From 40300d6fe677aecc2b3a648c4f48795feefb9ac2 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Wed, 22 Sep 2010 20:38:56 +0000
Subject: [PATCH] Fix whitespace and remove old comments

svn path=/; revision=45
---
 .../inparanoid_output_parse.pl                | 45 +++++++++----------
 1 file changed, 22 insertions(+), 23 deletions(-)

diff --git a/interactome_scripts/inparanoid_output_parse.pl b/interactome_scripts/inparanoid_output_parse.pl
index 111c57e..bd58591 100755
--- a/interactome_scripts/inparanoid_output_parse.pl
+++ b/interactome_scripts/inparanoid_output_parse.pl
@@ -99,31 +99,31 @@ foreach my $input_file (@files) {
 
 	
 		
-		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 (
-			`id` INT( 11 ) NOT NULL ,
-			`bit_score` INT( 11 ) NOT NULL ,
-			`species` VARCHAR( 255 ) NOT NULL ,
-			`score` FLOAT( 11 ) NOT NULL ,
-			`gene` VARCHAR( 255 ) NOT NULL ,
-			INDEX ( `id` )
-			) TYPE = MYISAM");
-		my $sth = $dbh->prepare("insert into $safe_species_table (id, bit_score, species, score, gene) values (?,?,?,?,?)");
-	
+	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 (
+		`id` INT( 11 ) NOT NULL ,
+		`bit_score` INT( 11 ) NOT NULL ,
+		`species` VARCHAR( 255 ) NOT NULL ,
+		`score` FLOAT( 11 ) NOT NULL ,
+		`gene` VARCHAR( 255 ) NOT NULL ,
+		INDEX ( `id` )
+		) TYPE = MYISAM");
+	my $sth = $dbh->prepare("insert into $safe_species_table (id, bit_score, species, score, gene) values (?,?,?,?,?)");
+
 	
 		
-		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 $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 = "";
 
@@ -152,7 +152,6 @@ foreach my $input_file (@files) {
 		next if ($gene =~ /\.7[0-9]$/);
 		next if ($gene =~ /\.8[0-9]$/);
 		next if ($gene =~ /\.9[0-9]$/);
-		# assume there are never more than 29 isomers
 	
 		if(!defined($id_hash{$clust_id})) {
 			if ($clust_id ne $clust_id_prev) {
-- 
2.34.1