From a1474a3f2c44ed397dd49daf59b2fa8c4e82fec4 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Wed, 6 Jul 2011 23:53:02 +0000
Subject: [PATCH] Switch to using dbconnect method from DbiFloret module

svn path=/; revision=113
---
 interactome_scripts/supercluster.pl | 36 +++++++++--------------------
 1 file changed, 11 insertions(+), 25 deletions(-)

diff --git a/interactome_scripts/supercluster.pl b/interactome_scripts/supercluster.pl
index 4425ee5..d30dbef 100755
--- a/interactome_scripts/supercluster.pl
+++ b/interactome_scripts/supercluster.pl
@@ -23,7 +23,11 @@ use warnings;
 use strict;
 
 use DBI;
-use Term::Screen::ReadLine;
+use Term::ReadKey;
+
+use lib "$ENV{HOME}/scripts/jaiswallab/interactome_scripts";
+
+use DbiFloret;
 
 if(-e "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl") {
 	require "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl";
@@ -31,33 +35,15 @@ if(-e "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl") {
 	require "$ENV{HOME}/bin/find_species.pl";
 }
 
-# define the database handle to be used 
-
-my $screen = Term::Screen::ReadLine->new();
-	# clear the screen
-	$screen->clrscr;
-	# ask for username
-	$screen->at(0,0)->puts("Username: ");
-	my $username = $screen->readline(ROW => 0, COL=>11);
-
-	# ask for password, replace character presses with stars
-	$screen->at(1,0)->puts("Password: ");
-	my $password = $screen->readline(ROW => 1, COL => 11, PASSWORD => 1);
+my $dbh = DbiFloret::dbconnect;
 	
-	# Ask for the minimum score for the paralogy cutoff
-	$screen->at(2,0)->puts("Minimum paralogy score: ");
-	my $min_score = $screen->readline(ROW => 2, COL => 24);
-
-	$screen->at(3,0);
-	undef $screen;
+print "Minimum paralogy score: ";
+chomp(my $min_score = <STDIN>);
 	
 if($min_score eq "") {
 	$min_score = 0;
 }
-	
-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";
+
 	
 	
 #### Note to self ####
@@ -83,8 +69,8 @@ my $super_id = 0; #initialize the super cluster id
 my %super_hash;
 my %big_count_hash;
 	
-#my @species  = ("Ath", "Brachy", "C_elegans", "Chlamy", "Danio", "E_coli", "Fragaria", "Glycine", "Human", "Maize", "Mouse", "Neurospora", "Oryza_sativa", "Physcomitreall", "Poplar", "P_persica", "Sacc_cerevisiae", "Sacc_pombe", "Selaginella", "Sorghum", "Synechosystis", "Vitis");
-my @species = all_species_array();
+my @species  = ("Arabidopsis_lyrata", "Arabidopsis_thaliana", "Carica_papaya", "Citrus_clementina", "Citrus_sinensis", "Eucalyptus_grandis", "Fragaria_vesca", "Malus_domestica", "Oryza_sativa", "Populus_trichocarpa", "Prunus_persica", "Vitis_vinifera");
+#my @species = all_species_array();
 my $num_species = @species;
 
 for (my $i=0; $i<$num_species-1; $i++) {
-- 
2.34.1