#!/usr/bin/perl -w
#
# Script para ler os dados de intensidade gerados pelo GenePix
# Uso:
#		gpr_parser.pl nome-da-hibridizacao arquivo.gpr
#

use DBI;

($lamina,$filename) = ($ARGV[0],$ARGV[1]);

unless (defined($lamina) && defined($filename)) {
  die("  use:\n    gpr_parser.pl lamina filename\n");
}

$dbh = DBI->connect('DBI:mysql:microarray','mentus','kafka')
        || die('Couldn\'t connect to MySQL server.');


open(GPR,$filename) || die("Not able to make filehandle: $!\n");

$cont = 0;
while($inp = <GPR>) {
   chomp($inp);
   @vec = split(/\t/,$inp);
   if (@vec < 41) {
     if ($inp =~ m/Type=(.*)\"/) {
        $type = $1;
     }
     elsif ($inp =~ m/RatioFormulation=(.*)\"/) {
        $ratio_form = $1;
     }
     elsif ($inp =~ m/ImageOrigin=(\d+),\s*(\d+)/) {
        $x_origin = $1;
        $y_origin = $2;
     }
     elsif ($inp =~ m/PixelSize=(\d+)/) {
        $pixel_size = $1;
     }
     next;
   }

  elsif($cont == 0) {
     $cont = 1;

 undef2null($pixel_size,$x_origin,$y_origin,$type,$ratio_form);
 
 $q1 = "INSERT INTO lamina VALUES (\'$lamina\',$pixel_size,$x_origin,$y_origin,\'$type\',\'$ratio_form\')";
  $sth = $dbh->prepare($q1);
  $sth->execute;

    $q2 = "CREATE TABLE $lamina (block_number INT(5),colum INT(5),row INT(5),x INT(10),y INT(10),dia INT(5),F635_Median INT(10),F635_Mean INT(10),F635_SD INT(10),B635_Median INT(10),B635_Mean INT(10),B635_SD INT(10),PMQ_B635_p_1SD INT(10),PMQ_B635_p_2SD INT(10),F635_PER_Sat INT(10),F532_Median INT(10),F532_Mean INT(10),F532_SD INT(10),B532_Median INT(10),B532_Mean INT(10),B532_SD INT(10),PMQ_B532_p_1SD REAL,PMQ_B532_p_2SD REAL,F532_PER_Sat REAL,Ratio_of_Medians REAL,Ratio_of_Means REAL,Median_of_Ratios REAL,Mean_of_Ratios REAL,Ratios_SD REAL,Rgn_Ratio REAL,Rgn_R_SQRD REAL,F_Pixels INT(10),B_Pixels INT(10),Sum_of_Medians INT(10),Sum_of_Means INT(10),Log_Ratio REAL,F635_Median_m_B635 INT(10),F532_Median_m_B532 INT(10),F635_Mean_m_B635 INT(10),F532_Mean_m_B532 INT(10),Flags INT(4),PRIMARY KEY(block_number,row,colum))";
    $ctr = $dbh->prepare($q2);
    $ctr->execute;


    next;
  }

 for($i=0;$i<5;$i++) {
   $tmp[$i] = shift(@vec);
  }
 for($i=2;$i>-1;$i--) {
  unshift(@vec,$tmp[$i]);
 }

 foreach $value (@vec) {
   $value =~ s/Error/NULL/g;
 }
 $vec = join(',',@vec);
 $vec =~ s/\s+$//g;


 $q3 = "INSERT INTO $lamina VALUES($vec)";
 $ins = $dbh->prepare($q3);
 $ins->execute; 

}

sub undef2null {
  foreach (@_) {
    if (!defined($_)) {
     $_ = 'NULL';
   }
 }
}