#! /usr/bin/perl
# Master list variables
$| = 1;
use DBD::Pg;
use DBI;
use vars qw($master_file $master_out $master_out_a @master $master_order $master_family
            $master_subfamily $master_genus $master_species $master $dbmain $dbname
	    $statement $conn $str $current_order $current_family $current_subfamily
	  $current_genus $current_species);
$dbname = 'bioseqdb';
$dbhost = '192.168.0.8';
$dbuser = '';
$dbpasswd = '';
$master_file = '/home/flarson/Master_Species_List-2008-2.csv';
$master_out = '/home/flarson/Master_vs_NCBI.txt';
$master_out_e = '/home/flarson/Master_vs_NCBI_errors.txt';
# Parse the master list to compare
Parse_Master();
#print "connected to $dbname, state is $str\n";
#@row_ary  = $conn->selectrow_array($statement);
#print "@row_ary\n";

sub Parse_Master {
  open(MAS, '<::encoding(iso-8859-1)',$master_file ) || die "Can not open $master_file";
  open(MASO, '>::encoding(iso-8859-1)',$master_out ) || die "Can not open $master_out";
  open(MASE, '>::encoding(iso-8859-1)',$master_out_e ) || die "Can not open $master_out_e";
  $conn = DBI->connect("dbi:Pg:dbname=$dbname;host=$dbhost;","$dbuser","$dbpasswd");
  $str = $conn->state;
  while(<MAS>) {
    undef(@master);
    undef($master_order);
    undef($master_family);
    undef($master_subfamily);
    undef($master_genus);
    undef($master_species);
    @master = split(/\,/,$_);
    chomp(@master);
    foreach (@master) {
      s/^\s+//;
      s/\s+$//;
    }
    next if $master[0] eq 'Order';
#       print MASO "$master[4]\n";
#       print MASO "@master\n";
    if($master[0] ne $current_order)  {
      if ($order_isolates) {
	print MASO "      $genus_isolates isolates found in genus $current_genus\n";
	print MASO "    $subfamily_isolates isolates found subfamily $current_subfamily\n";
	print MASO "  $family_isolates isolates found in family $current_family\n";
	print MASO "$order_isolates isolates found in order $current_order\n";
	undef($genus_isolates);
	undef($subfamily_isolates);
	undef($family_isolates);
	undef($order_isolates);
      }
      $current_order = $master[0];
      $name = $master[0];
      $statement = "select taxon_id,name,name_class from taxon_name where name like '$name'";
      #print "$statement\n";
      my @master_order = $conn->selectrow_array($statement);
      print MASO "Order:$master[0] Taxon_ID:$master_order[0] Name_class:$master_order[2]\n";# if ($master_order);
      if(($master[0] ne $master_order[1]) && ($master[0] ne 'Unassigned')) {
	print MASE "Order:$master[0]\n";
	$ordercount++;
	$name1 = substr $name, 0, 1, '%';
	$statement = "select taxon_id,name,name_class from taxon_name where name like '$name'";
	my @guess_order = $conn->selectrow_array($statement);
	print MASE "Possible matches: @guess_order\n" if($guess_order[1]);
      }
    }
    if(($master[1] ne $current_family) && ($master[1] ne 'Unassigned')) {
      if ($family_isolates) {
	print MASO "      $genus_isolates isolates found in genus $current_genus\n";
	print MASO "    $subfamily_isolates isolates found subfamily $current_subfamily\n";
	print MASO "  $family_isolates isolates found in family $current_family\n";
	undef($genus_isolates);
	undef($subfamily_isolates);
	undef($family_isolates);
      }
      $current_family = $master[1];
      $name = $master[1];
      $statement = "select taxon_id,name,name_class from taxon_name where name like '$name'";
      #print "$statement\n";
      my @master_family = $conn->selectrow_array($statement);
      print MASO "  Family:$master[1] Taxon_ID:$master_family[0] Name_class:$master_family[2]\n";# if ($master_family);
      if($master[1] ne $master_family[1]) {
	print MASE "Family:$master[1]\n" ;
	$familycount++;
	$name1 = substr $name, 0, 1, '%';
	$statement = "select taxon_id,name,name_class from taxon_name where name like '$name'";
	my @guess_family = $conn->selectrow_array($statement);
	print MASE "Possible matches: @guess_family\n" if($guess_family[1]);
      }
    }
    if(($master[2] ne $current_subfamily) && ($master[2] ne 'Unassigned')) {
      if ($subfamily_isolates) {
	print MASO "      $genus_isolates isolates found in genus $current_genus\n";
	print MASO "    $subfamily_isolates isolates found subfamily $current_subfamily\n";
	undef($genus_isolates);
	undef($subfamily_isolates);
      }
      $current_subfamily = $master[2];
      $name = $master[2];
      $statement = "select taxon_id,name,name_class from taxon_name where name like '$name'";
      #print "$statement\n";
      my @master_subfamily = $conn->selectrow_array($statement);
      print MASO "    Subfamily:$master[2] Taxon_ID:$master_subfamily[0] Name_class:$master_subfamily[2]\n";# if ($master_subfamily);
      if($master[2] ne $master_subfamily[1]) {
	print MASE "Subfamily:$master[2]\n" ;
	$subfamilycount++;
	$name1 = substr $name, 0, 1, '%';
	$statement = "select taxon_id,name from taxon_name where name like '$name'";
	my @guess_subfamily = $conn->selectrow_array($statement);
	print MASE "Possible matches: @guess_subfamily\n" if($guess_subfamily[1]);
      }
    }
    if(($master[3] ne $current_genus) && ($master[3] ne 'Unassigned')) {
      if ($genus_isolates) {
	print MASO "      $genus_isolates isolates found in genus $current_genus\n";
	undef($genus_isolates);
      }
      $current_genus = $master[3];
      $name = $master[3];
      $statement = "select taxon_id,name,name_class from taxon_name where name like '$name'";
      #print "$statement\n";
      my @master_genus = $conn->selectrow_array($statement);
      print MASO "      Genus:$master[3] Taxon_ID:$master_genus[0] Name_class:$master_genus[2]\n";# if ($master_genus);
      if($master[3] ne $master_genus[1]) {
	print MASE "Genus:$master[3]\n" ;
	$genuscount++;
	$name1 = substr $name, 0, 1, '%';
	$statement = "select taxon_id,name,name_class from taxon_name where name like '$name'";
	my @guess_genus = $conn->selectrow_array($statement);
	if($guess_genus[1]) {
	  print MASE "Possible matches: @guess_genus\n" ;
	} elsif ($master[3] eq 'Omicronpapillomavirus') {
	  $name2 = 'Omikronpapillomavirus';
	  $statement = "select taxon_id,name,name_class from taxon_name where name like '$name2'";
	  my @guess_genus = $conn->selectrow_array($statement);
	  print MASE "Possible matches: @guess_genus\n" if($guess_genus[1]);
	}
      }
    }
    if(($master[4] ne $current_species) && ($master[4] ne 'Unassigned')) {
      $current_species = $master[4];
      $name = $master[4];
      $name =~ s/\'/\\'/g;
      $statement = "select taxon_id,name,name_class from taxon_name where name like '$name'";
      #print "$statement\n";
      my @master_species = $conn->selectrow_array($statement);
      undef($species_count);
      if($master_species[0]) {
	$species_taxid = $master_species[0];
	$count_stmt = "select COUNT(DISTINCT(accession)) from bioentry join taxon_name using (taxon_id) where taxon_name.taxon_id='$species_taxid'";
	$species_count = $conn->selectrow_array($count_stmt);
	#print "$master_species[0] $master_species[1]: $species_count\n";
	$genus_isolates += $species_count;
	$subfamily_isolates += $species_count;
	$family_isolates += $species_count;
	$order_isolates += $species_count;
	$total_isolates += $species_count;
      }
      print MASO "          Species:$master[4] Taxon_ID:$master_species[0] Name_class:$master_species[2] Isolates found:$species_count\n";
      if($master[4] ne $master_species[1]) {
	print MASE "Species:$master[4]\n" ;
	$speciescount++;
	$name1 = substr $name, 0, 1, '%';
	$statement = "select taxon_id,name,name_class from taxon_name where name like '$name'";
	my @guess_species = $conn->selectrow_array($statement);
	print MASE "Possible matches: @guess_species\n" if($guess_species[1]);
      }
    }
  }
  print MASO "      $genus_isolates isolates found in genus $current_genus\n";
  print MASO "    $subfamily_isolates isolates found subfamily $current_subfamily\n";
  print MASO "  $family_isolates isolates found in family $current_family\n";
  print MASO "$order_isolates isolates found in order $current_order\n";
  print MASO "ICTV orders not found in NCBI taxonomy: $ordercount\n";
  print MASO "ICTV families not found in NCBI taxonomy: $familycount\n";
  print MASO "ICTV subfamilies not found in NCBI taxonomy: $subfamilycount\n";
  print MASO "ICTV genuses not found in NCBI taxonomy: $genuscount\n";
  print MASO "ICTV species not found in NCBI taxonomy: $speciescount\n";
  print MASO "Total isolate entries found in common taxonomy: $total_isolates\n";
  print MASE "ICTV orders not found in NCBI taxonomy: $ordercount\n";
  print MASE "ICTV families not found in NCBI taxonomy: $familycount\n";
  print MASE "ICTV subfamilies not found in NCBI taxonomy: $subfamilycount\n";
  print MASE "ICTV genuses not found in NCBI taxonomy: $genuscount\n";
  print MASE "ICTV species not found in NCBI taxonomy: $speciescount\n";
  print MASE "Total isolate entries found in common taxonomy: $total_isolates\n";
  close(MAS);
  close(MASO);
  close(MASE);
}