#usr/bin/perl -T

use strict;
use warnings;
use diagnostics;
use LWP;
use DBI;
use Data::Dumper;

########################
# Let user make a choice
########################
TOP:
print "Typ the number of the disease you want the\n";
print "genes to be calculated and compared of.\n";
print "1\tAlzheimer disease (5, 6)\n";
print "2\tBardet Biedl (syndrome 1, 2, 3, 5)\n";
print "3\tBreast cancer (type 4)\n";
print "4\tdiabetes mellitus, noninsulin-dependent (3)\n";
print "5\tHypertension (essential, susceptibility to, 2)\n";
print "6\tInflammatory bowel disease (7)\n";
print "7\tSystemic lupus erythematosus (susceptibility to, 3)\n";
print "8\tmuscular dystrophy, limb-girdle (autosomal recessive) (type 1D, 1H)\n";
print "9\tparkinsons disease (type 3, 4, autosomal dominant, Lewy body)\n";
print "10\tprostate cancer (susceptibility to)\n";

##</code><code>##

########################
# Define for which keywords to go looking in the different databases
########################
my $choice = <STDIN>;
chomp($choice);

if ($choice == 1) {
        #get_g2d('Alzheimer disease-5');
        #get_g2d('Alzheimer disease 6');
        get_pocus('alz');
        #get_dgp('alz 10q');
        #get_dgp('alz 12p11.23-q13.12');
}
elsif ($choice == 2) {
        #get_g2d('Bardet-Biedl syndrome 1');
        #get_g2d('Bardet-Biedl syndrome 2');
        #get_g2d('Bardet-Biedl syndrome 3');
        #get_g2d('Bardet-Biedl syndrome 5');
        get_pocus('bb');
        #get_dgp('bb 11q13');
        #get_dgp('bb 16q21');
        #get_dgp('bb 2q31');
        #get_dgp('bb 3p13-p12');
}
elsif ($choice == 3) {
        #get_g2d('Breast cancer, type 4');
        get_pocus('bc');
        #get_dgp('bc 13q21');
}
elsif ($choice == 4) {
        #get_g2d('Diabetes mellitus, noninsulin-dependent, 3');
        get_pocus('niddm');
        #get_dgp('niddm 20q12-q13');
}
elsif ($choice == 5) {
        #get_g2d('Hypertension, essential, susceptibility to, 2');
        get_pocus('h');
        #get_dgp('h 15q');
}
elsif ($choice == 6) {
        #get_g2d('Inflammatory bowel disease 7');
        get_pocus('ibd');
        #get_dgp('ibd 1p36');
}
elsif ($choice == 7) {
        #get_g2d('Systemic lupus erythematosus, susceptibility to, 3')
+;
        get_pocus('sle');
        #get_dgp('sle 4p16-15.2');
}
elsif ($choice == 8) {
        #get_g2d('Muscular dystrophy, limb-girdle, type 1D');
        #get_g2d('Muscular dystrophy, limb-girdle, type 2H');
        get_pocus('md');
        #get_dgp('md 7q');
        #get_dgp('md 9q31-q33');
}
elsif ($choice == 9) {
        #get_g2d('Parkinson disease, type 3');
        #get_g2d('Parkinson disease 4, autosomal dominant, Lewy body')
+;

        #get_pocus('pd');
        #get_dgp('pd 4p15');
}
elsif ($choice == 10) {
        #get_g2d('Prostate cancer, susceptibility to');
        get_pocus('pc');
        #get_dgp('pc 143000001-160000000');
}
else { print "Type a number between 1 and 10.\n"; 
        goto TOP
}

##</code><code>##

####################
# open file with results from POCUS database, parse it,
# and retrieve gene-name and score.
####################

my @results=();
sub get_pocus {
        my @disease_name_pocus = @_;
        print "Getting the genes and rankings from the POCUS analysis for:\n";
        print "$disease_name_pocus[0]\n";
        open (POCUS, "/home/jeroen/POCUS/results_100.out") || die "couldn't open the file: $!\n";
                while (<POCUS>) {
                        push @results, [ split ];
                }

                open (MARKER, ">marker.list.txt") || die $!;
                        for (my $i = 0; $i < scalar @results; $i++) {
                                if ($results[$i]->[0] eq $disease_name_pocus[0]) {
                                       if ($results[$i]->[1] ne $results[($i+1)]->[1]){
                                        print MARKER "$results[$i]->[1]\t$results[$i]->[4]\n";
                                       }
                                }
                        }
}
close(MARKER);

##</code><code>##

##################
# Make connection with Ensembl, and retrieve start, end  and rank.
##################


my $datasource = "DBI:mysql:homo_sapiens_core_23_34e:ensembldb.ensembl.org";
my $dbh=();
my $sth=();  # database and statement handles
my @rows;         # to get results or queries
my $row_count;    # to see how much we get back
my $username = "anonymous";
my $password = "";
my $marker = 'marker_list.txt';

# connect to database:
$dbh = DBI->connect($datasource, $username, $password, {RaiseError => 1});

open (LIST, "<$marker") or die ("Couldn't open file $marker: $!.\n");

while (<LIST>){
    my ($ensemblID, $score) = $_;


    # select all sequence entries:

    $row_count = 0;
    $sth = $dbh->prepare (qq{
        SELECT gene_stable_id.stable_id, gene.seq_region_start, gene.seq_region_end, gene.seq_region_strand
        FROM gene, gene_stable_id
        WHERE gene_stable_id.gene_id = gene.gene_id
        AND gene_stable_id.stable_id ="$ensemblID"
    });
    $sth->execute ();

    # read results:
    while (@rows = $sth->fetchrow_array () ) {
        $row_count++;
        print join ("\t", @rows), "\n";
    }

    unless ( $row_count ) {
        print "This gene doesn't appear to be placed on the current assembly.\n";
    }

# tidy up:
close(LIST);
$sth->finish ();
$dbh->disconnect ();
}