#! /usr/bin/perl -w

use strict;

my $usage=<<USG;
 usage: $0 <db-name>

    e.g. $0 cellcircuits_dev

USG

die $usage if(@ARGV != 1);

my $dbname = shift @ARGV;
my $ccdev = "mysql --user=mdaly --password=mdalysql $dbname";

my $results_dir = 'results';
my $sql_dir     = 'sql';

my $insert_into_enrichment_sql_FILE = 'insert_into_enrichment-$dbname-7nov06.sql';

## this block is specific to updating the database with a new GO version
if(0){
    my $gwt_file = "genes_with_term-$dbname-7nov06.tab";
    
print STDERR "\n\nNOTE: Loading the enrichment table takes 5-6 hours!!\n\n";
print STDERR "./precompute_genes_with_term.pl $dbname > $gwt_file\n";
print        `./precompute_genes_with_term.pl $dbname > $gwt_file\n`;
    
    my $tmp_out = "n_genes_beneath_tmp-$dbname-7nov06";
    open TMP_OUT, "> $tmp_out" or die "Cannot open $tmp_out: $!\n";
    
    open F, "< $gwt_file" or die "Cannot open $gwt_file: $!\n";
    while(<F>)
    {
	next if($. == 1);
	chomp;
	my @l = split(/\t/);
	my $term_acc        = $l[5];
	my $n_genes_beneath = $l[7];
	my $genus           = $l[1];
	my $species         = $l[2];
	
	my $organism = join " ", $genus, $species;
	
	printf TMP_OUT "%s\n", join "\t", $term_acc, $n_genes_beneath, $organism;
	
    }
    close F;

    my $n_genes_beneath_file = "n_genes_beneath_BY_GO_term_accession-$dbname-7nov06.tab";
    print STDERR "sort $tmp_out > $n_genes_beneath_file\n";
    print        `sort $tmp_out > $n_genes_beneath_file\n`;

    print STDERR "rm $tmp_out\n";
    print        `rm $tmp_out\n`;

#exit;
#}

my @pubs = qw(
	      Begley2002_MCR
	      Bernard2005_PSB
	      de_Lichtenberg2005_Science
	      Gandhi2006_NG
	      Hartemink2002_PSB
	      Haugen2004_GB
	      Ideker2002_BINF
	      Kelley2005_NBT/between_pathway/full
	      Kelley2005_NBT/between_pathway/restricted
	      Kelley2005_NBT/within_pathway
	      Sharan2005_PNAS/pairwise-cd
	      Sharan2005_PNAS/pairwise-yc
	      Sharan2005_PNAS/pairwise-yd
	      Sharan2005_PNAS/three-way
	      Suthram2005_Nature
	      Yeang2005_GB
	      );

my $pubs_list = join " ", @pubs;

print STDERR "./compute_enrichment.pl $dbname $n_genes_beneath_file $pubs_list\n";
print        `./compute_enrichment.pl $dbname $n_genes_beneath_file $pubs_list\n`;




print STDERR "./bin/generate_enrichment_insert_SQL_v1.pl $dbname $results_dir > $sql_dir/$insert_into_enrichment_sql_FILE\n";
print        `./bin/generate_enrichment_insert_SQL_v1.pl $dbname $results_dir > $sql_dir/$insert_into_enrichment_sql_FILE\n`;
}

print STDERR "cat $sql_dir/create_enrichment.sql | $ccdev\n";
print        `cat $sql_dir/create_enrichment.sql | $ccdev\n`;

print STDERR "cat $sql_dir/$insert_into_enrichment_sql_FILE | $ccdev\n";
print        `cat $sql_dir/$insert_into_enrichment_sql_FILE | $ccdev\n`;