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NOVOPlasty2.5.5.pl
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NOVOPlasty2.5.5.pl
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#!/usr/bin/env perl
######################################################
# SOFTWARE COPYRIGHT NOTICE AGREEMENT #
# Copyright (C) {2015-2017} {Nicolas Dierckxsens} #
# All Rights Reserved #
# See file LICENSE for details. #
######################################################
# NOVOPlasty - The Organelle Assembler
use Getopt::Long;
use strict;
my $left = '9';
my $right = '15';
my $insert_range = '1.8';
my $insert_range_back = '1.8';
my $noseed = "";
my $iterations = "1000000";
my $startprint = "1000000";
my $startprint2 = "1000000";
my $high_coverage = "yes";
my $coverage_cut_off = '1000';
my $max_memory;
my $option = '1';
my $insert_size_correct;
my $overlap;
my $insert_range_b;
my $insert_range_c;
my $genome_range_low;
my $genome_range_high;
my $genome_range ;
my $seed_input0;
my $seed_input;
my $insert_size;
my $project;
my $read_length;
my $type;
my $encrypt = "no";
my $paired;
my $print_log;
my $bad_read;
my %contigs_id;
my %contigs_end;
my $contig_num = '1';
my $id = "";
my $id_pair = "";
my $id_match = "";
my $id_pair_match = "";
my $contig_end_check;
my %seed;
my %seed_old;
my $counttest1 = '0';
my $indel_split = '0';
my $indel_split_skip;
my %indel_split_skip;
my %indel_split;
my $indel_split_back = '0';
my $indel_split_skip_back;
my %indel_split_skip_back;
my %indel_split_back;
my $insert_range2 = $insert_range;
my $SNR_read;
my $SNR_read_back;
my $SNR_read2;
my $SNR_read_back2;
my %best_extension_prev;
my %best_extension_back_prev;
my %contig_gap_min;
my %contig_gap_max;
my %contig_count;
my $contig_count;
my $progress_before;
my $contig_id2;
my $contig_id1;
my $contig_id3;
my $contig_id4;
my %seed_split;
my $lastbit_contig_prev;
my $split_forward;
my %old_id;
my %old_id2;
my %old_rep;
my %old_rep_old;
my %SNR_length;
my @insert_size;
my %regex;
my %regex_back;
my %regex1;
my %regexb;
my %regex2b;
my %noback;
my %noforward;
my %SNR;
my %SNR_back;
my $SNR_nucleo;
my $SNR_nucleo_back;
my %id_bad;
my $y ='1';
my %position;
my %position_back;
my %bad_read;
my %position_adjust;
my %read_end_tmp;
my %read_end_b_tmp;
my %read_short_end_tmp;
my %read_short_zone_tmp;
my %read_start_tmp;
my %read_start_b_tmp;
my %read_short_start_tmp;
my %read_short_zone_start_tmp;
my %tree;
my %contig_id2;
my %contig_id1;
my %contig_id3;
my %contig_id4;
my %hash;
my %hash2b;
my %hash2c;
my @row;
my %row;
my %match_rep;
my %count_rep;
my %before;
my %before_back;
my %first_before;
my %SNP_active;
my %first_before_back;
my %SNP_active_back;
my %filter_before1;
my %filter_before2;
my %filter_before3;
my %filter_before4;
my %filter_before1_pair;
my %filter_before2_pair;
my %filter_before3_pair;
my %filter_before4_pair;
my %nosecond;
my %repetitive_pair;
my %count_reads;
my %count_reads_all;
my $assembly_length = '1';
my $assembly_success;
my %seeds_check;
my $reads12;
my $reads1;
my $reads2;
my $config;
my $read;
my $deletion;
my $deletion_back;
my $reference_guided;
my $reference_guided_back;
my $contig_read2;
my $contig_read1;
my $first_contig_start;
my $first_contig_start_reverse;
my $finish;
my $repetitive_detect;
my $repetitive_detect_back;
my $repetitive_detect2;
my $repetitive_detect_back2;
my $contig_end;
my $repetitive;
my $before_repetitive;
my $before_repetitive_short;
my $CP_check;
my $before_extension1;
my $before_extension2;
my $before_extension_back1;
my $before_extension_back2;
my $id_split1;
my $id_split2;
my $id_split3;
my $before;
my $before_back;
my $end_repetitive_tmp4;
my $first_before;
my $SNP_active;
my $first_before_back;
my $SNP_active_back;
my $nosecond;
my $first_contig_id;
my $no_contig_id2;
my $no_contig_id1;
my $no_contig_id3;
my $no_contig_id4;
my $rep_detect2;
my $hasL;
my $no_next_seed;
my $count_split;
my @firstSNP_max;
my %yuyu_option;
my %yuyu_option_back;
my $yuyu_option_A;
my $yuyu_option_C;
my $yuyu_option_T;
my $yuyu_option_G;
my $yuyu_option_A_back;
my $yuyu_option_C_back;
my $yuyu_option_T_back;
my $yuyu_option_G_back;
my $extensions_before;
my $before_shorter_skip;
my %before_shorter_skip;
my $before_shorter_skip_back;
my %before_shorter_skip_back;
my $SNR_next_seed;
my $jump_rep;
my %jump_rep;
my $jump_rep_back;
my %jump_rep_back;
my $AT_rich_before;
my $AT_rich_before_back;
my $insert_range_shorter;
my $cp_input;
my $merge_now;
GetOptions (
"c=s" => \$config,
) or die "Incorrect usage!\n";
open(CONFIG, $config) or die "Error: $!\nCan't open the configuration file, please check the manual!\n";
my $ln ='0';
while (my $line = <CONFIG>)
{
if ($ln eq '0')
{
$project = substr $line, 23;
chomp $project;
}
if ($ln eq '1')
{
$insert_size = substr $line, 23;
chomp $insert_size;
}
if ($ln eq '2')
{
$insert_size_correct = substr $line, 23;
chomp $insert_size_correct;
}
if ($ln eq '3')
{
$read_length = substr $line, 23;
chomp $read_length;
}
if ($ln eq '4')
{
$type = substr $line, 23;
chomp $type;
}
if ($ln eq '5')
{
$genome_range = substr $line, 23;
chomp $genome_range;
my @words = split /-/, $genome_range;
$genome_range_low = $words[0];
$genome_range_high = $words[1];
}
if ($ln eq '6')
{
$overlap = substr $line, 23;
chomp $overlap;
}
if ($ln eq '7')
{
$insert_range_b = substr $line, 23;
chomp $insert_range_b;
}
if ($ln eq '8')
{
$insert_range_c = substr $line, 23;
chomp $insert_range_c;
}
if ($ln eq '9')
{
$paired = substr $line, 23;
chomp $paired;
}
if ($ln eq '10')
{
$max_memory = substr $line, 23;
chomp $max_memory;
}
if ($ln eq '11')
{
$coverage_cut_off = substr $line, 23;
chomp $coverage_cut_off;
}
if ($ln eq '12')
{
$print_log = substr $line, 23;
chomp $print_log;
}
if ($ln eq '13')
{
$reads12 = substr $line, 23;
chomp $reads12;
}
if ($ln eq '14')
{
$reads1 = substr $line, 23;
chomp $reads1;
}
if ($ln eq '15')
{
$reads2 = substr $line, 23;
chomp $reads2;
}
if ($ln eq '16')
{
$seed_input0 = substr $line, 23;
chomp $seed_input0;
}
if ($ln eq '17')
{
$cp_input = substr $line, 23;
chomp $seed_input0;
}
$ln++;
}
close CONFIG;
if ($print_log eq '1' || $print_log eq '2')
{
$startprint2 = '0';
$startprint = '1000000000';
}
my $USAGE = "\nUsage: perl NOVOPlasty.pl -c config_example.txt";
print "\n\n-----------------------------------------------";
print "\nNOVOPlasty: The Organelle Assembler\n";
print "Version 2.5.5\n";
print "Author: Nicolas Dierckxsens, (c) 2015-2016\n";
print "-----------------------------------------------\n\n";
print OUTPUT4 "\n\n-----------------------------------------------";
print OUTPUT4 "\nNOVOPlasty: The Organelle Assembler\n";
print OUTPUT4 "Version 2.5.5\n";
print OUTPUT4 "Author: Nicolas Dierckxsens, (c) 2015-2016\n";
print OUTPUT4 "-----------------------------------------------\n\n";
sub build_partial {
my $A = "";
my $G = "";
my $T = "";
my $C = "";
my ($str) = (@_);
my @re;
undef @re;
my $v = length($str);
my $m = '2';
my $star = substr $str, 0,1;
if ($star eq "*")
{
substr $str, 0,1, ".";
}
while ($m < $v)
{
my $str9 = substr $str, $m+1;
my $str6 = substr $str, 0, $m;
my $x = '0';
my $y = length($str6);
while ($x < $y)
{
my $str8 = substr $str6, $x+1;
my $str7 = substr $str6, 0, $x;
$A = $str7.".".$str8.".".$str9;
push @re, $A;
$x++;
}
$m++;
}
my $re = join ('|' , @re);
qr/$re/;
}
sub build_partialb {
my $A = "";
my $G = "";
my $T = "";
my $C = "";
my ($str) = (@_);
my @re;
undef @re;
my $v = length($str);
my $m = '2';
while ($m < $v)
{
my $str9 = substr $str, $m+1;
my $str6 = substr $str, 0, $m;
my $x = '0';
my $y = length($str6);
while ($x < $y)
{
my $str8 = substr $str6, $x+1;
my $str7 = substr $str6, 0, $x;
$A = $str7.".".$str8.".".$str9;
push @re, $A;
$x++;
}
$m++;
}
@re;
}
sub build_partial2b
{
my $A = "";
my (%str) = (@_);
my %re;
undef %re;
foreach my $str (keys %str)
{
my $v = length($str)-1;
my $m = '2';
while ($m < $v)
{
my $str9 = substr $str, $m+1;
my $str6 = substr $str, 0, $m;
my $x = '0';
my $y = length($str6);
while ($x < $y)
{
my $str8 = substr $str6, $x+1;
my $str7 = substr $str6, 0, $x;
$re{$str7."A".$str8."A".$str9} = undef;
$re{$str7."A".$str8."C".$str9} = undef;
$re{$str7."A".$str8."T".$str9} = undef;
$re{$str7."A".$str8."G".$str9} = undef;
$re{$str7."C".$str8."A".$str9} = undef;
$re{$str7."C".$str8."C".$str9} = undef;
$re{$str7."C".$str8."T".$str9} = undef;
$re{$str7."C".$str8."G".$str9} = undef;
$re{$str7."T".$str8."A".$str9} = undef;
$re{$str7."T".$str8."C".$str9} = undef;
$re{$str7."T".$str8."T".$str9} = undef;
$re{$str7."T".$str8."G".$str9} = undef;
$re{$str7."G".$str8."A".$str9} = undef;
$re{$str7."G".$str8."C".$str9} = undef;
$re{$str7."G".$str8."T".$str9} = undef;
$re{$str7."G".$str8."G".$str9} = undef;
$x++;
}
$m++;
}
}
%re;
}
sub build_partial3b {
my $A = "";
my @str = @_;
my $str = $str[0];
my $reverse = $str[1];
my %re;
my %re2;
my %re3;
undef %re;
undef %re2;
undef %re3;
my $hasdot = $str =~ tr/\.//;
my $hasstar = $str =~ tr/\*//;
$re2{$str} = undef;
if ($hasstar > 0)
{
foreach my $str (keys %re2)
{
if ($reverse eq "reverse")
{
my $str2 = $str;
$str2 =~ s/\*.//g;
$re3{$str2} = undef;
}
else
{
my $str2 = $str;
$str2 =~ s/.\*//g;
$re3{$str2} = undef;
}
if ($reverse eq "reverse")
{
$str =~ tr/\*//d;
my $temp_sre = $str;
$str = substr $temp_sre, 0, -$hasstar;
$re3{$str} = undef;
}
else
{
$str =~ tr/\*//d;
my $temp_sre = $str;
$str = substr $temp_sre, $hasstar;
$re3{$str} = undef;
}
}
}
else
{
%re3 = %re2;
}
if ($hasdot > 0)
{
foreach my $str (keys %re3)
{
$hasdot = $str =~ tr/\.//;
if ($hasdot eq '1')
{
if ($str =~ m/^(\w*)\.(\w*)$/)
{
my $str7 = $1;
my $str8 = $2;
$re{$str7."A".$str8} = undef;
$re{$str7."C".$str8} = undef;
$re{$str7."T".$str8} = undef;
$re{$str7."G".$str8} = undef;
}
}
elsif ($hasdot eq '2')
{
if ($str =~ m/^(\w*)\.(\w*)\.(\w*)$/)
{
my $str7 = $1;
my $str8 = $2;
my $str9 = $3;
$A = $str7."A".$str8."A".$str9; #two substitutions
$re{$A} = undef;
$A = $str7."A".$str8."C".$str9;
$re{$A} = undef;
$A = $str7."A".$str8."T".$str9;
$re{$A} = undef;
$A = $str7."A".$str8."G".$str9;
$re{$A} = undef;
$A = $str7."C".$str8."A".$str9; #two substitutions
$re{$A} = undef;
$A = $str7."C".$str8."C".$str9;
$re{$A} = undef;
$A = $str7."C".$str8."T".$str9;
$re{$A} = undef;
$A = $str7."C".$str8."G".$str9;
$re{$A} = undef;
$A = $str7."T".$str8."A".$str9; #two substitutions
$re{$A} = undef;
$A = $str7."T".$str8."C".$str9;
$re{$A} = undef;
$A = $str7."T".$str8."T".$str9;
$re{$A} = undef;
$A = $str7."T".$str8."G".$str9;
$re{$A} = undef;
$A = $str7."G".$str8."A".$str9; #two substitutions
$re{$A} = undef;
$A = $str7."G".$str8."C".$str9;
$re{$A} = undef;
$A = $str7."G".$str8."T".$str9;
$re{$A} = undef;
$A = $str7."G".$str8."G".$str9;
$re{$A} = undef;
}
}
elsif ($hasdot eq '3')
{
my $str1 = $str;
my $x = '0';
my @combi = ('A','C','T','G');
while ($x < 4)
{
$str1 = $str;
$str1 =~ s/\./$combi[$x]/;
my $x2 = '0';
while ($x2 < 4)
{
my $str2 = $str1;
$str2 =~ s/\./$combi[$x2]/;
my $x3 = '0';
while ($x3 < 4)
{
my $str3 = $str2;
$str3 =~ s/\./$combi[$x3]/;
$re{$str3} = undef;
$x3++;
}
$x2++;
}
$x++;
}
}
elsif ($hasdot eq '4')
{
my $str1 = $str;
my $x = '0';
my @combi = ('A','C','T','G');
while ($x < 4)
{
$str1 = $str;
$str1 =~ s/\./$combi[$x]/;
my $x2 = '0';
while ($x2 < 4)
{
my $str2 = $str1;
$str2 =~ s/\./$combi[$x2]/;
my $x3 = '0';
while ($x3 < 4)
{
my $str3 = $str2;
$str3 =~ s/\./$combi[$x3]/;
my $x4 = '0';
while ($x4 < 4)
{
my $str4 = $str3;
$str4 =~ s/\./$combi[$x4]/;
$re{$str4} = undef;
$x4++;
}
$x3++;
}
$x2++;
}
$x++;
}
}
elsif ($hasdot eq '5')
{
my $str1 = $str;
my $x = '0';
my @combi = ('A','C','T','G');
while ($x < 4)
{
$str1 = $str;
$str1 =~ s/\./$combi[$x]/;
my $x2 = '0';
while ($x2 < 4)
{
my $str2 = $str1;
$str2 =~ s/\./$combi[$x2]/;
my $x3 = '0';
while ($x3 < 4)
{
my $str3 = $str2;
$str3 =~ s/\./$combi[$x3]/;
my $x4 = '0';
while ($x4 < 4)
{
my $str4 = $str3;
$str4 =~ s/\./$combi[$x4]/;
my $x5 = '0';
while ($x5 < 4)
{
my $str5 = $str4;
$str5 =~ s/\./$combi[$x5]/;
$re{$str5} = undef;
$x5++;
}
$x4++;
}
$x3++;
}
$x2++;
}
$x++;
}
}
elsif ($hasdot eq '6')
{
my $str1 = $str;
my $x = '0';
my @combi = ('A','C','T','G');
while ($x < 4)
{
$str1 = $str;
$str1 =~ s/\./$combi[$x]/;
my $x2 = '0';
while ($x2 < 4)
{
my $str2 = $str1;
$str2 =~ s/\./$combi[$x2]/;
my $x3 = '0';
while ($x3 < 4)
{
my $str3 = $str2;
$str3 =~ s/\./$combi[$x3]/;
my $x4 = '0';
while ($x4 < 4)
{
my $str4 = $str3;
$str4 =~ s/\./$combi[$x4]/;
my $x5 = '0';
while ($x5 < 4)
{
my $str5 = $str4;
$str5 =~ s/\./$combi[$x5]/;
my $x6 = '0';
while ($x6 < 4)
{
my $str6 = $str5;
$str6 =~ s/\./$combi[$x6]/;
$re{$str6} = undef;
$x6++;
}
$x5++;
}
$x4++;
}
$x3++;
}
$x2++;
}
$x++;
}
}
elsif ($hasdot eq '7')
{
my $str1 = $str;
my $x = '0';
my @combi = ('A','C','T','G');
while ($x < 4)
{
$str1 = $str;
$str1 =~ s/\./$combi[$x]/;
my $x2 = '0';
while ($x2 < 4)
{
my $str2 = $str1;
$str2 =~ s/\./$combi[$x2]/;
my $x3 = '0';
while ($x3 < 4)
{
my $str3 = $str2;
$str3 =~ s/\./$combi[$x3]/;
my $x4 = '0';
while ($x4 < 4)
{
my $str4 = $str3;
$str4 =~ s/\./$combi[$x4]/;
my $x5 = '0';
while ($x5 < 4)
{
my $str5 = $str4;
$str5 =~ s/\./$combi[$x5]/;
my $x6 = '0';
while ($x6 < 4)
{
my $str6 = $str5;
$str6 =~ s/\./$combi[$x6]/;
my $x7 = '0';
while ($x7 < 4)
{
my $str7 = $str6;
$str7 =~ s/\./$combi[$x7]/;
$re{$str7} = undef;
$x7++;
}
$x6++;
}
$x5++;
}
$x4++;
}
$x3++;
}
$x2++;
}
$x++;
}
}
elsif ($hasdot eq '8')
{
my $str1 = $str;
my $x = '0';
my @combi = ('A','C','T','G');
while ($x < 4)
{
$str1 = $str;
$str1 =~ s/\./$combi[$x]/;
my $x2 = '0';
while ($x2 < 4)
{
my $str2 = $str1;
$str2 =~ s/\./$combi[$x2]/;
my $x3 = '0';
while ($x3 < 4)
{
my $str3 = $str2;
$str3 =~ s/\./$combi[$x3]/;
my $x4 = '0';
while ($x4 < 4)
{
my $str4 = $str3;
$str4 =~ s/\./$combi[$x4]/;
my $x5 = '0';
while ($x5 < 4)
{
my $str5 = $str4;
$str5 =~ s/\./$combi[$x5]/;
my $x6 = '0';
while ($x6 < 4)
{
my $str6 = $str5;
$str6 =~ s/\./$combi[$x6]/;
my $x7 = '0';
while ($x7 < 4)
{
my $str7 = $str6;
$str7 =~ s/\./$combi[$x7]/;
my $x8 = '0';
while ($x8 < 4)
{
my $str8 = $str7;
$str8 =~ s/\./$combi[$x8]/;
$re{$str8} = undef;
$x8++;
}
$x7++;
}
$x6++;
}
$x5++;
}
$x4++;
}
$x3++;
}
$x2++;
}
$x++;
}
}
else
{
$re{$str} = undef;
}
}
}
else
{
%re = %re3;
}
%re;
}
sub build_partial3c {
my $A = "";
my @str = @_;
my $str = $str[0];
my $reverse = $str[1];
my %re2;
my %re;
undef %re2;
undef %re;
my $hasstar = $str =~ tr/\*//;
$re2{$str} = undef;
if ($hasstar > 0)
{
foreach my $str (keys %re2)
{
if ($reverse eq "reverse")
{
my $str2 = $str;
$str2 =~ s/\*.//g;
$re{$str2} = undef;
}
else
{
my $str2 = $str;
$str2 =~ s/.\*//g;
$re{$str2} = undef;
}
if ($reverse eq "reverse")
{
$str =~ tr/\*//d;
my $temp_sre = $str;
$str = substr $temp_sre, 0, -$hasstar;
$re{$str} = undef;
}
else
{
$str =~ tr/\*//d;
my $temp_sre = $str;
$str = substr $temp_sre, $hasstar;
$re{$str} = undef;
}
}
}
else
{
%re = %re2;
}
%re;
}
sub uniq
{
my %seen;
grep !$seen{$_}++, @_;
}
sub encrypt
{
my @value = @_;
my $value = $value[0];
$value =~ s/AA/0/g;
$value =~ s/CC/1/g;
$value =~ s/TT/2/g;
$value =~ s/GG/3/g;
$value =~ s/AC/4/g;
$value =~ s/AG/5/g;
$value =~ s/AT/6/g;
$value =~ s/CT/7/g;
$value =~ s/CA/8/g;
$value =~ s/CG/9/g;
$value =~ s/TA/Z/g;
$value =~ s/TC/U/g;
$value =~ s/TG/I/g;
$value =~ s/GA/O/g;
$value =~ s/GC/P/g;
$value =~ s/GT/Q/g;
return $value;
}
sub decrypt
{
my @value = @_;
my $value = $value[0];
$value =~ s/Q/GT/g;
$value =~ s/P/GC/g;
$value =~ s/O/GA/g;
$value =~ s/I/TG/g;
$value =~ s/U/TC/g;
$value =~ s/Z/TA/g;
$value =~ s/9/CG/g;
$value =~ s/8/CA/g;
$value =~ s/7/CT/g;
$value =~ s/6/AT/g;
$value =~ s/5/AG/g;
$value =~ s/4/AC/g;
$value =~ s/3/GG/g;
$value =~ s/2/TT/g;
$value =~ s/1/CC/g;
$value =~ s/0/AA/g;
return $value;
}
sub IUPAC
{
my @snps = @_;
my $A = $snps[0];
my $C = $snps[1];
my $T = $snps[2];
my $G = $snps[3];
my $iupac;
if ($A + $C > 0.93*($A+$C+$T+$G))
{
$iupac = "M";
}
elsif ($A + $G > 0.93*($A+$C+$T+$G))
{
$iupac = "R";
}
elsif ($A + $T > 0.93*($A+$C+$T+$G))
{
$iupac = "W";
}
elsif ($C + $G > 0.93*($A+$C+$T+$G))
{
$iupac = "S";
}
elsif ($C + $T > 0.93*($A+$C+$T+$G))
{
$iupac = "Y";
}
elsif ($G + $T > 0.93*($A+$C+$T+$G))
{
$iupac = "K";
}
elsif ($A + $C + $G eq ($A+$C+$T+$G))
{
$iupac = "V";
}
elsif ($A + $C + $T eq ($A+$C+$T+$G))
{