/usr/lib/x86_64-linux-gnu/perl5/5.24/TFBS/Tools/SetOperations.pm is in libtfbs-perl 0.7.0+dfsg-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 | package TFBS::Tools::SetOperations;
use strict;
use Bio::Root::Root;
use vars qw'@ISA';
@ISA = qw'Bio::Root::Root';
sub new {
my ($caller, @args) = @_;
my $self = bless {}, ref $caller || $caller;
my ($index_by, $strict, $output_type, $pairs) =
$self->_rearrange([qw'INDEX_BY STRICT OUTPUT_TYPE PAIRS'], @args);
$self->index_by($index_by);
$self->strict($strict);
$self->output_type($output_type);
$self->pairs($pairs);
return $self;
}
sub union {
my ($self, @sets) = @_;
my %union_index =
map {$self->_index($_)} $self->_sets_to_arrayrefs(@sets);
$self->_output(\%union_index);
}
sub intersection {
my ($self, @sets) = @_;
my @set_arrayrefs = $self->_sets_to_arrayrefs(@sets);
#this would be faster, but we might want to retain the exact objects
# that were present in
#my @set_arrayrefs = sort {@$a <=> @$b} $self->_sets_to_arrayrefs(@sets);
my %intersection_index = $self->_index(shift @set_arrayrefs);
foreach my $set_arrayref (@set_arrayrefs) {
my %curr_set_index = $self->_index($set_arrayref);
my @help_array = %curr_set_index;
foreach my $key (keys %intersection_index) {
if (!exists $curr_set_index{$key}) {
delete $intersection_index{$key} ;
}
}
}
$self->_output(\%intersection_index);
}
sub difference {
# pairs only for now
my ($self, @sets) = @_;
my ($set1, $set2) = $self->_sets_to_arrayrefs(@sets);
if (!defined $set2) {
$self->throw ("'difference' needs exactly two sets as arguments");
}
my %diff_index1 = $self->_index($set1);
my %diff_index2 = $self->_index($set2);
foreach my $key (keys %diff_index1) {
if (exists $diff_index2{$key}) {
delete $diff_index1{$key};
delete $diff_index2{$key};
}
}
wantarray ? ($self->_output(\%diff_index1), $self->_output(\%diff_index2))
: $self->_output(\%diff_index1);
}
sub index_by {
my $self = shift;
# By default, we are dealing with Bio::SeqFeatureI objects
my @DEFAULTS = qw(primary_tag source_tag start end score strand);
if (@_) {
if(!defined $_[0]) {
$self->{_index_by} = \@DEFAULTS;
}
elsif (ref($_[0]) eq "ARRAY") {
$self->{_index_by} = $_[0];
}
else {
$self->{_index_by} = [@_];
}
}
return @{$self->{_index_by}};
}
sub strict {
my $self = shift;
if (@_) {
if ($self->{_strict} = shift) {
$self->{_index_fn} = \&_index_strict;
}
else {
$self->{_index_fn} = \&_index_by_annotation;
}
}
return $self->{_strict};
}
sub output_type {
my $self = shift;
if (@_) {
unless ($self->{_output_type} = shift) {
$self->{_output_type} = "arrayref"
}
}
return $self->{_output_type};
}
sub pairs {
my $self = shift;
if (@_) {
if ($self->{_pairs} = shift and !$self->strict) {
$self->{_index_fn} = \&_index_by_pair_annotation;
}
}
return $self->{_pairs};
}
sub _index {
my ($self) = @_;
$self->{_index_fn}->(@_);
}
sub _index_strict {
my ($self, $set_arrayref) = @_;
my %index_hash = (map {$_, $_} @$set_arrayref);
return %index_hash;
}
sub _index_by_pair_annotation {
my ($self, $set_arrayref) = @_;
my %index_hash;
foreach my $member (@$set_arrayref) {
my @index_elements = ($self->_get_index_elements($member->feature1),
$self->_get_index_elements($member->feature2));
$index_hash{join("::", @index_elements)} = $member;
}
return %index_hash;
}
sub _index_by_annotation {
my ($self, $set_arrayref) = @_;
my %index_hash;
foreach my $member (@$set_arrayref) {
my @index_elements = $self->_get_index_elements($member);
$index_hash{join("::", @index_elements)} = $member;
}
return %index_hash;
}
sub _get_index_elements {
my ($self, $set_member) = @_;
my @index_elements;
foreach my $method ($self->index_by) {
if (ref($method) eq 'CODE') {
push @index_elements, $method->($set_member);
}
else {
eval { push @index_elements, $set_member->$method; };
if ($@) {
$self->throw(sprintf("Could not use '%s' for indexing a %s object. The original error was:\n",
$method, ref($set_member)).$@)
}
}
}
return @index_elements;
}
sub _sets_to_arrayrefs {
my ($self, @sets) = @_;
my @set_arrayrefs;
foreach my $set (@sets) {
if (ref($set) eq "ARRAY") {
push @set_arrayrefs, $set;
}
elsif(ref($set) and $set->can("Iterator")) {
my @set_elements;
my $it = $set->Iterator;
while (my $set_el = $it->next) { push @set_elements, $set_el }
push @set_arrayrefs, \@set_elements;
}
else {
$self->throw("Set must be an aray reference or have an ".
"Iterator method. Got ".(ref($set or $set)). "instead.");
}
}
return @set_arrayrefs;
}
sub _output {
my ($self, $hashref) = @_;
if ($self->output_type eq "arrayref") {
return [values %$hashref];
}
elsif ($self->output_type eq "array") {
return %$hashref;
}
elsif ($self->output_type eq "matrix_set") {
my $setobj = TFBS::MatrixSet->new;
$setobj->add_Matrix(values %$hashref);
return $setobj;
}
elsif ($self->output_type eq "site_set") {
my $setobj = TFBS::SiteSet->new;
$setobj->add_site(values %$hashref);
return $setobj;
}
else {
$self->throw($self->output_type." is not a supported output type");
}
}
1;
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