From fc06d7e1f4a9780bc9c9e31b5e28810ee21f0908 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Thu, 16 Sep 2010 22:01:52 +0000
Subject: [PATCH] Added --new option for creating a new version of the database

svn path=/; revision=35
---
 .../inparanoid_output_parse.pl                | 46 +++++++++++++++----
 1 file changed, 38 insertions(+), 8 deletions(-)

diff --git a/interactome_scripts/inparanoid_output_parse.pl b/interactome_scripts/inparanoid_output_parse.pl
index 8c035b5..111c57e 100755
--- a/interactome_scripts/inparanoid_output_parse.pl
+++ b/interactome_scripts/inparanoid_output_parse.pl
@@ -21,6 +21,11 @@ use warnings;
 use DBI;
 use Term::Screen::ReadLine;
 
+use Getopt::Long;
+my $new = '';
+GetOptions ('new' => \$new);
+
+
 require "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl";
 
 # open the file to be parsed, assume this is all sqltable* files in directory
@@ -29,6 +34,8 @@ my @files = glob("sqltable*");
 
 # define the database handle to be used 
 
+my $database;
+
 my $screen = Term::Screen::ReadLine->new();
 	# clear the screen
 	$screen->clrscr;
@@ -42,11 +49,33 @@ my $screen = Term::Screen::ReadLine->new();
 
 	$screen->at(2,0);
 	undef $screen;
-	
-my $dbh = DBI->connect('DBI:mysql:inparanoid_data;host=floret.cgrb.oregonstate.edu', $username, $password,
-	{ RaiseError=> 1, AutoCommit=>1 }
-	) or die "Failed to connect to database: $DBI::errstr";
-	
+	if($new) {
+		$database = "";
+		my $dbh_temp = DBI->connect("DBI:mysql:$database;host=floret.cgrb.oregonstate.edu", $username, $password,
+		{ RaiseError=> 1, AutoCommit=>1 }
+		) or die "Failed to connect to database: $DBI::errstr";
+		$dbh_temp->do("drop database inparanoid_data");
+		$dbh_temp->do("create database inparanoid_data");
+		$dbh_temp->disconnect;
+	}
+	my $dbh = DBI->connect("DBI:mysql:inparanoid_data;host=floret.cgrb.oregonstate.edu", $username, $password,
+		{ RaiseError=> 1, AutoCommit=>1 }
+		) or die "Failed to connect to database: $DBI::errstr";
+		
+		
+my $clust_table = "clusters";
+my $safe_clust_table = $dbh->quote_identifier($clust_table);
+
+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");
+}
+		
+my $tot_file_count = scalar @files;
+my $file_counter = 1;
 	
 # start the database entries
 foreach my $input_file (@files) {
@@ -60,11 +89,12 @@ foreach my $input_file (@files) {
 	$species_1 = find_species($species_1);
 	$species_2 = find_species($species_2);
 	my $species_table = $species_1."_".$species_2;
-	my $clust_table = "clusters";
+	
 
 	my %id_hash;
 	
-	print "Working on $species_table\n";
+	print "Working on $species_table: file $file_counter/$tot_file_count\n";
+	$file_counter++;
 
 
 	
@@ -82,7 +112,7 @@ foreach my $input_file (@files) {
 		my $sth = $dbh->prepare("insert into $safe_species_table (id, bit_score, species, score, gene) values (?,?,?,?,?)");
 	
 	
-		my $safe_clust_table = $dbh->quote_identifier($clust_table);
+		
 		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");
-- 
2.34.1