Hello wonderful Perlmonks! I created a large number of files with the data layout shown below. I foolishly didn't anticipate the problem of having a newline between each line of text. 

 
0 26 2 2699645 1 3 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

0 21 7 2699676 3 1 1 1 3 1 3 1 1 3 1 1 1 1 3 1 1 3 1 1 3 1 1 1 1 1 1 1

0 14 14 2699968 1 1 3 3 1 1 1 3 3 1 3 1 1 3 1 3 3 1 1 3 1 3 3 3 1 1 3 
+3

0 13 15 2700027 1 1 3 3 1 1 1 3 3 1 3 1 1 3 1 3 3 1 1 3 1 3 3 3 3 1 3 
+3

0 26 2 2700157 1 3 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

0 17 11 2700202 3 3 1 1 3 3 3 1 1 3 3 1 1 1 3 1 3 3 1 1 3 1 1 1 1 1 1 
+1

0 18 10 2700302 3 1 1 1 3 1 3 3 1 3 3 1 1 1 3 1 3 3 1 1 3 1 1 1 1 1 1 
+1

0 15 13 2700608 1 3 3 3 1 3 1 1 3 1 1 3 1 3 1 3 1 1 1 3 1 1 1 3 1 3 3 
+3

0 15 13 2700613 1 1 3 3 1 3 1 1 3 1 1 3 1 3 3 3 1 1 1 3 1 1 1 3 1 3 3 
+3

[download]

The problem this yields is in my next set of files. The blank lines return values of 0 each time they are encountered

2699645    2
    0
2699676    7
    0
2699968    14

[download]

Is there a way to program out these new lines between strings , in addition to the split command for single spaces? Below is my relevant code for the split command. 

while($count < 155){

    my $output_file = "$output_dir"."compute_minor_alleles_28_males.".
+"$count".".txt";
    open(OUT, ">$output_file");
    print OUT "position\tminor allele frequency\n";

    my $input_file = "$input_dir"."temp_file_". "$count."."txt";
    
    open (CG, "<$input_file") or die "Cannot open $input_file:$!\n";
    while (my $cg = <CG>){
        
        if ($cg =~ /NA/){
            next;
        }
        
        chomp($cg);    #get rid of newline character
        @info =  split(" ", $cg);

[download]

In reply to Getting Rid of Newlines Between Strings by ccelt09

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