From: elserj <elserj@localhost>
Date: Tue, 16 Dec 2014 23:38:23 +0000 (+0000)
Subject: Switch to using DBIFloret
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=9a404610ddb6cf43d0f327941340cf2fa53deeda;p=old-jaiswallab-svn%2F.git

Switch to using DBIFloret

svn path=/; revision=597
---

diff --git a/interactome_scripts/inparanoid_orthologs.pl b/interactome_scripts/inparanoid_orthologs.pl
index 194a427..40228cf 100755
--- a/interactome_scripts/inparanoid_orthologs.pl
+++ b/interactome_scripts/inparanoid_orthologs.pl
@@ -3,36 +3,21 @@
 use warnings;
 use strict;
 
-use DBI;
-use Term::Screen::ReadLine;
 
 if ($#ARGV != 0) {
 	print "usage: inparanoid_orthologs.pl output_file\n";
 	exit;
 }
-open(outfile,">$ARGV[0]") || die "Error: file '$ARGV[0]' can not be opened\n";
+open(OUTFILE,">$ARGV[0]") || die "Error: file '$ARGV[0]' can not be opened\n";
 
 # define the database handle to be used 
+use lib "$ENV{HOME}/scripts/jaiswallab/interactome_scripts";
 
-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);
+use DbiFloret;
 
-	# ask for password, replace character presses with stars
-	$screen->at(1,0)->puts("Password: ");
-	my $password = $screen->readline(ROW => 1, COL => 11, PASSWORD => 1);
-
-	$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";
+my $dbh = DbiFloret::dbconnect;
 	
-my @species = ("Maize", "Oryza_sativa", "Ath", "Sorghum", "Brachy");
+my @species = ("Arabidopsis_thaliana", "Populus_trichocarpa");
 my $num_species = @species;
 
 for (my $i=0; $i<$num_species-1; $i++) {
@@ -88,12 +73,21 @@ for (my $i=0; $i<$num_species-1; $i++) {
 		
 		foreach my $key (keys %species_1_gene_hash) {
 			if(defined($species_2_gene_hash{$key})) {
-				print outfile "$species_1_gene_hash{$key}\t$species_2_gene_hash{$key}\n";
+				my @species_1_gene_array = split(" ", $species_1_gene_hash{$key});
+				my @species_2_gene_array = split(" ", $species_2_gene_hash{$key});
+				foreach my $gene_1 (@species_1_gene_array) {
+					print OUTFILE "$gene_1\t@species_2_gene_array" ."\n";
+				}
+				#foreach my $gene_1 (@species_1_gene_array) {
+				#	foreach my $gene_2 (@species_2_gene_array) {
+				#		print OUTFILE "$gene_1\t$gene_2\n";
+				#	}
+				#}
 			}
 		}
 		$sth->finish();
 	}
 }
 
-close(outfile);
+close(OUTFILE);