Program to query inparanoid database and retrieve orthologs and paralogs

svn path=/; revision=15

diff --git a/interactome_scripts/find_ortho_inpara.pl b/interactome_scripts/find_ortho_inpara.pl
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+++ b/interactome_scripts/find_ortho_inpara.pl
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+#!/usr/bin/perl
+
+#####################################################################
+#    Written by Justin Elser 4/14/10                                #
+#                                                                   #
+#    This program takes an input file with a list of genes and      #
+#      finds the orthologs (and paralogs if the score in sth_get_ortho #
+#      is changed).                                                 #
+#                                                                   #
+#####################################################################
+
+use strict;
+use warnings;
+
+use lib "$ENV{HOME}/scripts/jaiswallab/interactome_scripts";
+
+use DbiFloret;
+
+my $dbh = DbiFloret::dbconnect;
+
+#my @species_array = ("Ath", "Oryza_sativa", "Sorghum", "Maize", "Glycine");
+my @species_array = ("Ath", "Maize");
+my $spec_array_size = @species_array;
+
+# read in list of genes from csv file given as argument
+my $in_file = $ARGV[0];
+
+open (in_file, "$in_file");
+
+my @in_gene_array;
+
+while(<in_file>) {
+       my $in_gene = $_;
+       chomp $in_gene; 
+       $in_gene .= ".1"; # add the suffix back so that the gene matches the db
+       push(@in_gene_array, $in_gene);
+       
+}
+close(in_file);
+
+open(out_file, ">flower_ortho.txt");
+
+for (my $i = 1; $i<$spec_array_size; $i++) {
+       
+       my $table = $species_array[0] . "_" . $species_array[$i];
+       print out_file "$species_array[$i]\t$table\n";
+       
+       # set up the db query statement
+       my $sth_get_id = $dbh->prepare("select id from $table where gene = ?");
+       
+       # set up db query statement to get the orthologs using the cluster id
+       my $sth_get_ortho = $dbh->prepare("select gene from $table where id = ? and species = '$species_array[$i]' and score = '1'");
+       
+       foreach my $gene (@in_gene_array) {
+               
+               my $rv1 = $sth_get_id->execute($gene);
+               if (!$rv1) {
+                       next;
+               }
+               
+               while (my $id = $sth_get_id->fetchrow_array()) {
+                       my $rv2 = $sth_get_ortho->execute($id);
+                       if (!$rv2) {
+                               next;
+                       }
+                       
+                       while (my $ortho = $sth_get_ortho->fetchrow_array()) {
+                               print out_file "$gene\t$ortho\n";
+                       }
+               }
+       }
+}
+
+close(out_file);