diff orthologs/evolmap.pl @ 0:5b9a38ec4a39 draft default tip

First commit of old repositories

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/orthologs/evolmap.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,86 @@
+#!/usr/bin/perl
+
+my $evolmapPath = "\/home\/galaxy\/galaxy_dist\/tool-data\/shared\/jars\/evolmap";
+
+my $file = "Options.txt";	     
+
+my $tree_Input = $ARGV[0];
+my $tag_Input = ".dat";
+my $protein_Input = $ARGV[1];
+my $database_name_Input = "dataout";
+my $read_database_Input = $ARGV[3];
+my $Blastall_Input = $ARGV[4];
+my $read_blast_scores_Input = $ARGV[5];
+my $alignments_Input = $ARGV[6];
+my $bit_scores_Input = $ARGV[7];
+my $read_scores_Input = $ARGV[8];
+my $read_ancestors_Input = $ARGV[9];
+my $view_ancestors_Input = "false";
+my $sfa_Input = $ARGV[10];
+my $ortholog_threshold_Input = $ARGV[11];
+my $diverged_threshold_Input = $ARGV[12];
+my $diverged_std_Input = $ARGV[13];
+my $avg_of_paralogs_Input = $ARGV[14];
+#my $numDiffGenes = $ARGV[15];
+
+my $temp = $tree_Input;
+$temp =~ tr/(),/ /;
+my @genes = split(' ', $temp);
+my $size = @genes;
+
+my @treeFiles;
+my $argIndex = 15;
+my $count;
+for($count = 0; $count < $size; $count++) {
+	$treeFiles[$count] = $ARGV[$argIndex];
+	$argIndex++;
+}
+
+my $tree_copy = "";
+my $index = 0;
+my $flag = 1;
+for($count = 0; $count < length($tree_Input); $count++) {
+	if(substr($tree_Input, $count, 1) eq '(' || substr($tree_Input, $count, 1) eq ')' || substr($tree_Input, $count, 1) eq ',') {
+		$tree_copy = $tree_copy.substr($tree_Input, $count, 1);
+		$flag = 1;
+	}
+	else {
+		if($flag) {
+			$tree_copy = $tree_copy.$treeFiles[$index];
+			$index++;
+		}
+		$flag = 0;
+	}
+}
+
+$tree_copy =~ s/\Q.dat\E//g;
+
+open(CONFIG, '>'.$file);
+
+print CONFIG "processors = 10\n";
+#print CONFIG "tree = ".$tree_Input."\n";
+print CONFIG "tree = ".$tree_copy."\n";
+print CONFIG "tag = ".$tag_Input."\n";
+print CONFIG "protein = ".$protein_Input."\n";
+print CONFIG "database_name = ".$database_name_Input."\n";
+print CONFIG "read_database = ".$read_database_Input."\n";
+print CONFIG "Blastall = ".$Blastall_Input."\n";
+print CONFIG "read_blast_scores = ".$read_blast_scores_Input."\n";
+print CONFIG "alignments = ".$alignments_Input."\n";
+print CONFIG "bit_scores = ".$bit_scores_Input."\n";
+print CONFIG "read_scores = ".$read_scores_Input."\n";
+print CONFIG "read_ancestors = ".$read_ancestors_Input."\n";
+print CONFIG "view_ancestors = ".$view_ancestors_Input."\n";
+print CONFIG "sfa = ".$sfa_Input."\n";
+print CONFIG "ortholog_threshold = ".$ortholog_threshold_Input."\n";
+print CONFIG "diverged_threshold = ".$diverged_threshold_Input."\n";
+print CONFIG "diverged_std = ".$diverged_std_Input."\n";
+print CONFIG "avg_of_paralogs = ".$avg_of_paralogs_Input."\n";
+
+close(CONFIG);
+
+if($read_ancestors_Input eq "false" || $read_scores_Input eq "false") {
+	my $run = qx/java -jar -Xms8000m -Xmx8000m $evolmapPath\/EvolMAP.jar $file/;
+	print $run;
+}
+