/usr/lib/perl5/TFBS/ConservationProfile.pm is in libtfbs-perl 0.6.0+dfsg-1.
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 | package TFBS::ConservationProfile;
use strict;
use Bio::Root::Root;
use vars qw'@ISA';
@ISA = qw'Bio::Root::Root';
sub new {
my ($caller, %args) = @_;
my $self = bless {parameters=>{},
alignment => undef,
ref_sequence => undef,
%args
} ,ref $caller || $caller;
if (!defined($self->{conservation}) or ref($self->{conservation}) ne "ARRAY") {
$self->throw("conservation: argument missing or wrong object type");
}
return $self;
}
sub param {
my ($self, $param, $value) = @_;
if (!defined $param) {
return keys %{$self->{parameters}};
}
elsif (defined $value) {
$self->{parameters}->{$param} = $value;
}
return $self->{parameters}->{$param};
}
sub alignment {
$_[0]->{alignment}
}
sub ref_sequence {
$_[0]->{ref_sequence}
}
sub conserved_regions_as_gff {
my ($self, %args) = @_;
my @features = $self->conserved_regions_as_features;
my $output = "";
foreach my $f (@features) {
$output .= $f->gff_string."\n";
}
return $output;
}
sub conserved_regions_as_features {
my ($self, %args) = @_;
my ($excl_feature_ref, $cutoff) =
$self->_rearrange([qw(exclude_features cutoff)], %args);
$cutoff = ($cutoff or $self->param("cutoff") or 0.7);
print STDERR "CURRENT CUTOFF $cutoff\n";
my @conservation = $self->conservation;
my ($START, $END);
if ($self->ref_sequence and $self->ref_sequence->isa("Bio::LocatableSeq")) {
$START = $self->ref_sequence->start;
$END = $self->ref_sequence->end;
}
else {
$START = $self->alignment->get_seq_by_pos($self->param("ref_seq_nr" or 1))->start;
$END = $self->alignment->get_seq_by_pos($self->param("ref_seq_nr" or 1))->end;
}
if ($excl_feature_ref and ref($excl_feature_ref) eq "ARRAY") {
foreach my $f (@$excl_feature_ref) {
my ($s, $e) = ($f->start, $f->end);
next if ($e<$START or $s>$END);
$s = $START if $s<$START;
$e = $END if $e>$END;
map { $conservation[$_] = 0 } ($s-$START..$e-$START);
}
}
# obtain a list of positions with threshold
my @cons_positions = ( (grep {$conservation[$_-$START]>=$cutoff} ($START..$#conservation+$START)), $END+1000);
# $END+1000 is a dummy position that simplifies the procedure
my @features;
my $region_start = $cons_positions[0];
my $counter = 0;
foreach my $i (0..$#cons_positions ) {
if ($cons_positions[$i+1]-$cons_positions[$i]>10) { # 10 can be changed to max allowed gap in a conserved region
$counter++;
my $f = Bio::SeqFeature::Generic->new(-start=>$region_start,
-end =>$cons_positions[$i],
-primary => "CR$counter",
-score => $cons_positions[$i]-$region_start+1
);
push @features, $f;
print STDERR $features[-1]->gff_string."\n";
$region_start = $cons_positions[$i+1];
}
}
return @features;
}
sub conserved_regions_as_feature_pairs {
}
sub conservation {
my ($self, $start, $end) = @_;
if (!defined $start) {
return @{$self->{conservation}}
}
else {
my ($START, $END);
if ($self->alignment) {
my $ref_seq_nr = ($self->param("ref_seq_nr") or 1);
$START = $self->alignment->get_seq_by_pos($ref_seq_nr)->start;
$END = $self->alignment->get_seq_by_pos($ref_seq_nr)->end;
}
else {
$START = 1;
}
if (defined $end) {
my ($pad_start, $pad_end) = (0, 0);
if ($start < $START) { $pad_start = $START-$start; $start = $START; }
if ($end > $END) { $pad_end = $end-$END; $end = $END }
return (_blank_array($pad_start),
@{$self->{conservation}}[$start-$START, $end-$START],
_blank_array($pad_end)
);
}
elsif ($start< $START) {
return undef;
}
else {
return $self->{conservation}->[$start-$START];
}
}
}
sub _blank_array {
my ($length) = @_;
my @arr = map {undef} (0..$length);
pop @arr;
return @arr
}
sub conserved_sequences {
}
sub conserved_subalignments {
}
1;
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