find_SNPs1.pl

Invoke using:

http://cougar:8080/tigr-scripts/projects/find_SNPs1.pl?file=TB.mum.out




#!/usr/bin/perl

use strict;
use CGI qw/:standard/;
print header;

my $file = param('file');

print "<HTML>\n";
print "<h2>Parsing the contents of this file: $file</H2>\n";

use strict;

my $insert_size = 1;

my (@list);

open(F_IN, $file) || print "was not able to open file\n";
while(<F_IN>) {
    if (!/>/) {
	s/^\s*//;
	my($x1, $x2, $l) = split(/\s+/);
	push(@list, $x1 . " " . $x2 . " " . $l);
    }
}
close(F_IN);

@list = sort numerically (@list);

my $first_time = 1;
my $old_pos;

my @list2;

my $count_snps = 0;
foreach my $row (@list) {
    my ($x1, $x2, $l) = split(/\s/,$row);

    if ($first_time != 1) {
	if (($x1 - $old_pos) == $insert_size) {
	    $count_snps++;
	    push(@list2, $old_pos);
	}
    }

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

print "SNP Count: $count_snps\n";

print "<TABLE BORDER = 1>\n";
print "<TR><TH>Position</TH></TR>\n";

foreach my $p (@list2) {
    print "<TR><TD>$p</TD></TR>\n";
}

print "</TABLE>\n";
sub numerically {
    $a <=> $b;
}

Finding if SNPs are in coding regions

Was done in this program.
left right