From 92b0ea999162dcc642df14905c616a4df4421f87 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Wed, 2 Dec 2015 22:29:33 +0000
Subject: [PATCH] Initial version of SNP venn statistics script

svn path=/; revision=638
---
 interactome_scripts/SNP_venn_stats.pl | 135 ++++++++++++++++++++++++++
 1 file changed, 135 insertions(+)
 create mode 100755 interactome_scripts/SNP_venn_stats.pl

diff --git a/interactome_scripts/SNP_venn_stats.pl b/interactome_scripts/SNP_venn_stats.pl
new file mode 100755
index 0000000..ade720e
--- /dev/null
+++ b/interactome_scripts/SNP_venn_stats.pl
@@ -0,0 +1,135 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+# check for arguments and explain usage
+if ($#ARGV !=3) {
+	print "usage: SNP_venn_stats.pl file_1 file_2 file_3 output_file\n";
+	exit;
+}
+
+my $file_1 = $ARGV[0];
+my $file_2 = $ARGV[1];
+my $file_3 = $ARGV[2];
+my $output_file = $ARGV[3];
+
+my %file1hash;
+my %file2hash;
+my %file3hash;
+
+# This will change the way the hash is keyed.  A "0" will key with only the position, a "1" will include the snp value
+my $include_snp = 0;
+
+open(FILE1, "$file_1");
+while(<FILE1>) {
+		my $line = $_;
+		chomp $line;
+		my ($chrom,$pos,$ref,$snp) = split("\t", $line);
+		my $key;
+		
+		if($include_snp) {
+				$key = "$chrom" . "x" . "$pos";
+		}else{
+				$key = "$chrom" . "x" . "$pos" . "y" . "$snp";
+		}
+		$file1hash{$key} = $snp;
+}
+close(FILE1);
+
+
+open(FILE2, "$file_2");
+while(<FILE2>) {
+		my $line = $_;
+		chomp $line;
+		my ($chrom,$pos,$ref,$snp) = split("\t", $line);
+		my $key;
+		
+		if($include_snp) {
+				$key = "$chrom" . "x" . "$pos";
+		}else{
+				$key = "$chrom" . "x" . "$pos" . "y" . "$snp";
+		}
+		$file2hash{$key} = $snp;
+}
+close(FILE2);
+
+open(FILE3, "$file_3");
+while(<FILE3>) {
+		my $line = $_;
+		chomp $line;
+		my ($chrom,$pos,$ref,$snp) = split("\t", $line);
+		my $key;
+		
+		if($include_snp) {
+				$key = "$chrom" . "x" . "$pos";
+		}else{
+				$key = "$chrom" . "x" . "$pos" . "y" . "$snp";
+		}
+		$file3hash{$key} = $snp;
+}
+close(FILE3);
+
+my $count_file_1 = 0;
+my $count_file_2 = 0;
+my $count_file_3 = 0;
+
+my $count_file_12 = 0;
+my $count_file_13 = 0;
+my $count_file_23 = 0;
+my $count_file_21 = 0;
+
+my $count_file_123 = 0;
+
+foreach my $key (keys %file1hash) {
+		#check if also in file2
+		if(defined($file2hash{$key})) {
+				# and file3
+				if(defined($file3hash{$key})) {
+						$count_file_123++;
+				}else{# it's only in file1 and file2
+						$count_file_12++;
+				}
+				#check if in file3
+		}elsif(defined($file3hash{$key})) {
+				$count_file_13++;
+		#it's only in file1
+		}else{$count_file_1++;
+		}
+}
+
+foreach my $key (keys %file2hash) {
+		#check if in file3
+		if(defined($file3hash{$key})) {
+				$count_file_23++;
+		}
+		if(defined($file1hash{$key})) {
+				$count_file_21++;
+		}
+}
+
+
+# Get total counts in each file/hash
+my $total_count_file_1 = scalar(keys %file1hash);
+my $total_count_file_2 = scalar(keys %file2hash);
+my $total_count_file_3 = scalar(keys %file3hash);
+
+# calculate the count of those only in file2 and file3
+$count_file_2 = $total_count_file_2 - $count_file_123 - $count_file_12 - $count_file_23;
+$count_file_3 = $total_count_file_3 - $count_file_123 - $count_file_13 - $count_file_23;
+				
+				
+open (OUTFILE, ">$output_file");
+
+print OUTFILE "Total count in $file_1\t=\t$total_count_file_1\n";
+print OUTFILE "Total count in $file_2\t=\t$total_count_file_2\n";
+print OUTFILE "Total count in $file_3\t=\t$total_count_file_3\n";
+print OUTFILE "In $file_1 only\t=\t$count_file_1\n";
+print OUTFILE "In $file_2 only\t=\t$count_file_2\n";
+print OUTFILE "In $file_3 only\t=\t$count_file_3\n";
+print OUTFILE "In $file_1 and $file_2\t=\t$count_file_12\n";
+print OUTFILE "In $file_1 and $file_3\t=\t$count_file_13\n";
+print OUTFILE "In $file_2 and $file_3\t=\t$count_file_23\n";
+print OUTFILE "In all three files\t=\t$count_file_123\n";
+
+close(OUTFILE);
-- 
2.34.1