Moved the "clusters" table select statement outside the loop. Fixes random stalls...

svn path=/; revision=47

diff --git a/interactome_scripts/inparanoid_output_parse.pl b/interactome_scripts/inparanoid_output_parse.pl
index bd58591a460af9feae03ec3d51f6989e37651a31..bb8de08839c331f818bcd420fe3fec271051af71 100755 (executable)
--- a/interactome_scripts/inparanoid_output_parse.pl
+++ b/interactome_scripts/inparanoid_output_parse.pl
@@ -66,12 +66,24 @@ my $screen = Term::Screen::ReadLine->new();
 my $clust_table = "clusters";
 my $safe_clust_table = $dbh->quote_identifier($clust_table);
 
+my %id_hash;
 if($new) {
        $dbh->do("create table $safe_clust_table (
                `id` INT( 11 ) NOT NULL AUTO_INCREMENT,
                `clust_id` VARCHAR( 255 ) NOT NULL ,
                INDEX ( `id` )
                ) TYPE = MYISAM");
+}else{ # if not new load, grab the data from the clusters table
+       my $sth_id_dump = $dbh->prepare("select * from clusters");
+       # put the clusters table data into a hash
+       print "before dump\n";
+       $sth_id_dump->execute();
+       print "after dump\n";
+       while(my @ids = $sth_id_dump->fetchrow_array) {
+               if(!defined($id_hash{$ids[1]})) {
+                       $id_hash{$ids[1]} = $ids[0];
+               }
+       }
 }
                
 my $tot_file_count = scalar @files;
@@ -91,14 +103,12 @@ foreach my $input_file (@files) {
        my $species_table = $species_1."_".$species_2;
        
 
-       my %id_hash;
        
        print "Working on $species_table: file $file_counter/$tot_file_count\n";
        $file_counter++;
 
 
        
-               
        my $safe_species_table = $dbh->quote_identifier($species_table);
        $dbh->do("drop table if exists $safe_species_table");
        $dbh->do("CREATE TABLE $safe_species_table (
@@ -113,17 +123,11 @@ foreach my $input_file (@files) {
 
        
                
-       my $sth_id_dump = $dbh->prepare("select * from clusters");
+       
        my $sth_id_add = $dbh->prepare("insert into $safe_clust_table (id, clust_id) values (?,?)");
        my $sth_get_id = $dbh->prepare("select last_insert_id(id) from clusters order by id desc limit 1");
 
-       # put the clusters table data into a hash
-       $sth_id_dump->execute();
-       while(my @ids = $sth_id_dump->fetchrow_array) {
-               if(!defined($id_hash{$ids[1]})) {
-                       $id_hash{$ids[1]} = $ids[0];
-               }
-       }
+       
        
        my $clust_id_prev = "";
 
@@ -140,7 +144,6 @@ foreach my $input_file (@files) {
                $clust_id = "$species_1"."___".$species_2."___".$clust_id;
                $species = find_species($species);
                my $gene = find_gene($gene_header,$species);
-               
                # skip isomers that are not .1
                next if ($gene =~ /\.[2-9]$/);
                next if ($gene =~ /\.1[0-9]$/);
@@ -156,7 +159,6 @@ foreach my $input_file (@files) {
                if(!defined($id_hash{$clust_id})) {
                        if ($clust_id ne $clust_id_prev) {
                                $sth_id_add->execute(undef, $clust_id);
-                       
                                $sth_get_id->execute();
                                my @new_id = $sth_get_id->fetchrow_array;
                                $id = $new_id[0];
@@ -168,7 +170,6 @@ foreach my $input_file (@files) {
        
                
                $sth->execute($id, $bit_score, $species, $score, $gene);
-       
                $clust_id_prev = $clust_id;