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|
#!/usr/bin/perl
use POSIX;
my $nTotal = 0;
my $nClean = 0;
my $flowSeq = "TACG";
my $primer = &translateIUPAC($ARGV[0]);
my $out = $ARGV[1];
my $minFlows=360;
if($ARGV[2] ne undef){
$minFlows = $ARGV[2];
}
my $maxFlows=720;
if($ARGV[3] ne undef){
$maxFlows = $ARGV[3];
}
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++;
}
$length = $newLength*4;
my $read = flowToSeq($length,@flows);
if($length >= $minFlows && $read=~/^TCAG.*(${primer}.*)/){
if($length > $maxFlows){
$length = $maxFlows;
}
printf DFILE "$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/W/\[AT\]/g;
$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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