--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloconversion/change_sp.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,70 @@
+#!/usr/bin/perl -w
+use strict;
+
+my $infile = $ARGV[0];
+my $changefile = $ARGV[1];
+my $outfile = $ARGV[2];
+
+open(IN, "$infile") or exit;
+open(CHANGE, "$changefile");
+open(OUT, ">$outfile") or exit;
+
+
+my %speciesFor;	#Hash to associate code with species name
+
+while (<CHANGE>) 
+{
+	chomp;
+	my $currentinput = "$_";
+	if($currentinput =~m /\t/){     #must have a tab otherwise wrong file format
+		if($currentinput =~m /\t\t/){
+			print OUT "ERROR: file contains 2 tabs in a row.  Check phytab format.\n";
+                        die("ERROR: file contains 2 tabs in a row. Check it is in phytab format");
+                }else{
+                        my @changepair = split(/\t/, $currentinput);
+                        my $codename=$changepair[0];
+                        my $sp_name = $changepair[1];
+                        if (exists $speciesFor{$codename}) {
+                        	print OUT "ERROR: Species name specification for $codename is duplicated\n";
+                                die("ERROR: Species name specifiation for for $codename is duplicated\n");
+                        }else{
+                        	$speciesFor{$codename}=$sp_name;
+			}
+                }
+        }else{
+		die "ERROR: Species conversion table  must be genefamily\tmodel and contain no blank lines\n";
+        }
+}
+while (<IN>) {
+	chomp;
+	my $currentinput = "$_";
+	if($currentinput =~m /\t/){     #must have a tab otherwise wrong file format
+		if($currentinput =~m /\t\t/){
+			print OUT "ERROR: file contains 2 tabs in a row.  Check phytab format.\n";
+                        die;
+                }else{
+                        my @changepair = split(/\t/, $currentinput);
+                        my $sp_name=$changepair[0];
+
+                        if (exists $speciesFor{$sp_name}) {
+				$currentinput =~s /$sp_name/$speciesFor{$sp_name}/ ;
+                        	print OUT $currentinput."\n";
+                        }else{
+				print OUT $currentinput."\n";
+			}
+                }
+        }else{
+		die "ERROR: Input a PHYTAB file in Tabular format\n";
+        }
+}
+close(IN);
+close(OUT);
+close(CHANGE);
+
+sub change
+{
+
+	my $changetext = shift;
+	$changetext =~ s/ /_/g;
+	return $changetext;
+}