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#!/usr/bin/perl
# split a wiggle file in single contig files
my $usage = "split_wiggle.pl in.wig outputPath prefix\n";
if (@ARGV != 2) {
print $usage;
exit;
}
$inFile = $ARGV[0];
$outPath = $ARGV[1];
if(defined($ARGV[2])){
$prefix = $ARGV[2];
}else{$prefix="split_";}
$outFile = $outPath."/".$prefix;
open(IN, "<", $inFile) or die "Could not open file $inFile!\n";
$counter = 0;
while(<IN>){
if($_=~m/track name/){$headerLine = $_;
}elsif($_=~m/variableStep/){
if($counter>=1){
close(OUT) or die "Could not close File $thisFile!\n";
}
$counter = $counter + 1;
$thisFile = $outFile.$counter;
open(OUT, ">", $thisFile) or die "Could not open File $thisFile!\n";
print OUT $headerLine;
print OUT $_;
}else{print OUT $_;}
}
close(OUT) or die "Could not close file $outFile\n";
close(IN) or die "Could not close file $inFile\n";
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