methods => {
score => 'greaterthan 500',
percent_id => 90,
}
);
my $filtered_results = $filter->filter_results($features);
Description
This module will take a hash keyed on method name with the
value either being a straight cut off which it is then assumed
all features should have a value greater than or if the cut off
number is prefaced with either lessthan or greaterthan you can
vary what comparison is made. It is important to note that
features passed in must beable to call the method specified in
as the key and all cut offs must be numeric
Methods
Methods description
Arg [1] : Bio::EnsEMBL::Analysis::Tools::BasicFilter
Arg [2] : arryref of objects
Function : to filter objects on specific criteria
Returntype: arrayref of objects
Exceptions: throws if not passed an arrayref or if objects
cant do the specified methods
Example : |
Arg [1] : Bio::EnsEMBL::Analysis::Tools::BasicFilter
Arg [2] : object
Arg [3] : string which is method to call on object
Arg [4] : cutoff object needs to have value greater or
lesser than
Function : returns object if method returns value greater
or lesser than specific cutoff
Returntype: object
Exceptions: none
Example : |
Arg [1] : Bio::EnsEMBL::Analysis::Tools::BasicFilter
Arg [2] : hashref containing a list of method names and cut
off values
Function : container method
Returntype: hashref
Exceptions: throw if not passed a hashref
Example : |
Arg [1] : hashref, containing list of method names and
cut off values
Function : create a Bio::EnsEMBL::Analysis::Tools::
BasicFilter object
Returntype: Bio::EnsEMBL::Analysis::Tools::BasicFilter
Exceptions: none
Example : see docs above |
Methods code
sub filter_results
{ my ($self, $features) = @_;
if(!$features || ref($features) ne 'ARRAY'){
throw("Must pass filter_results an arrayref not ".
$features." BasicFilter::filter_results");
}
my $methods = $self->methods;
my @filtered_features;
FEATURE:foreach my $feature(@$features){
foreach my $method(keys(%$methods)){
throw("The features passed in ".$feature->[0].
" must have the method specified ".$method)
unless($feature->can($method));
my $value = $methods->{$method};
my @values = split /\s+/, $value;
my ($checkmethod, $cutoff);
if(@values == 1){
$cutoff = $values[0];
$checkmethod = 'greaterthan';
}elsif(@values == 2){
$cutoff = $values[1];
$checkmethod = $values[0];
}else{
throw("String ".$value." from ".$method." key isn't ".
"in the expected format\n");
}
throw("Cut off ".$cutoff." must be a numeric value from".
" ".$method." ")
unless($cutoff =~ /\d+/);
next FEATURE unless($self->$checkmethod($feature,
$method,
$cutoff));
}
push(@filtered_features, $feature);
}
return\@ filtered_features;} | sub greaterthan
{ my ($self, $feature, $method, $cutoff) = @_;
return $feature if($feature->$method > $cutoff);
}
1; } | sub lessthan
{ my ($self, $feature, $method, $cutoff) = @_;
return $feature if($feature->$method < $cutoff); } | sub methods
{ my ($self, $methods) = @_;
if($methods){
throw("The value passed into BasicFilter::methods ".
"must be a hash ref not a ".$methods)
if(ref($methods) ne 'HASH');
$self->{'methods'} = $methods;
}
return $self->{'methods'};} | sub new
{ my ($class, @args) = @_;
my $self = bless {},$class;
my ($methods) = rearrange(['METHODS'], @args);
$self->methods($methods);
return $self;} | General documentation