find_SNPs2.pl

Note, I cheated and did not make this run under cgi-bin. Invoke the program like this on the unix command line: 
 % cat TB.mum.out | find_SNPs2.pl TBCDC1551.ppt 

#!/usr/local/perl

use strict;

my $insert_size = 1;

my (@list, %array);

open(F_IN, $ARGV[0]) || die "cant open: $ARGV[0]";
while(<F_IN>) {
    if (/^\s*([0-9]+)\.\.([0-9]+)/) {
	my $start = $1;
	my $stop = $2;

	my($i);
	for($i=$start;$i<$stop+1;$i++) {
	    $array{$i} = "coding";
	}
    }    
}
close(F_IN);

while(<STDIN>) {
    if (!/>/) {
	s/^\s*//;
	my($x1, $x2, $l) = split(/\s+/);
	push(@list, $x1 . " " . $x2 . " " . $l);
    }
}

@list = sort numerically (@list);

my $first_time = 1;
my $old_pos;

foreach my $row (@list) {
    my ($x1, $x2, $l) = split(/\s/,$row);

    if ($first_time != 1) {
	if (($x1 - $old_pos) == $insert_size) {
	    if ($array{$old_pos} eq "coding") {
		print "Pos $old_pos was coding\n";
	    }
	    else {
		print "Pos $old_pos was noncoding\n";
	    }
	}
    }

    $first_time = 0;
    $old_pos = $x1 + $l;
}


sub numerically {
    $a <=> $b;
}
left right