--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/matrix2fisher.pl	Fri Dec 09 11:56:56 2011 -0500
@@ -0,0 +1,139 @@
+#!/usr/bin/perl
+# This script takes a matrix as input and generates an R script to look for 
+# simularity between rows.
+#
+# 'tab2list' is a complement to list2tab. It reads a 2-dimensional table and
+# produces a list in the form: row label - column label - value.
+#
+use Getopt::Long;
+
+$keycols = 1;
+$usage = 0;
+@cis;
+%hash;
+open OUT, "> FISH/Fisher_pre.txt";
+open OUT2, "> FISH/Fisher_pre_named.txt";
+GetOptions("keycols=i" => \$keycols, "usage" => \$usage, "help"=>\$usage);
+
+if ($usage) {
+  print STDERR "usage: tab2list < infile > outfile
+  Options:
+    --keycols=X  ... How many cols from left are to be kept (default: 1)\n";
+  exit 0;
+}
+
+$keycols--;
+
+$_ = <>;
+chomp;
+@headline = split /\t/, $_;
+@anim = @headline;
+shift(@anim);
+while (<>) {
+  chomp;
+  @line = split /\t/, $_;
+  $head = "";
+  foreach my $i (0 .. $keycols) {
+    $head .= "$line[$i]\t";
+  }
+  chop $head;
+push (@cis,$head);
+
+  foreach my $i ($keycols+1 .. $#line) {
+ #   print "$head\t$headline[$i]\t$line[$i]\n";
+ $value=$head."|".$headline[$i];
+ $hash{$value}=$line[$i];
+
+}
+}
+foreach (@cis){
+#print "$_";
+}
+
+print "\n";
+foreach (@anim){
+#print "$_";
+}
+
+print "\n";
+foreach (keys %hash) {
+#        print "The key $_ $hash{$_}\n";
+}
+
+%seen;
+$first=0;
+$second=0;
+$third=0;
+$fourth=0;
+
+foreach $x(@cis){
+foreach $y(@cis){
+$first=0;
+$second=0;
+$third=0;
+$fourth=0;
+if ($x eq $y){
+next;}
+$z = $x."|".$y;
+if (exists $seen{$z}){
+next;}
+$seen{$z}= '1';
+$z2 = $y."|".$x;
+$seen{$z2}= '1';
+foreach $a(@anim) {
+$b =$x."|".$a;
+$c =$y."|".$a;
+if (($hash{$b}==0) and ($hash{$c}==0)){
+$fourth = $fourth + 1;
+}
+elsif (($hash{$b}==0) and ($hash{$c}==1)){
+$third = $third + 1;
+}
+elsif (($hash{$b}==1) and ($hash{$c}==0)){
+$second = $second + 1;
+}
+elsif (($hash{$b}==1) and ($hash{$c}==1)){
+$first = $first + 1;
+}
+#print "$a|$x|$y\n";
+#print "$hash{$b}|$hash{$c}\n";
+}
+print OUT "object__object\t$first\t$second\t$third\t$fourth\n";
+print OUT2 "$x"."__"."$y\t$first\t$second\t$third\t$fourth\n";
+}
+}
+close OUT;
+close OUT2;
+open SOURCE, "< FISH/Fisher_pre.txt";
+open OUT, "> FISH/Fisher.R";
+while (defined($line = <SOURCE>)) {
+chomp $line;
+    @field= split(/\t/, $line);
+print OUT "$field[0] <- matrix(c($field[1],$field[2],$field[3],$field[4]), nr=2, dimnames=list(c(\"cis\", \"nocis\"), c(\"pheno\", \"notpheno\")))\n$field[0]\nfisher.test($field[0]".",alternative = \"greater\")\n";
+}
+#system "module load R";
+#system "R < FISH/Fisher.R --vanilla > FISH/fisher_dump.txt";
+open (my $fisher_dump, ">", "FISH/fisher_dump.txt") || die "Unable to open FISH/fisher_dump.txt. $!\n";
+open (my $out, "Rscript --vanilla FISH/Fisher.R | ");
+while (<$out>) {
+    print $fisher_dump $_;
+}
+close($out);
+close($fisher_dump);
+close OUT;
+
+open SOURCE, "< FISH/fisher_dump.txt";
+open OUT, "> FISH/R_result.txt";
+while (defined($line = <SOURCE>)) {
+   chomp ($line); 
+   @field= split(/\t/, $line);
+           if ($field[0] =~ m/data/){
+           print OUT "$field[0]\t";
+           }
+           if ($field[0] =~ m/p-value/){
+           print OUT "$field[0]\n";
+           }
+   }
+close OUT;
+print "cooperation analyses complete";
+