Updated scripts

svn path=/; revision=17

diff --git a/interactome_scripts/find_ortho_super.pl b/interactome_scripts/find_ortho_super.pl
index 45cbfa92e9dc0774c5f72f8e8ce1615942ea893e..ca7af464eace6c72f8df69c28fcb0f640d8346b6 100755 (executable)
--- a/interactome_scripts/find_ortho_super.pl
+++ b/interactome_scripts/find_ortho_super.pl
@@ -52,6 +52,10 @@ 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) {
                
@@ -61,12 +65,23 @@ for (my $i = 1; $i<$spec_array_size; $i++) {
                }
                
                while (my $id = $sth_get_id->fetchrow_array()) {
-                       my $rv2 = $sth_get_ortho->execute($id);
-                       if (!$rv2) {
+                       #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) {
                                next;
                        }
                        
-                       while (my $ortho = $sth_get_ortho->fetchrow_array()) {
+                       while (my ($ortho, $species) = $sth_get_ortho->fetchrow_array()) {
                                print out_file "$gene\t$ortho\n";
                        }
                }

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 17c7a8841d7d7071ff9d598790de8cefc71abfdb..1e6c16ed760aa23786d6fbb6dbe24851cccec97a 100755 (executable)
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -32,8 +32,10 @@ sub find_species {
                $temp = "Neurospora";
        }elsif ($temp =~ /Oryza\_sativa/) {
                $temp = "Oryza_sativa";
+       }elsif ($temp =~ /Cpapaya/) {
+               $temp = "Carica_papaya";
        }elsif ($temp =~ /Physcomit/) {
-               $temp = "Physcomitreall";
+               $temp = "Physcomitrella";
        }elsif ($temp =~ /Populus/) {
                $temp = "Poplar";
        }elsif ($temp =~ /Ppersica/) {
@@ -41,13 +43,13 @@ sub find_species {
        }elsif ($temp =~ /cerevisiae/) {
                $temp = "Sacc_cerevisiae";
        }elsif ($temp =~ /pombe/) {
-               $temp = "Sacc_pombe";
+               $temp = "Schizo_pombe";
        }elsif ($temp =~ /Selaginella/) {
                $temp = "Selaginella";
        }elsif ($temp =~ /Sorghum/) {
                $temp = "Sorghum";
-       }elsif ($temp =~ /Synechosystis/) {
-               $temp = "Synechosystis";
+       }elsif ($temp =~ /Synechocystis/) {
+               $temp = "Synechocystis";
        }elsif ($temp =~ /Vitis\_vinifera/) {
                $temp = "Vitis";
        }else {
@@ -100,7 +102,7 @@ sub find_gene {
        }elsif ($species eq "Oryza_sativa") {
                my ($isomer,$temp,$type) = split(/\|/,$gene_header);
                $gene = $isomer;
-       }elsif ($species eq "Physcomitreall") {
+       }elsif ($species eq "Physcomitrella") {
                my ($name,$locus_id,$chrom_id,$prot_id) = split(/\|/,$gene_header);
                $gene = $prot_id; #???
        }elsif ($species eq "Poplar") {
@@ -112,7 +114,7 @@ sub find_gene {
        }elsif ($species eq "Sacc_cerevisiae") {
                my ($gene_id,$temp) = split(/\s/,$gene_header);
                $gene = $gene_id;
-       }elsif ($species eq "Sacc_pombe") {
+       }elsif ($species eq "Schizo_pombe") {
                my ($gene_id,$temp) = split(/\s/,$gene_header);
                $gene = $gene_id;
        }elsif ($species eq "Selaginella") {
@@ -121,7 +123,7 @@ sub find_gene {
        }elsif ($species eq "Sorghum") {
                my ($name,$locus_id,$scaff_id,$prot_id) = split(/\|/,$gene_header);
                $gene = $prot_id; #???
-       }elsif ($species eq "Synechosystis") {
+       }elsif ($species eq "Synechocystis") {
                my ($gene_id,$type,$temp) = split(" ",$gene_header);
                $gene = $gene_id; #???
        }elsif ($species eq "Vitis") {