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|
#!/usr/bin/perl
my $fastaFile = shift;
my $distFile = shift;
my $cutoff = shift;
my @Seq = ();
my $total = 0;
my @id = ();
open(FILE, $fastaFile) or die "Can't open $fastaFile\n";
my $seq = "";
while($line = <FILE>){
chomp($line);
if($line =~ />(.*)/){
$id[$count] = $1;
if($seq ne ""){
$Seq[$count - 1] = $seq;
$seq = "";
}
$count++;
}
else{
$seq .= $line;
}
}
$Seq[$count - 1] = $seq;
$total = $count;
open(FILE, $distFile) or die "Can't open $distFile\n";
for($i = 0; $i < $total; $i++){
$line = <FILE>;
chomp($line);
@tokens = split(/ /,$line);
$id = $tokens[0];
$id =~ /.*_(.*)/;
$freq = $1;
$x = $tokens[1];
$y = $tokens[2];
$p = $tokens[4];
if($p < $cutoff){
printf STDERR ">$id[$i]\n$Seq[$i]\n";
}
else{
printf STDOUT ">$id[$i]\n$Seq[$i]\n";
}
}
close(FILE);
|
