I have a data frame that looks like this: 

0 25 27 60454 2 2 3 2 2 3 3 3 2 3 1 1 2 1 2 2 3 3 2 1 2 1 1 1 2 3
0 19 33 60466 2 2 3 2 2 2 3 3 3 3 1 1 2 1 2 3 3 3 2 1 2 3 2 2 3 3
0 25 27 60692 2 2 3 2 2 3 3 3 2 3 1 1 2 1 2 2 3 3 2 1 2 1 1 1 2 3
0 50 2 60727 1 1 1 1 1 2 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
0 48 4 60814 1 1 1 1 1 1 2 1 1 3 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1
0 46 6 60866 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 2 2 2 1 1 1 1 1 1 1 2
0 25 27 60882 2 2 3 2 2 3 3 3 2 3 1 1 2 1 2 2 3 3 2 1 2 1 1 1 2 3
0 48 4 60888 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 1 2
0 50 2 60909 1 1 1 1 1 2 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

[download]

and it goes on this way for quite a while. I want to separate and reprint lines from the data frame, sorting by the values in 4th column. My sorting parameters are the intervals specified in another data frame:

chrX    1    1000001
chrX    100001    1100001
chrX    200001    1200001
chrX    300001    1300001
chrX    400001    1400001
chrX    500001    1500001
chrX    600001    1600001
chrX    700001    1700001
chrX    800001    1800001

[download]

so I'd want all lines with 4th column values within an interval to be printed to it's own text file. I can do this when the intervals don't overlap using the code below, but when the intervals overlap as they do above I lose data from overlapping regions 


my $placeholder = 0;
my $count = 0;

#my $window = "1Mbwindow_overlapping100kb";

my $interval_directory = "/Users/logancurtis-whitchurch/Desktop/IB_Sen
+ior_Thesis/galaxy_chrX_data/";

my $input_interval = "$interval_directory"."chrX_"."$window".".txt";

my $cg_input = "/Users/logancurtis-whitchurch/Desktop/IB_Senior_Thesis
+/CompleteGenomics/All26.females/CGS.All26.txt";

#my $output_directory = "/Users/logancurtis-whitchurch/Desktop/IB_Seni
+or_Thesis/temps/overlapping/1Mb/";

open (INTERVAL, "$input_interval") or die "can't open $input_interval\
+n"; 
my $interval = <INTERVAL>;

my (@find_interval, $start, $end);

open (CG, "<$cg_input") or die "can't open $cg_input\n";
my @SNPs = <CG>;
close(CG);
            
foreach my $interval (<INTERVAL>){
            
    @find_interval = split(/\t/, $interval);
    $start = $find_interval[1]; 
    $end = $find_interval[2];    
        
    my $tmp = "temp_file_"."$count".".txt";
    my $output_file = "$output_directory" . "$tmp";

    open (OUT, ">>$output_file");    
        
    my $switch = 1; 
    while ($switch == 1) {
        my @get_SNPs = split(/\t/, $SNPs[$placeholder]);
        my $position = $get_SNPs[3];
                        
        if (($position < $start) && ($position < $end)) {
            $placeholder++;    
        }
                
        if (($position >= $start) && ($position <= $end)) {
            print OUT "@get_SNPs";
            $placeholder++;
        }
        else {
            $switch =! 1;                
        }
    }
    $count++;
}
close(INTERVAL);

[download]

In reply to Sorting Data By Overlapping Intervals by ccelt09

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