From 7eb3d9a9bd6ab77defd10933335c358d166934fe Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Thu, 10 Mar 2016 21:42:40 +0000
Subject: [PATCH] Input species order no longer matters.  Added extra argument
 to make it detect which species to search for in sql statement

svn path=/; revision=643
---
 interactome_scripts/find_ortho_inpara.pl | 33 +++++++++++++++++-------
 1 file changed, 23 insertions(+), 10 deletions(-)

diff --git a/interactome_scripts/find_ortho_inpara.pl b/interactome_scripts/find_ortho_inpara.pl
index 600cd27..748d7a5 100755
--- a/interactome_scripts/find_ortho_inpara.pl
+++ b/interactome_scripts/find_ortho_inpara.pl
@@ -12,28 +12,41 @@
 use strict;
 use warnings;
 
-if($#ARGV != 3) {
-	print "usage: find_ortho_inpara.pl species_1 species_2 input_gene_list output_file\n";
+if($#ARGV != 4) {
+	print "usage: find_ortho_inpara.pl species_1 species_2  input_species input_gene_list output_file\n";
 	exit;
 }
 
 use lib "$ENV{HOME}/scripts/jaiswallab/interactome_scripts";
 
+
+my @temp_array = ($ARGV[0], $ARGV[1]);
+my @species_array = sort @temp_array;
+my $spec_array_size = @species_array;
+
+
 use DbiFloret;
 
 my $dbh = DbiFloret::dbconnect;
 
-my @species_array = ($ARGV[0], $ARGV[1]);
-#my @species_array = ("Arabidopsis_thaliana", "Zea_mays");
-#my @species_array = ("Ath", "Maize");
-my $spec_array_size = @species_array;
-
 # similarity score to determine if we should keep the paralogs.
 #  0.0 would keep all paralogs, 1.0 would restrict to strict orthologs
 my $sim_score = 0.1;
 
+# input species, needed to fix sth_get_ortho species_array index to the opposite
+my $in_species = $ARGV[2];
+my $species_index;
+if($in_species eq $species_array[0]) {
+		$species_index = 1;
+}elsif($in_species eq $species_array[1]) {
+		$species_index = 0;
+}else{
+		print "input_species doesn't match!!!/n";
+		die;
+}
+
 # read in list of genes from csv file given as argument
-my $in_file = $ARGV[2];
+my $in_file = $ARGV[3];
 
 open (in_file, "$in_file");
 
@@ -56,7 +69,7 @@ my %ortho_hash;
 
 for (my $i = 1; $i<$spec_array_size; $i++) {
 	
-	my $out_file = $ARGV[3]; # . "_$species_array[3].txt";
+	my $out_file = $ARGV[4]; # . "_$species_array[3].txt";
 	open(out_file, ">$out_file");
 	
 	my $table = $species_array[0] . "_" . $species_array[$i];
@@ -68,7 +81,7 @@ for (my $i = 1; $i<$spec_array_size; $i++) {
 	my $sth_get_id = $dbh->prepare("select id from $safe_table where gene like ?");
 	
 	# set up db query statement to get the orthologs using the cluster id
-	my $sth_get_ortho = $dbh->prepare("select gene, score from $safe_table where id = ? and species = '$species_array[1]' and score >= '$sim_score'");
+	my $sth_get_ortho = $dbh->prepare("select gene, score from $safe_table where id = ? and species = '$species_array[$species_index]' and score >= '$sim_score'");
 	
 	foreach my $gene (@in_gene_array) {
 		
-- 
2.34.1