Fixed scripts for Mamathas needs, and added better use of vars

svn path=/; revision=25

diff --git a/interactome_scripts/find_ortho_inpara.pl b/interactome_scripts/find_ortho_inpara.pl
index 08fca807156b5928ec2039a56248db0de83a53ba..a7876e4367c3cba91d290fdb182ab0761eb2ecc8 100755 (executable)
--- a/interactome_scripts/find_ortho_inpara.pl
+++ b/interactome_scripts/find_ortho_inpara.pl
@@ -12,16 +12,25 @@
 use strict;
 use warnings;
 
+if($#ARGV != 1) {
+       print "usage: find_ortho_inpara.pl input_gene_list output_file_prefix\n";
+       exit;
+}
+
 use lib "$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 @species_array = ("Ath", "Oryza_sativa", "Sorghum", "Maize", "Glycine", "Brachy", "Poplar");
+#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 = 0.0;
+
 # read in list of genes from csv file given as argument
 my $in_file = $ARGV[0];
 
@@ -33,25 +42,29 @@ while(<in_file>) {
        my $in_gene = $_;
        chomp $in_gene; 
        $in_gene =~ s/\s//g;
-       $in_gene .= ".1"; # add the suffix back so that the gene matches the db
+       if ($in_gene !~ /\.\d$/) {
+               $in_gene .= ".1"; # add the suffix back so that the gene matches the db
+       }
        push(@in_gene_array, $in_gene);
        #print "$in_gene\n";
        
 }
 close(in_file);
 
-open(out_file, ">Ath_ortho.txt");
 
 for (my $i = 1; $i<$spec_array_size; $i++) {
        
+       my $out_file = $ARGV[1] . "_$species_array[$i].txt";
+       open(out_file, ">$out_file");
+       
        my $table = $species_array[0] . "_" . $species_array[$i];
-       print out_file "$species_array[$i]\t$table\n";
+       print out_file "gene\tortho_gene\tscore\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, score from $table where id = ? and species = '$species_array[$i]' and score >= '0.0'");
+       my $sth_get_ortho = $dbh->prepare("select gene, score from $table where id = ? and species = '$species_array[$i]' and score >= '$sim_score'");
        
        foreach my $gene (@in_gene_array) {
                
@@ -72,6 +85,7 @@ for (my $i = 1; $i<$spec_array_size; $i++) {
                        }
                }
        }
+       close(out_file);
 }
 
-close(out_file);
+

diff --git a/interactome_scripts/find_ortho_super.pl b/interactome_scripts/find_ortho_super.pl
index ca7af464eace6c72f8df69c28fcb0f640d8346b6..d4a3a516c732be5d5b8946f52b434dcf750b963a 100755 (executable)
--- a/interactome_scripts/find_ortho_super.pl
+++ b/interactome_scripts/find_ortho_super.pl
@@ -1,25 +1,30 @@
 #!/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).                                                 #
-#                                                                   #
-#####################################################################
+###########################################################################
+#    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) from the supercluster table                            #
+#                                                                         #
+###########################################################################
 
 use strict;
 use warnings;
 
+if($#ARGV != 1) {
+       print "usage: find_ortho_super.pl input_gene_list output_file_prefix\n";
+       exit;
+}
+
 use lib "$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 @species_array = ("Ath", "Oryza_sativa", "Sorghum", "Maize", "Glycine", "Brachy");
+#my @species_array = ("Ath", "Maize");
 my $spec_array_size = @species_array;
 
 # read in list of genes from csv file given as argument
@@ -33,17 +38,20 @@ while(<in_file>) {
        my $in_gene = $_;
        chomp $in_gene; 
        $in_gene =~ s/\s//g;
-       $in_gene .= ".1"; # add the suffix back so that the gene matches the db
+       if ($in_gene !~ /\.\d$/) {
+               $in_gene .= ".1"; # add the suffix back so that the gene matches the db
+       }
        push(@in_gene_array, $in_gene);
        #print "$in_gene\n";
        
 }
 close(in_file);
 
-open(out_file, ">Ath_ortho_super.txt");
-
 for (my $i = 1; $i<$spec_array_size; $i++) {
        
+       my $out_file = $ARGV[1] . "_$species_array[$i].txt";
+       open(out_file, ">$out_file");
+       
        my $table = "super_clust";
        #print out_file "$species_array[$i]\t$table\n";
        
@@ -53,10 +61,7 @@ for (my $i = 1; $i<$spec_array_size; $i++) {
        # set up db query statement to get the orthologs using the cluster id
        my $sth_get_ortho = $dbh->prepare("select gene from $table where super_id = ? and species = '$species_array[$i]'");
        #my $sth_get_ortho = $dbh->prepare("select gene,species from $table where super_id = ?");
-       
-       # setup query to make sure there is an ortholog gene in the cluster
-       my $sth_check_ortho = $dbh->prepare("select species from $table where super_id = ? and species = '$species_array[0]'");
-       
+
        foreach my $gene (@in_gene_array) {
                
                my $rv1 = $sth_get_id->execute($gene);
@@ -65,19 +70,9 @@ for (my $i = 1; $i<$spec_array_size; $i++) {
                }
                
                while (my $id = $sth_get_id->fetchrow_array()) {
-                       #my $rv2 = $sth_check_ortho->execute($id);
-                       #if (!$rv2) {
-                       #       next;
-                       #}
-                       #my $check = $sth_check_ortho->fetchrow_array();
-                       #print "$id\t$check\n";
-                       #if ($check ne "$species_array[0]") {
-                       #       print "no match\t\t$id\t$check\n";
-                       #       next;
-                       #}
-                       
-                       my $rv3 = $sth_get_ortho->execute($id);
-                       if (!$rv3) {
+
+                       my $rv2 = $sth_get_ortho->execute($id);
+                       if (!$rv2) {
                                next;
                        }
                        
@@ -86,6 +81,6 @@ for (my $i = 1; $i<$spec_array_size; $i++) {
                        }
                }
        }
+       close(out_file);
 }
 
-close(out_file);