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Update NOVOPlasty2.6.1.pl
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@ndierckx
ndierckx authored Jul 24, 2017
1 parent fa56968 commit 0048b8e
Showing 1 changed file with 104 additions and 12 deletions.
116 changes: 104 additions & 12 deletions NOVOPlasty2.6.1.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -358,13 +358,13 @@

print "\n\n-----------------------------------------------";
print "\nNOVOPlasty: The Organelle Assembler\n";
print "Version 2.6.1\n";
print "Author: Nicolas Dierckxsens, (c) 2015-2016\n";
print "Version 2.6.2\n";
print "Author: Nicolas Dierckxsens, (c) 2015-2017\n";
print "-----------------------------------------------\n\n";
print OUTPUT4 "\n\n-----------------------------------------------";
print OUTPUT4 "\nNOVOPlasty: The Organelle Assembler\n";
print OUTPUT4 "Version 2.6.1\n";
print OUTPUT4 "Author: Nicolas Dierckxsens, (c) 2015-2016\n";
print OUTPUT4 "Version 2.6.2\n";
print OUTPUT4 "Author: Nicolas Dierckxsens, (c) 2015-2017\n";
print OUTPUT4 "-----------------------------------------------\n\n";


Expand Down Expand Up @@ -1360,6 +1360,26 @@ sub correct
push @read_matches2, $extensions;
}
}
my $count_cor2 = '0';
$count_cor2++ for (@read_matches2);

if ($count_cor2 < 4)
{
if ($y > $startprint2)
{
print OUTPUT5 "\nBAD_READ\n";
}
if ($y eq '1')
{
$bad_read = "yes";
goto FIRST_SEED;
}
else
{
goto CORRECT_END;
}
}

my $l = '0';
while ($l < length($read_correct))
{
Expand Down Expand Up @@ -1684,7 +1704,7 @@ sub correct

print OUTPUT4 "\n\n-----------------------------------------------";
print OUTPUT4 "\nNOVOPlasty: The Organelle Assembler\n";
print OUTPUT4 "Version 2.6.1\n";
print OUTPUT4 "Version 2.6.2\n";
print OUTPUT4 "Author: Nicolas Dierckxsens, (c) 2015-2016\n";
print OUTPUT4 "-----------------------------------------------\n\n";

Expand Down Expand Up @@ -3424,11 +3444,9 @@ sub correct
print OUTPUT5 "DETECT_REPETITIVE2\n";
}
my $repetitive_test_stop = substr $read_short_end2, -30;
my $end_repetitive_stop = substr $read, -$insert_size-550;
my $end_repetitive_stopb = substr $read, -8000,-200;
my $check_repetitive_stop = $end_repetitive_stop =~ s/$repetitive_test_stop/$repetitive_test_stop/g;
my $check_repetitive_stopb = $end_repetitive_stopb =~ s/$repetitive_test2b/$repetitive_test2b/g;
if ($check_repetitive_stop > 3 || $check_repetitive_stopb > 2)
if ($check_repetitive_stopb > 2)
{
$noforward = "stop";
$noforward{$id} = "stop";
Expand Down Expand Up @@ -8082,6 +8100,28 @@ sub correct
print OUTPUT5 "\nDELETE SPLIT2\n\n";
}
}
else
{
my $best_extension1_tmpi = $best_extension1;
my $best_extension2_tmpi = $best_extension2;
$best_extension1_tmpi =~ tr/N|K|R|Y|S|W|M|B|D|H|V|\.//d;
$best_extension2_tmpi =~ tr/N|K|R|Y|S|W|M|B|D|H|V|\.//d;
if ($SNR_read eq "yes" && length($best_extension1_tmpi) < 7 && length($best_extension2_tmpi) < 7)
{
$SNR_next_seed = "yes";
$noforward{$id} = "stop";
delete $seed{$id_split2};
delete $seed{$id};
delete $seed{$id_split1};
delete $seed{$id_split3};
$noforward = "stop";
if ($y > $startprint2)
{
print OUTPUT5 "SNR_NEXT_SEED\n";
}
goto BACK;
}
}
INDEL:
$id = $id_original;
$split = "";
Expand Down Expand Up @@ -10364,9 +10404,13 @@ sub correct
$seed{$id} = $read;
$seeds_check{$id} = undef;
$read_new = $read;
$read_new1 = $read;
$read_new1 = $read;

if ($SNR_read eq "yes" && length($best_extension1) < 7 && length($best_extension2) < 7)
my $best_extension1_tmpi = $best_extension1;
my $best_extension2_tmpi = $best_extension2;
$best_extension1_tmpi =~ tr/N|K|R|Y|S|W|M|B|D|H|V|\.//d;
$best_extension2_tmpi =~ tr/N|K|R|Y|S|W|M|B|D|H|V|\.//d;
if ($SNR_read eq "yes" && length($best_extension1_tmpi) < 7 && length($best_extension2_tmpi) < 7)
{
$SNR_next_seed = "yes";
$noforward{$id} = "stop";
Expand Down Expand Up @@ -15621,6 +15665,54 @@ sub correct
print OUTPUT5 "FINISH3\n";
}
}
elsif ($no_next_seed ne "yes" && $contig_num eq '1' && exists($old_id{$id}) && (($SNR_next_seed eq "yes" && ($last_chance_back eq "yes" || $noback eq "stop")) || ($nosecond eq "" && $CP_check ne "yes" && length($read) > $read_length+150 && $circle eq "" && (($last_chance eq "yes" || $noforward eq "stop") && ($last_chance_back eq "yes" || $noback eq "stop")) || ($AT_rich eq "yes" && $count_seed ne "0") || ($bad_read eq "yes" && $count_seed ne "0"))))
{
my $start_point = '500';
my $check_repetitive = '3';

while ($check_repetitive > 2)
{
my $check_for_rep = substr $seed_old{$old_id{$id}}, 0, $start_point+200;
my $repetitive = substr $check_for_rep, $start_point, 15;
$check_repetitive = $check_for_rep =~ s/$repetitive/$repetitive/g;
if ($check_repetitive > 2)
{
$start_point += 20;
if ($y > $startprint2)
{
print OUTPUT5 "DETECT_REPETITIVE_IN_START_SEQUENCE\n";
}
}
}
$first_contig_start = substr $seed_old{$old_id{$id}}, $start_point, $overlap;
my $check_start = $first_contig_start =~ tr/N|K|R|Y|S|W|M|B|D|H|V|\.//;
while ($check_start > 0)
{
$start_point += 10;
$first_contig_start = substr $seed_old{$old_id{$id}}, $start_point, $overlap;
$check_start = $first_contig_start =~ tr/N|K|R|Y|S|W|M|B|D|H|V|\.//;
}
if ($y > $startprint2)
{
print OUTPUT5 $first_contig_start." CONTIG_START6a\n";
}

foreach my $seedie (keys %seed)
{
my $seedie_part = substr $seed{$seedie}, 0, 1000;
my $check_seedie = $seedie_part =~ s/$first_contig_start/$first_contig_start/;
if ($check_seedie > 0)
{
delete $seed{$seedie};
}
}
$merge_now = "yes2";
if ($y > $startprint2)
{
print OUTPUT5 "MERGE NOW\n";
}
goto MERGE;
}


elsif ($no_next_seed ne "yes" && (($SNR_next_seed eq "yes" && ($last_chance_back eq "yes" || $noback eq "stop")) || ($nosecond eq "" && $CP_check ne "yes" && length($read) > $read_length+150 && $circle eq "" && (($last_chance eq "yes" || $noforward eq "stop") && ($last_chance_back eq "yes" || $noback eq "stop")) || ($AT_rich eq "yes" && $count_seed ne "0") || ($bad_read eq "yes" && $count_seed ne "0"))))
Expand Down Expand Up @@ -16718,9 +16810,9 @@ sub correct
$start_next_contig =~ tr/N|K|R|Y|S|W|M|B|D|H|V/\./;
my $start_next_contig2 = $start_next_contig;
my $x1 = length($start_next_contig);
$start_next_contig =~ s/.*.$end_assembly//;
$start_next_contig =~ s/.*$end_assembly//;
my $x2 = length($start_next_contig);
$start_next_contig2 =~ s/.*.$end_assembly2//;
$start_next_contig2 =~ s/.*$end_assembly2//;
my $x2b = length($start_next_contig2);
if ($x1-$x2 ne '0')
{
Expand Down

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