/usr/share/perl5/PAI_scripts/overlap.pm is in alien-hunter 1.7-5.
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 | =head1 NAME
PAI_scripts::overlap
=head1 SYNOPSIS
merges predictions
=head1 AUTHOR
George Vernikos <gsv(at)sanger.ac.uk>
=head1 LICENSE
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
=cut
package PAI_scripts::overlap;
use Exporter;
@ISA = ("Exporter");
@EXPORT = qw (&overlap);
sub overlap{
$cutoff=$_[0];
$scoresRef=$_[1];
$prevFrom=0;
$prevTo=0;
$check=0;
%joinedScores;
$b=0;
$bb=0;
$count=0;
#if cutoff = 0 don't join at all - return them as they are
if($cutoff==0){
foreach $z ($scoresRef){
foreach $key (keys %$z){
$joinedScores{$key}="$z->{$key}";
}
}
}
else{
foreach $z ($scoresRef){
foreach $key (keys %$z){
$scores{$key}="$z->{$key}";
}
}
@keys2 = sort {$a <=> $b} keys %scores;
$numkeys= keys %scores;
for($i=0;$i<=$numkeys-1;$i++){
if($scores{$keys2[$i]}>=$cutoff){
$aboveCut[$b]=$keys2[$i];
$b++
}
}
#if there is only one window with score > T
if($b==1){
$joinedScores{$aboveCut[$b-1]}=$scores{$aboveCut[$b-1]};
}
for($c=0;$c<=$b;$c++){
($from,$to)=split /\.\./, $aboveCut[$c];
if(($prevTo>=$from) | ($prevTo==0)){
if($c>0){
$count++;
$joinedScore+=$scores{$aboveCut[$c]};
}
}
else{
$check=1;
}
#that's for the last windows where there is no next window to make check=1
if($c==$b){
#because it's doing once more the loop
$count--;
$check=1;
}
if ($check==1){
($fromF,$toF)=split /\.\./, $aboveCut[$c-1-$count];
($fromL,$toL)=split /\.\./, $aboveCut[$c-1];
#to add also the 1st win score
$joinedScore+=$scores{$aboveCut[$c-1-$count]};
$average=$joinedScore/($count+1);
$average=sprintf("%.3f",$average);
#for the first window; there is no previous window
if($c>0){
$joinedScores{"$fromF..$toL"}=$average;
}
$count=0;
$check=0;
$joinedScore=0;
}
$prevFrom=$from;
$prevTo=$to;
}
}#else
return (\%joinedScores);
}
1;
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