/usr/share/perl5/changepointCaller.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 | =head1 NAME
changepointCaller
=head1 SYNOPSIS
changepointCaller - it calls the PAI_scripts::changePoint
=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
use FindBin;
use lib $FindBin::Bin;
package changepointCaller;
use PAI_scripts::changePoint;
use Exporter;
@ISA = ("Exporter");
@EXPORT = qw (&changepointCaller);
sub changepointCaller{
$SeqFile=$_[0];
$tabFile=$_[1];
$Genlen=readGenomeSeq($SeqFile);
open file1, $tabFile
or die "dead";
open file2, ">$tabFile.opt"
or die "dead";
open file3, ">$tabFile.opt.plot"
or die "dead";
$count=`grep -c misc_feature $tabFile`;
$st=1;
$to_prev=0;
while(<file1>){
chomp($_);
if (m#(\d+)\.\.(\d+)#){
$left=$1;
$right=$2;
$c++;
print "\n optimizing prediction $c out of $count\n";
#it calls changepoint
($newLeft,$newRight)=changepoint($left,$right,$tabFile);
print " opt boundaries: $newLeft..$newRight\n";
$from=$newLeft;
$to=$newRight;
#if overlap after the HMM optimization of two consequtive regions
#then re-update the plot file not to print extra bases
if($to_prev>=$from){
$from=$to_prev+1;
$newLeft=$to_prev+1;
}
$to_prev=$to;
}
if (m#(colour=\d+ \d+ \d+)#){
$colour=$1;
}
if (m#(note=.+)#){
$note=$1;
}
if (m#score=(\d+\.*\d+)#){
$score=$1;
print file2 "FT misc_feature $newLeft..$newRight
FT /$colour
FT /algorithm=\"alien_hunter\"
FT /$note
FT /score=$score\n";
#begin -> from
for($i=$st;$i<$from;$i++){
print file3 "0\n";
}
#from -> to
for($i=$from;$i<=$to;$i++){
print file3 "$score\n";
}
$st=$to+1;
}
}#while
#to -> end
for($i=$st;$i<=$Genlen;$i++){
print file3 "0\n";
}
close file1;
close file2;
close file3;
return ();
}
1;
|