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Sim-it1.3.6.pl
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#!/usr/bin/env perl
######################################################
# SOFTWARE COPYRIGHT NOTICE AGREEMENT #
# Copyright (C) {2020-2023} {Nicolas Dierckxsens} #
# All Rights Reserved #
# See file LICENSE for details. #
######################################################
# Sim-it - The Sequence Simulator
# nicolasdierckxsens@hotmail.com
use strict;
use Getopt::Long;
use Time::HiRes qw(time);
use Parallel::ForkManager;
print "\n\n-----------------------------------------------";
print "\nSim-it\n";
print "Version 1.3.6\n";
print "Author: Nicolas Dierckxsens, (c) 2020-2023\n";
print "-----------------------------------------------\n\n";
my $reference = "";
my $ref_database = "";
my $project = "";
#NC_000001.11
my $kmer = '30';
my $chromosome = "";
my $start_end = '250';
my $detection_limit = '30';
my $fraction = '2000';
my $left = '40';
my $right = '30';
my $reference_size = '0';
my $count_contigs = '1';
my $length_fasta_line = "";
my $SVs_whitin_1_line = "";
my $SVs_whitin_1_line_length = "";
my %SV;
undef %SV;
my $time_check1 = '0';
#error_profile-----
my $AAGA = '0';
my $AAGC = '0';
my $AAGT = '0';
my $AAGG = '0';
#------------------
#my $time_np = '0';
#my $time_np1 = '0';
#my $time_np2 = '0';
#my $time_np3 = '0';
#my $time_sv = '0';
my $VCF_input = "";
my %VCF_input;
undef %VCF_input;
my %VCF_input2;
undef %VCF_input2;
my %VCF_output;
undef %VCF_output;
my $next_pos = "";
my $next_type = "";
my $next_length = "";
my $next_hap = "";
my $next_seq = "";
my $VCF_input_now = "";
my $next_length_minus = '0';
my $next_length_minus_save = '0';
my $hap = "";
my $SEQ = "";
my %sequences;
undef %sequences;
my %sequences_final;
undef %sequences_final;
my %sequences_foreign;
undef %sequences_foreign;
my %foreign_contigs;
undef %foreign_contigs;
my $sequences_foreign = "";
my $DEL_input = "";
my $INS_input = "";
my $DUP_input = "";
my $INV_input = "";
my $TRA_input = "";
my $DEL_range = "";
my $INS_range = "";
my $INV_range = "";
my $DUP_range = "";
my $DUP_copies = "";
my $TRA_range = "";
my $CSUB_input = "";
my $CSUB_range = "";
my $IDUP_input = "";
my $IDUP_range = "";
my $heterozygosity = "";
my $haplotype1 = "";
my $haplotype2 = "";
my $haplotype1_print = "";
my $haplotype2_print = "";
my $finish_var = "";
my $finish_var_np = "";
my $variation_haplo = "";
my $haplo_merged = "";
my $haplo_merged_print = "";
my $ref_haplo = "";
my $pos_hap1 = '0';
my $pos_hap2 = '0';
my $pos_hap_merged = '0';
my $new_contig = "";
my $shortest_seq = '0';
my $shortest_seq1 = '0';
my $shortest_seq2 = '0';
my $seq_done = '0';
my $seq_done1 = '0';
my $seq_done2 = '0';
my $NP_coverage = '0';
my $NP_coverage1 = '0';
my $NP_coverage2 = '0';
my $NP_range = "";
my $NP_average = "";
my $NP_accuracy = "";
my $NP_error_profile = "";
my $maxProcs = 8;
my %graph_DEL;
undef %graph_DEL;
my %graph_INS;
undef %graph_INS;
my %graph_INV2;
undef %graph_INV2;
my %merge_command;
my $config = "";
my $output = "";
my $batch_file;
my $last_var = "";
my $test = "";
my $ambigious_replace = "";
my @nucs = ("A","C","T","G");
GetOptions (
"c=s" => \$config,
"o=s" => \$output,
) or die "Incorrect usage!\n\nUsage: perl NOVOLoci1.0.pl -c config.txt -o output_path\n\n";
open(CONFIG, $config) or die "Error: Can't open the configuration file, please check the manual!\n\nUsage: perl Sim-it.pl -c config.txt -o output_path\n\n";
my $last_output = substr $output, -1, 1;
if ($last_output ne "/" && $output ne "")
{
$output .= "/";
}
if (-d $output)
{}
else
{
mkdir $output;
}
while (my $line = <CONFIG>)
{
chomp($line);
$line =~ tr/\r//d;
$line =~ s/\R/\012/;
if ($line =~ m/.*Project name\s+\=\s+(.*?)(Reference sequence.*)*$/)
{
$project = $1;
chomp $project;
my $project_tmp = $project;
my $ggg;
if ($project =~ m/batch\:(.*)/)
{
my $batch_file_tmp = $1;
if ($batch_file eq "")
{
$batch_file = $batch_file_tmp;
print "Batch file detected...\n\n";
open(BATCH, $batch_file) or die "Error: $!\nCan't open the batch file, please check the manual!\n";
$ggg = "yes";
}
while (my $line = <BATCH>)
{
$project = $line;
chomp $project;
last;
}
if ($project eq $project_tmp || $project eq "")
{
goto EXIT;
}
elsif ($ggg ne "yes")
{
print "\n\n------------------------------\n------------------------------\n";
print " NEXT SAMPLE\n";
print "------------------------------\n------------------------------\n\n\n";
}
}
}
if ($line =~ m/.*Reference sequence\s+\=\s+(.*?)(Replace ambiguous nts.*)*$/)
{
$reference = $1;
chomp $reference;
if ($reference eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$reference = $line;
chomp $reference;
last;
}
}
}
if ($line =~ m/.*Replace ambiguous nts\(N\)\s+\=\s+(.*?)(Max threads.*)*$/)
{
$ambigious_replace = $1;
chomp $ambigious_replace;
if ($ambigious_replace eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$ambigious_replace = $line;
chomp $ambigious_replace;
last;
}
}
}
if ($line =~ m/.*Max threads\s+\=\s+(.*?)(Structural variation:.*)*$/)
{
$maxProcs = $1;
chomp $maxProcs;
if ($maxProcs eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$maxProcs = $line;
chomp $maxProcs;
last;
}
}
}
if ($line =~ m/.*VCF input\s+\=\s+(.*?)(Foreign sequences.*)*$/)
{
$VCF_input = $1;
chomp $VCF_input;
if ($VCF_input eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$VCF_input = $line;
chomp $VCF_input;
last;
}
}
}
if ($line =~ m/.*Foreign sequences\s+\=\s+(.*?)(Deletions.*)*$/)
{
$sequences_foreign = $1;
chomp $sequences_foreign;
if ($sequences_foreign eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$sequences_foreign = $line;
chomp $sequences_foreign;
last;
}
}
}
if ($line =~ m/.*Deletions\s+\=\s+(.*?)(Length \(bp\).*)*$/)
{
$DEL_input = $1;
chomp $DEL_input;
$last_var = "DEL";
if ($DEL_input eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$DEL_input = $line;
chomp $DEL_input;
last;
}
}
}
if ($line =~ m/.*Length \(bp\)\s+\=\s+(.*?)(Insertions.*)*$/ && $last_var eq "DEL")
{
$DEL_range = $1;
chomp $DEL_range;
if ($DEL_range eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$DEL_range = $line;
chomp $DEL_range;
last;
}
}
}
if ($line =~ m/.*Insertions\s+\=\s+(.*?)(Length \(bp\).*)*$/)
{
$INS_input = $1;
chomp $INS_input;
$last_var = "INS";
if ($INS_input eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$INS_input = $line;
chomp $INS_input;
last;
}
}
}
if ($line =~ m/.*Length \(bp\)\s+\=\s+(.*?)(Tandem duplications.*)*$/ && $last_var eq "INS")
{
$INS_range = $1;
chomp $INS_range;
if ($INS_range eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$INS_range = $line;
chomp $INS_range;
last;
}
}
}
if ($line =~ m/.*Tandem duplications\s+\=\s+(.*?)(Length \(bp\).*)*$/)
{
$DUP_input = $1;
chomp $DUP_input;
$last_var = "DUP";
if ($DUP_input eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$DUP_input = $line;
chomp $DUP_input;
last;
}
}
}
if ($line =~ m/.*Length \(bp\)\s+\=\s+(.*?)(Copies.*)*$/ && $last_var eq "DUP")
{
$DUP_range = $1;
chomp $DUP_range;
if ($DUP_range eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$DUP_range = $line;
chomp $DUP_range;
last;
}
}
}
if ($line =~ m/.*Copies\s+\=\s+(.*?)(Inversions.*)*$/)
{
$DUP_copies = $1;
chomp $DUP_copies;
if ($DUP_copies eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$DUP_copies = $line;
chomp $DUP_copies;
last;
}
}
}
if ($line =~ m/.*Inversions\s+\=\s+(.*?)(Length \(bp\).*)*$/)
{
$INV_input = $1;
chomp $INV_input;
$last_var = "INV";
if ($INV_input eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$INV_input = $line;
chomp $INV_input;
last;
}
}
}
if ($line =~ m/.*Length \(bp\)\s+\=\s+(.*?)(Complex substitutions.*)*$/ && $last_var eq "INV")
{
$INV_range = $1;
chomp $INV_range;
if ($INV_range eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$INV_range = $line;
chomp $INV_range;
last;
}
}
}
if ($line =~ m/.*Complex substitutions\s+\=\s+(.*?)(Length \(bp\).*)*$/)
{
$CSUB_input = $1;
chomp $CSUB_input;
$last_var = "CSUB";
if ($CSUB_input eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$CSUB_input = $line;
chomp $CSUB_input;
last;
}
}
}
if ($line =~ m/.*Length \(bp\)\s+\=\s+(.*?)(Complex SVs.*)*$/ && $last_var eq "CSUB")
{
$CSUB_range = $1;
chomp $CSUB_range;
if ($CSUB_range eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$CSUB_range = $line;
chomp $CSUB_range;
last;
}
}
}
if ($line =~ m/.*Inverted duplications\s+\=\s+(.*?)(Length \(bp\).*)*$/)
{
$IDUP_input = $1;
chomp $IDUP_input;
$last_var = "IDUP";
if ($IDUP_input eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$IDUP_input = $line;
chomp $IDUP_input;
last;
}
}
}
if ($line =~ m/.*Length \(bp\)\s+\=\s+(.*?)(Heterozygosity.*)*$/ && $last_var eq "IDUP")
{
$IDUP_range = $1;
chomp $IDUP_range;
if ($IDUP_range eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$IDUP_range = $line;
chomp $IDUP_range;
last;
}
}
}
if ($line =~ m/.*Heterozygosity\s+\=\s+(.*?)(Long Read simulation:.*)*$/)
{
$heterozygosity = $1;
chomp $heterozygosity;
if ($heterozygosity eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$heterozygosity = $line;
chomp $heterozygosity;
last;
}
}
}
#Read simulation input----------------------------------------------------------------------------------------
if ($line =~ m/.*Sequencing depth\s+\=\s+(.*?)(Average length.*)*$/)
{
$NP_coverage = $1;
chomp $NP_coverage;
if ($NP_coverage eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$NP_coverage = $line;
chomp $NP_coverage;
last;
}
}
}
if ($line =~ m/.*Median length\s+\=\s+(.*?)(Length range.*)*$/)
{
$NP_average = $1;
chomp $NP_average;
if ($NP_average eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$NP_average = $line;
chomp $NP_average;
last;
}
}
}
if ($line =~ m/.*Length range\s+\=\s+(.*?)(Accuracy.*)*$/)
{
$NP_range = $1;
chomp $NP_range;
if ($NP_range eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$NP_range = $line;
chomp $NP_range;
last;
}
}
}
if ($line =~ m/.*Accuracy\s+\=\s+(.*?)(Error profile.*)*$/)
{
$NP_accuracy = $1;
chomp $NP_accuracy;
if ($NP_accuracy eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$NP_accuracy = $line;
chomp $NP_accuracy;
last;
}
}
}
if ($line =~ m/.*Error profile\s+\=\s+(.*?)$/)
{
$NP_error_profile = $1;
chomp $NP_error_profile;
if ($NP_error_profile eq "batch" && $batch_file ne "")
{
while (my $line = <BATCH>)
{
$NP_error_profile = $line;
chomp $NP_error_profile;
last;
}
}
last;
}
}
close CONFIG;
if ($reference eq "")
{
die "\nYou need to give a reference sequence!\n";
}
#Check input parameters----------------------------------------------------------------------------
my $SV_input = "";
if ($VCF_input ne "" || $DEL_input > '0' || $INS_input > '0' || $INV_input > '0' || $TRA_input > '0' || $DUP_input > '0' || $CSUB_input > '0' || $IDUP_input > '0')
{
$SV_input = "yes";
}
if ($SV_input eq "")
{
$heterozygosity = "";
}
if ($SV_input ne "" && $heterozygosity eq "")
{
$heterozygosity = '60%';
}
if ($DEL_input > 0 && $DEL_range ne "" && $DEL_range =~ m/^\d+\-\d+$/)
{}
elsif ($DEL_input > 0 && $DEL_range ne "")
{
die "\n\nThe length parameter of the Deletions input is not in a correct format should be for example (30-150000), $!\n";
}
elsif ($DEL_input > 0)
{
$DEL_range = "30-150000";
}
if ($INS_input > 0 && $INS_range ne "" && $INS_range =~ m/^\d+\-\d+$/)
{}
elsif ($INS_input > 0 && $INS_range ne "")
{
die "\n\nThe length parameter of the Inserions input is not in a correct format should be for example (30-100000), $!\n";
}
elsif ($INS_input > 0)
{
$INS_range = "30-100000";
}
if ($NP_error_profile eq "" && $NP_coverage ne "")
{
die "\n\nAn error profile should be given$!\n";
}
chomp($heterozygosity);
$heterozygosity =~ tr/,/./;
if ($heterozygosity =~ m/^(\d+\.*\d*)%*.*$/)
{
$heterozygosity = $1;
$heterozygosity /= 100;
}
if ($heterozygosity eq "")
{
$heterozygosity = "no";
}
elsif ($heterozygosity eq '0')
{
$heterozygosity = "no";
}
elsif ($heterozygosity <= 1)
{}
else
{
die "\nHeterozygosity: '$heterozygosity' has to be a value between 0 and 100 or left empty!\n";
}
chomp($maxProcs);
if ($maxProcs eq "" || ($maxProcs < 17 && $maxProcs > 0))
{}
else
{
die "\nMax Threads: '$maxProcs' has to be a value between 1 and 16 or left empty!\n";
}
chomp($NP_accuracy);
$NP_accuracy =~ tr/,/./;
if ($NP_accuracy =~ m/^(\d+\.*\d*)%*.*$/)
{
$NP_accuracy = $1;
}
if ($NP_accuracy eq "")
{}
elsif ($NP_accuracy <= 110 && $NP_accuracy > 69)
{}
else
{
die "\nAccuracy: '$NP_accuracy' has to be a value between 70 and 100 or left empty!\n";
}
#----------------------------------------------------------------------------------------------------
if (-d $output || $output eq "")
{
}
else
{
die "\nCan't open output directory $output, first create this directory,\n $!\n";
}
if ($SV_input ne "")
{
my $output_DEL = $output."graph_DEL_".$project.".txt";
open(OUTPUT_DEL, ">" .$output_DEL) or die "\nCan't open file $output_DEL, $!\n";
my $output_INS = $output."graph_INS_".$project.".txt";
open(OUTPUT_INS, ">" .$output_INS) or die "\nCan't open file $output_INS, $!\n";
my $output_INV2 = $output."graph_INV_".$project.".txt";
open(OUTPUT_INV2, ">" .$output_INV2) or die "\nCan't open file $output_INV2, $!\n";
}
my $output_LOG = $output."log_".$project.".txt";
open(OUTPUT_LOG, ">" .$output_LOG) or die "\nCan't open file $output_LOG, $!\n";
my $output_vcf = $output.$project.".vcf";
my $output_ref = $output.$project.".fasta";
my $output_hap1 = $output.$project."_haplotype1.fasta";
my $output_hap2 = $output.$project."_haplotype2.fasta";
print "\n\n";
print "---------------------------------CONFIG INPUT-----------------------------------\n\n";
print "\nInput parameters from the configuration file: *** Verify if everything is correct ***\n\n\n";
print "Project:\n";
print "-----------------------\n";
print "Project name = ".$project."\n";
print "Reference sequence = ".$reference."\n";
print "Replace ambiguous nts(N) = ".$ambigious_replace."\n";
print "Max threads = ".$maxProcs."\n\n\n";
print "Structural variation:\n";
print "-----------------------\n";
print "VCF input = ".$VCF_input."\n";
print "Foreign sequences = ".$sequences_foreign."\n\n";
print "Deletions = ".$DEL_input."\n";
print "Length (bp) = ".$DEL_range."\n\n";
print "Insertions = ".$INS_input."\n";
print "Length (bp) = ".$INS_range."\n\n";
print "Tandem duplications = ".$DUP_input."\n";
print "Length (bp) = ".$DUP_range."\n";
print "Copies = ".$DUP_copies."\n\n";
print "Inversions = ".$INV_input."\n";
print "Length (bp) = ".$INV_range."\n\n";
print "Complex substitutions = ".$CSUB_input."\n";
print "Length (bp) = ".$CSUB_range."\n\n";
print "Inverted duplications = ".$IDUP_input."\n";
print "Length (bp) = ".$IDUP_range."\n\n";
print "Heterozygosity = ".$heterozygosity."\n\n\n";
print "Long Read simulation:\n";
print "-----------------------\n";
print "Sequencing depth = ".$NP_coverage."\n";
print "Median length = ".$NP_average."\n";
print "Length range = ".$NP_range."\n";
print "Accuracy = ".$NP_accuracy."\n";
print "Error profile = ".$NP_error_profile."\n\n\n";
print OUTPUT_LOG "\n\n";
print OUTPUT_LOG "---------------------------------CONFIG INPUT-----------------------------------\n\n";
print OUTPUT_LOG "\nInput parameters from the configuration file: *** Verify if everything is correct ***\n\n\n";
print OUTPUT_LOG "Project:\n";
print OUTPUT_LOG "-----------------------\n";
print OUTPUT_LOG "Project name = ".$project."\n";
print OUTPUT_LOG "Reference = ".$reference."\n";
print OUTPUT_LOG "Replace ambiguous nts(N) = ".$ambigious_replace."\n";
print OUTPUT_LOG "Max threads = ".$maxProcs."\n\n\n";
print OUTPUT_LOG "Structural variation:\n";
print OUTPUT_LOG "-----------------------\n";
print OUTPUT_LOG "VCF input = ".$VCF_input."\n";
print OUTPUT_LOG "Foreign sequences = ".$sequences_foreign."\n\n";
print OUTPUT_LOG "Deletions = ".$DEL_input."\n";
print OUTPUT_LOG "Length (bp) = ".$DEL_range."\n\n";
print OUTPUT_LOG "Insertions = ".$INS_input."\n";
print OUTPUT_LOG "Length (bp) = ".$INS_range."\n\n";
print OUTPUT_LOG "Tandem duplications = ".$DUP_input."\n";
print OUTPUT_LOG "Length (bp) = ".$DUP_range."\n";
print OUTPUT_LOG "Copies = ".$DUP_copies."\n\n";
print OUTPUT_LOG "Inversions = ".$INV_input."\n";
print OUTPUT_LOG "Length (bp) = ".$INV_range."\n\n";
print OUTPUT_LOG "Complex substitutions = ".$CSUB_input."\n";
print OUTPUT_LOG "Length (bp) = ".$CSUB_range."\n\n";
print OUTPUT_LOG "Inverted duplications = ".$IDUP_input."\n";
print OUTPUT_LOG "Length (bp) = ".$IDUP_range."\n\n";
print OUTPUT_LOG "Heterozygosity = ".$heterozygosity."\n\n\n";
print OUTPUT_LOG "Long Read simulation:\n";
print OUTPUT_LOG "-----------------------\n";
print OUTPUT_LOG "Sequencing depth = ".$NP_coverage."\n";
print OUTPUT_LOG "Median length = ".$NP_average."\n";
print OUTPUT_LOG "Length range = ".$NP_range."\n";
print OUTPUT_LOG "Accuracy = ".$NP_accuracy."\n";
print OUTPUT_LOG "Error profile = ".$NP_error_profile."\n\n";
my $seq_depth = "";
my %seq_depth;
chomp($NP_coverage);
if ($NP_coverage =~ m/^\s*(\d+)\s*$/)
{
$NP_coverage = $1;
}
elsif ($NP_coverage eq "")
{
$NP_coverage = '0';
}
else
{
print "\n--------------------------READ SEQUENCING DEPTH FILE----------------------------\n\n";
print OUTPUT_LOG "\n--------------------------READ SEQUENCING DEPTH FILE----------------------------\n\n";
open(SEQ_DEPTH, $NP_coverage) or die "\nIncorrect coverage number or can't open sequencing depth file $NP_coverage, $!\n";
$seq_depth = $NP_coverage;
$NP_coverage = "";
my $total_coverage = '0';
my $total_coverage_tmp = '0';
my $count_line = '0';
my $hunderd = '1';
my $chr_prev = "";
while (my $line = <SEQ_DEPTH>)
{
chomp($line);
my @line = split /\t/, $line;
$total_coverage += $line[2];
$total_coverage_tmp += $line[2];
my $last_two = substr $line[1], -2;
if ($last_two eq "00" || ($chr_prev ne $line[0] && $chr_prev ne ""))
{
my $cov = sprintf("%.0f",($total_coverage_tmp/$hunderd));
my $pos = substr $line[1], 0, -2;
$seq_depth{$line[0]}{$pos} = $cov;
$total_coverage_tmp = '0';
$hunderd = '0';
}
$count_line++;
$hunderd++;
$chr_prev = $line[0];
}
$NP_coverage = $total_coverage/$count_line;
print "Average sequencing depth = ".$NP_coverage."\n\n";
print OUTPUT_LOG "Average sequencing depth = ".$NP_coverage."\n\n";
}
my $VCF_input_DEL = '0';
my $VCF_input_INS = '0';
my $VCF_input_INV = '0';
my $VCF_input_IDUP = '0';
my $VCF_input_DUP = '0';
my $VCF_input_TRA = '0';
my $VCF_input_CSUB = '0';
my $VCF_input_DEL_min = '100000000000000000';
my $VCF_input_INS_min = '100000000000000000';
my $VCF_input_INV_min = '100000000000000000';
my $VCF_input_IDUP_min = '100000000000000000';
my $VCF_input_DUP_min = '100000000000000000';
my $VCF_input_TRA_min = '100000000000000000';
my $VCF_input_CSUB_min = '100000000000000000';
my $VCF_input_DEL_max = '0';
my $VCF_input_INS_max = '0';
my $VCF_input_INV_max = '0';
my $VCF_input_IDUP_max = '0';
my $VCF_input_DUP_max = '0';
my $VCF_input_TRA_max = '0';
my $VCF_input_CSUB_max = '0';
my %TRA_hap1;
undef %TRA_hap1;
my %TRA_hap2;
undef %TRA_hap2;
my %TRA_hap_second;
undef %TRA_hap_second;
my %TRA_sequences;
undef %TRA_sequences;
if ($VCF_input ne "")
{
if ($sequences_foreign ne "")
{
open (INPUT_SEQ, $sequences_foreign) or die "Can't open file $sequences_foreign, $!\n";
my $id = "";
my $seq = "";
while (my $line_seq = <INPUT_SEQ>)
{
chomp $line_seq;
$line_seq =~ tr/\r//d;
$line_seq =~ s/\R/\012/;
my $first_tmp = substr $line_seq, 0, 1, "";
if ($first_tmp eq ">" && $id eq "")
{
$id = $line_seq;
}
elsif ($first_tmp eq ">")
{
$foreign_contigs{$id} = $seq;
$id = $line_seq;
}
elsif ($line_seq ne "" && $line_seq ne " ")
{
$seq .= $line_seq;
}
}
$foreign_contigs{$id} = $seq;
close INPUT_SEQ;
}
open (INPUT_VCF, $VCF_input) or die "Can't open file $VCF_input, $!\n";
while (my $line = <INPUT_VCF>)
{
if ($line =~ m/(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)*\s+(\S+)*.*/)
{
my $chr_tmp = $1;
my $start_pos_tmp = $2;
my $length_tmp = $3;
my $type_tmp = $4;
my $hap_tmp = $5;
my $SEQ_tmp = $6;
if ($SEQ_tmp ne "")
{
if (exists($foreign_contigs{$SEQ_tmp}))
{}
else
{
$sequences{$SEQ_tmp} = undef;
}
}
if ($type_tmp eq "DEL")
{
$VCF_input_DEL++;
if ($length_tmp < $VCF_input_DEL_min)
{
$VCF_input_DEL_min = $length_tmp;
}
if ($length_tmp > $VCF_input_DEL_max)
{
$VCF_input_DEL_max = $length_tmp;
}
}
if ($type_tmp eq "INS")
{
$VCF_input_INS++;
if ($length_tmp < $VCF_input_INS_min)
{
$VCF_input_INS_min = $length_tmp;
}
if ($length_tmp > $VCF_input_INS_max)
{
$VCF_input_INS_max = $length_tmp;
}
}
if ($type_tmp eq "DUP")
{
$VCF_input_DUP++;
if ($length_tmp < $VCF_input_DUP_min)
{
$VCF_input_DUP_min = $length_tmp;
}
if ($length_tmp > $VCF_input_DUP_max)
{
$VCF_input_DUP_max = $length_tmp;
}
}
if ($type_tmp eq "INV")
{
$VCF_input_INV++;
if ($length_tmp < $VCF_input_INV_min)
{
$VCF_input_INV_min = $length_tmp;
}
if ($length_tmp > $VCF_input_INV_max)
{
$VCF_input_INV_max = $length_tmp;
}
}
if ($type_tmp eq "CSUB")
{
$VCF_input_CSUB++;
if ($length_tmp < $VCF_input_CSUB_min)
{
$VCF_input_CSUB_min = $length_tmp;
}
if ($length_tmp > $VCF_input_CSUB_max)
{
$VCF_input_CSUB_max = $length_tmp;
}
}
if ($type_tmp eq "TRA")
{
$VCF_input_TRA++;
if ($length_tmp < $VCF_input_TRA_min)
{
$VCF_input_TRA_min = $length_tmp;
}
if ($length_tmp > $VCF_input_TRA_max)
{
$VCF_input_TRA_max = $length_tmp;
}
my @chr_tmp = split /\:/, $chr_tmp;
if (exists($TRA_hap1{$chr_tmp[1]}))
{
die "\n\nERROR: ".$line." You can only have one translocation per chromosome\n";
}
if (exists($TRA_hap2{$chr_tmp[1]}))
{
die "\n\nERROR: ".$line." You can only have one translocation per chromosome\n";
}
if ($hap_tmp ne '1')
{
$TRA_hap1{$chr_tmp[1]}{$chr_tmp[0]} = $length_tmp;
$TRA_hap1{$chr_tmp[0]}{$chr_tmp[1]} = $length_tmp;
$TRA_hap_second{$chr_tmp[1]} = undef;
}
if ($hap_tmp ne '0')
{
$TRA_hap2{$chr_tmp[1]}{$chr_tmp[0]} = $length_tmp;
$TRA_hap2{$chr_tmp[0]}{$chr_tmp[1]} = $length_tmp;
$TRA_hap_second{$chr_tmp[1]} = undef;
}
}
if ($type_tmp eq "IDUP" || $type_tmp eq "INV-DUP")
{
$VCF_input_IDUP++;
if ($length_tmp < $VCF_input_IDUP_min)
{
$VCF_input_IDUP_min = $length_tmp;
}
if ($length_tmp > $VCF_input_IDUP_max)
{
$VCF_input_IDUP_max = $length_tmp;
}
}
}
}
print "\n----------------------------------VCF INPUT------------------------------------\n\n";
print OUTPUT_LOG "\n----------------------------------VCF INPUT------------------------------------\n\n";
if ($VCF_input_DEL > 0)
{
print "Deletions = ".$VCF_input_DEL."\n";