/usr/share/ampliconnoise/Scripts/CleanBothM.pl is in ampliconnoise 1.29-6.
This file is owned by root:root, with mode 0o755.
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 | #!/usr/bin/perl
use POSIX;
my $nTotal = 0;
my $nClean = 0;
my $flowSeq = "TACG";
my $primer = &translateIUPAC($ARGV[0]);
my $revPrimer = &translateIUPAC($ARGV[1]);
my $out = $ARGV[2];
my $maxFlows = 800;
my $ffile = "${out}.fa";
my $dfile = "${out}.dat";
open(FFILE, ">${ffile}") or die "Can't open ${out}.fa\n";
open(DFILE, ">${dfile}") or die "Can't open ${out}.dat\n";
while(my $line = <STDIN>){
chomp($line);
if($line =~ />(.*)/){
my $id = $1;
#print "$id\n";
$line = <STDIN>;
chomp($line);
#print "$id $line\n";
my @flows = split(/ /,$line);
#print "@flows\n";
my $length = shift(@flows);
my $read;
my $newLength = 0;
#print "$length\n";
#print "$length @flows\n";
while($newLength*4 < $length){
my $signal = 0;
my $noise = 0;
for($j = 0; $j < 4; $j++){
my $f = $flows[$j + 4*$newLength];
if($f > 0.5){
$signal++;
if($f < 0.7 || $f > 6.49){
$noise++;
}
}
}
if($noise > 0 || $signal == 0){
last;
}
$newLength++;
}
$newLLength = 4*$newLength;
# print "$length $newLength $newLLength $noise\n";
if($newLength*4 > $length){
my $read = flowToSeq($length,@flows);
#print "$read $revPrimer\n";
if($read=~/^TCAG.*(${primer}.*${revPrimer}).*$/){
# print "Good\n";
printf DFILE "$id $length ";
for($j = 0; $j < $maxFlows; $j++){
printf DFILE "$flows[$j] ";
}
printf DFILE "\n";
printf FFILE ">$id\n";
printf FFILE "$1\n";
$nClean++;
goto found;
}
found : $nTotal++;
}
}
}
close(DFILE);
close(FFILE);
open my $in, '<', $dfile or die "Can't read old file: $!";
open my $out, '>', "$dfile.new" or die "Can't write new file: $!";
print $out "$nClean $maxFlows\n";
while( <$in> )
{
print $out $_;
}
close $out;
rename("$dfile.new", $dfile);
exit(0);
sub flowToSeq()
{
my ($length, @flowgram) = @_;
my $retSeq = "";
for(my $i = 0; $i < $length; $i++){
my $signal = floor($flowgram[$i] + 0.5);
my $base = substr($flowSeq, $i % 4, 1);
for(my $j = 0; $j < $signal; $j++){
$retSeq .= $base;
}
}
return $retSeq;
}
sub translateIUPAC()
{
my ($seq) = @_;
$seq=~s/B/\[CGT\]/g;
$seq=~s/S/\[GC\]/g;
$seq=~s/N/\[ACTG\]/g;
$seq=~s/Y/\[CT\]/g;
$seq=~s/R/\[AG\]/g;
$seq=~s/D/\[AGT\]/g;
$seq=~s/H/\[ACT\]/g;
$seq=~s/M/\[AC\]/g;
$seq=~s/K/\[GT\]/g;
$seq=~s/V/\[ACG\]/g;
return $seq;
}
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