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#!/usr/bin/perl
# This program aims to:
# 1) Run and merge the CNV prediction algorithms PennCNV, GNOSIS and QuantiSNP.
# PennCNV and QuantiSNP need to already be present on the machine prior to
# using this program.
# 2) Provide tools for further analysis of CNVs
# Upgrade ideas:
# * Remove concept of running differently with presence of logfile. Instead list
# column numbers as ARGVs with their absence trigerring the need for questions
# about column order
# * Add in PPV calculations
# * Remove the Rare algorithm since it is replaced by annotation and causes
# running issues (however it is used for PPV)
# * Add QuantiSNP 2.3 support
# * Add error message about theprobes pedfile at the start
# * Add high confidence settings to de novo algorithm
# * Include de novo algorithm in the pipeline
# * Add in regions of 2 algo overlap to summary file
# * Detect a partial run and continue where left off
use strict;
#use warnings;
use Data::Dumper;
use Getopt::Long;
use Parallel::ForkManager;
use POSIX;
use Tie::File;
#use LWP::Simple;
use Socket qw(:DEFAULT :crlf);
use Cwd qw(abs_path);
use Statistics::Distributions; #This requires installation: cpan, install Statistics::Distributions, quit
my $abspathin = &abs_path($0);
my $abspath = substr ($abspathin, 0, rindex($abspathin, '/'));
#print "My absolute path is $abspath\n";
###############################################################################
############### Process Initial Options ###############
###############################################################################
# Set the initial number options given, for error handling
my $num_opts = scalar @ARGV;
# configuration options
my ( $set_cfg , $data_opt , $ped_opt , $tag_opt , $threads_opt , $wd_opt, $probe_num );
# Multi-step analysis options
my ( $startall , $cnvall, $startquanton, $startmergeon, $startjenni );
# Individual analysis steps
my ( $annotatefxn, $nastychip, $chiperror, $clean, $convert, $denovoalg, $denovoalg2, $denovoalg3,
$run_gnosis, $homodelfind, $inquire, $mark_samples, $merge_prog, $ped_detail,
$pedmodify, $run_penncnv, $run_quantisnp, $run_quantisnp2, $format_qt2, $rarealg, $sexsift, $smallinquire,
$ppv_estimate, $fr_name, $sort_snp, $samplename, $cluster, $no_submit, $submit_batch, $force,
$chromocol, $startcol, $stopcol, $sampcol, $typecol, $algoname, $rarecol, $onecol, $fr_sum_all, $fr_sum_b, $fr_sum_c, $fr_sum_d,
$thesnpcol, $gendercol, $genecol, $headlinepres, $plot, $second_hit, $loci_find, $monitor_pbs );
my ($node_number) = 10;
# Informational options
my ( $help, $show_version );
# debugging / testing options
my ( $debugrun );
# timings
our $timeanddate = &showtime;
our $starttime = time;
# GetOpt!
GetOptions(
### Configuration Options ###
# Allows new locations to be added to the "directory_locations.cfg" file
'setup' => \$set_cfg,
# set data directory different than working directory
'data=s' => \$data_opt,
# set a custom pedfile other than 'pedfile' in the working directory
'ped=s' => \$ped_opt,
# specify the tag used for an analysis run
'tag=s' => \$tag_opt,
# specify the max number of threads to be used
'threads=i' => \$threads_opt,
# set a working directory different than `pwd`
'wd=s' => \$wd_opt,
# runs the sample using the cluster method
'clust' => \$cluster,
# Specifies if a header is present
'head=s' => \$headlinepres,
# Specifies the column with the chromosome
'chr=i' => \$chromocol,
# Specifies the column with the start position
'start=i' => \$startcol,
# Specifies the column with the stop position
'stop=i' => \$stopcol,
# Specifies the column with the sample name
'sampcol=i' => \$sampcol,
# Specifies the column with the CNV type
'type=i' => \$typecol,
# Specifies the column with the algo name
'algo=i' => \$algoname,
# Specifies the column with the % rare
'rarecol=i' => \$rarecol,
# Specifies the column with the % one
'onecol=i' => \$onecol,
# Specifies the column with the number of SNPs
'snpcol=i' => \$thesnpcol,
# Specifies the column with the gender
'gender=i' => \$gendercol,
# Specifies the file for using the cluster method
'samp=s' => \$samplename,
# Makes a PBS automation script without running it
'nosubmit' => \$no_submit,
# Runs a batch file through PBS
'submit' => \$submit_batch,
# Allows the number of nodes to be set
'node=s' => \$node_number,
#Looks for processes which have not finished
'monitorpbs' => \$monitor_pbs,
### Multi analysis steps ###
# Run the entire analysis pipeline
'run' => \$startall,
# Run the analysis pipeline after QT2
'run2' => \$startquanton,
# Run the analysis pipeline after QT2 format
'run3' => \$startmergeon,
# Run the analysis pipeline after QT2 format
'runjen' => \$startjenni,
# Run all three CNV algorithms
'cnvall' => \$cnvall,
### Individual analysis steps ###
# Annotation
'annotate' => \$annotatefxn ,
# Identifies chips that have failed as part of the pipeline
'badchip' => \$nastychip ,
# Looks for chips failing QC
'chiperror' => \$chiperror,
# Cleans up excess files after pipeline has compelted
'cleanup' => \$clean,
# Converts FinalReports to PennCNV and QuantiSNP input
'convert' => \$convert,
# Determines if CNVs are seen in parents
'denovo' => \$denovoalg,
# Determines if CNVs are seen in parents using raw data
'denovo2' => \$denovoalg2,
# Determines in CNVs are seen in parents using raw data and SNP summaries
'denovo3' => \$denovoalg3,
# Makes images of CNVs using R
'plot' => \$plot,
# Runs GNOSIS
'gnosis' => \$run_gnosis,
# Find homozygous deletions
'homodel' => \$homodelfind,
# Summaries files to human readable output
'inquire' => \$inquire,
# Marks CNVs according to whether a sample is present in another list
'marksamp' => \$mark_samples,
# Merges reformated results
'merge' => \$merge_prog,
# Annotates samples against a pedfile
'peddetail' => \$ped_detail,
# Modifies the pedfile to remove chips that have failed
'pedmod' => \$pedmodify,
# Runs PennCNV calling algorithm
'penncnv' => \$run_penncnv,
# Runs PPV estimation algorithm
'ppv' => \$ppv_estimate,
# Runs QuantiSNPv1.1 on multiple processors
'quantisnp' => \$run_quantisnp,
# Runs QuantiSNPv2.3 on multiple processors
'quantisnp2' => \$run_quantisnp2,
# Format QuantiSNPv2.3 results
'formatqt2' => \$format_qt2,
# Predicts whether CNVs are rare or common
'rare' => \$rarealg,
# Find overlapping transmitted variants from de novo hits
'secondhit' => \$second_hit,
# Determines the gender of samples
'sexsift' => \$sexsift,
# Summaries merged output files
'smallinq' => \$smallinquire,
# Loads the ChipIDs from FinalReports
'name' => \$fr_name,
# Sorts the SNPs in FinalReports to make files showing SNP order
'sortsnp' => \$sort_snp,
# Reduces a file to non-overlaping loci
'loci' => \$loci_find,
#Summary of LogR and BAF from mutliple chips
'frsum' => \$fr_sum_all,
#Summary of LogR and BAF from mutliple chips
'frsumb' => \$fr_sum_b,
#Summary of LogR and BAF from mutliple chips
'frsumc' => \$fr_sum_c,
#Summary of LogR and BAF from mutliple chips
'frsumd' => \$fr_sum_d,
### Informational options ###
# Prints out general help info
'help' => \$help,
# Prints out of the version of CNVision
'version' => \$show_version,
# Forces CNVision to run despite wrong penncnv/QT/annotation folders
'force' => \$force,
### Debug option ###
'debug' => \$debugrun
);
if (!$num_opts) {
print "No options were given\n";
exit;
}
#Pipeline Commands
my $pipeline_com = 1 if ($annotatefxn or $nastychip or $chiperror or $clean or $convert or $denovoalg or $denovoalg2 or $denovoalg3 or
$run_gnosis or $homodelfind or $inquire or $merge_prog or $ped_detail or $pedmodify or $run_penncnv or $run_quantisnp or $run_quantisnp2 or $format_qt2 or
$rarealg or $sexsift or $smallinquire or $denovoalg2 or $ppv_estimate or $startall or $startquanton or $startmergeon or $startjenni or $fr_sum_all or $fr_sum_b or $fr_sum_c or $fr_sum_d);
#Analysis Commands
my $analysis_com = 1 if ($annotatefxn or $fr_name or $plot or $second_hit or $loci_find);
#Simple commands
my $simple_com = 1 if ($fr_name or $show_version or $loci_find);
###############################################################################
############### Global Variable Declaration ###############
###############################################################################
# Many of the options look for FinalReport in file names, to change this alter
# the option below (eg $namematch = 'Hapmap_';)
our $namematch = 'FinalReport';
our $version = '0.11';
(our $progname = $0) =~ s|.*[/\\]||;
# Identifies operating system and directory seperator
# using a lone `cd` on a windows system is equivalent to `pwd` on unix-based
# operating systems. `cd` returns an empty string on *nix based OSes. Therefore:
# if $os_test is non-empty -> Windows
# if $os_test is empty -> unix-based (Unix, Linux or OS X)
our ($operating_system, $dir_sep);
chomp(my $os_test = `cd 2>tmperr`);
if ($os_test) {
($operating_system, $dir_sep) = qw(Windows \\);
} else {
($operating_system, $dir_sep) = qw(Unix /);
}
unlink 'tmperr' if (-e 'tmperr');
# Set location of directories that will be used
chomp(our $working_dir = $operating_system eq 'Windows' ? `cd` : `pwd`);
our $data_dir = $working_dir;
our $res_dir = '01_Raw_Results';
our $pro_dir = '02_Processed';
our $merge_dir = '03_Merged';
our $fin_dir = '04_Final_Results';
our $rin_dir = '05_Image_Data';
our $image_dir = '06_Images';
our $plink_dir = '07_Plink';
our $sum_dir = '08_FRSum';
# Run specific variables
our ($QTloc, $QT2loc, $MATloc, $PNloc, $ANloc);
our ($tag, $processors, $chip_type);
our (%sample_cols, %sample_idx);
our $strand = 'Top';
our $pedfile = $working_dir.$dir_sep.'pedfile';
# Final report columns indices (updated via fr_columns($header_line))
our ($patname, $snpcol, $chrcol, $chromodist, $gtcol1, $gtcol2, $theta,
$rvalue, $ballele, $log2col) = 0 .. 9;
# Contains gender info for subjects. Gets pulled in later, but perl is complaining
our %sexysex;
# CNV markers
our %cnvsnps;
# Forker PID-tracking array
our @pids;
# Using java interface?
our $javamethod = 0;
#Autoflush - allows communication with Java for questions
$| = 1;
# Run setup, if appropriate
if ($set_cfg) {
&set_conf();
exit;
}
###############################################################################
############### Load Configuration Files ###############
###############################################################################
# This loads the file "directory_locations.cfg" to determine the location of app
# directories; Note allows multiple entries and operating systems
# cat /apps1/cnvision/0.11/cnvision.conf | sed -e 's/Threads=8/Threads=XX/' | tee cnvision.conf
my $configure_file = "cnvision.conf";
if (-e $configure_file) {
#print "Config file in this directory\n";
&load_conf($configure_file);
} elsif (-e $abspath.$dir_sep.$configure_file) {
#print "Config file in CNVision directory\n";
&load_conf($abspath.$dir_sep.$configure_file);
} else {
print "Could not load directory config\n";
&set_conf();
&load_conf($configure_file);
}
unless (($PNloc and ($QTloc or $QT2loc) and $ANloc) or $force or $analysis_com) {
print "Unable to load one or more directory locations:\n";
print "PennCNV\n" unless ($PNloc);
print "QuantiSNP\n" unless ($QTloc or $QT2loc);
print "Annotation\n" unless ($ANloc);
exit;
}
###############################################################################
############### Set Run-Specific Variables ###############
###############################################################################
#print "=============================================================================\n";
#print " Welcome to CNVision v.$version\n";
#print "=============================================================================\n";
# Set location of datafile if not in the current directory
if ($data_opt) {
if (-d $data_opt) {
$data_dir = $data_opt;
print "Set data directory to $data_dir\n";
} else {
print "Invalid data directory: '$data_dir'\n";
exit;
}
}
# Set location of the pedfile if not in the current directory
$pedfile = $ped_opt if ($ped_opt and -e $ped_opt);
# If a job tag was passed with the variables, check for any existing results with
# that job name and continue with that name if not. If no tag was given on the
# command line, get it interactively from the user.
if (defined $tag_opt) {
if (-e "${tag_opt}_Logfile.txt") {
print "\nLoading run information from Logfile\n";
open LOG, '<', "${tag_opt}_Logfile.txt" or print $!;
while (my $line = <LOG>){
chomp $line;
my @tab = split /\t/, $line;
$data_dir = $tab[3] if ($tab[1] =~ /Data Dir/);
$ped_opt = $tab[3] if ($tab[1] =~ /Pedfile/);
$threads_opt = $tab[3] if ($tab[1] =~ /Processors/);
$chip_type = $tab[3] if ($tab[1] =~ /Chip/);
$probe_num = $tab[3] if ($tab[1] =~ /Probes/);
$tag = $tag_opt;
}
print "The data directory is:\t\t$data_dir\nThe pedfile is:\t\t\t$ped_opt\nThe number of processors is:\t$threads_opt\nThe chip type is:\t\t$chip_type\n\n";
} else {
while ($tag_opt =~ /[^\w\d-]/) {
print "Your job name contains illegal characters.\n";
print "Please use only a-z, A-Z, 0-9, _, -\n";
chomp ($tag_opt = <STDIN>);
}
$tag = $tag_opt;
#print "Creating a new job with the name: $tag\n";
}
} elsif ($force or $simple_com) { #Skip this
} else {
print "Please a choose a name for job. This name will be attached to all your result files:\n";
chomp(my $resp = <>);
while ($resp =~ /[^\w\d-]/) {
print "Your job name contains illegal characters.\n";
print "Please use only a-z, A-Z, 0-9, _, -\n";
chomp ($resp = <>);
}
$tag = $resp;
print "Creating a new job with the name: $tag\n";
}
my $newlog = -e "${tag}_Logfile.txt" ? 0 : 1;
# Set pedfile name. This can be done using the --ped option too
if ($ped_opt and -e $ped_opt){
$pedfile = $ped_opt;
} elsif ($force or $simple_com or $analysis_com) { #Skip this
} else {
my @pedfiles = <$data_dir/*pedfile*>;
my $pedfilecount = @pedfiles;
#my $pedout = join "\n", @pedfiles;
#print "Found $pedfilecount pedfiles, they are:\n$pedout\n";
my ($thepedfilename, $resp, $resp2, $done);
if ($pedfilecount == 1){
$pedfile = $pedfiles[0];
print "Using pedfile $pedfiles[0]; is this correct? [y/n]\n";
chomp($resp = <STDIN>);
while ($resp !~ /^(y(es)?|no?)$/i) {
print "'$resp' is an invalid response.\n";
print "Using pedfile $pedfiles[0]; is this correct? [y/n]\n";
chomp($resp = <STDIN>);
}
}
if ($pedfilecount != 1 or $resp =~ /n/i) {
print "Please specify the name of the pedfile.\n";
chomp($resp2 = <STDIN>);
do {
$done = 0;
if (-e $resp2) {
$done = 1;
}
elsif ($force){
$done = 1;
}
else {
print "Cannot find file '$resp2'.\n";
print "Please specify the name of the pedfile.\n";
chomp($resp2 = <STDIN>);
}
} until ($done == 1);
$pedfile = $resp2;
}
}
# load samples into tied array
our (@sample_files, $num_samples, @samples, @sample_names, %sample_build);
my ($prescount, $misscount) = (0,0);
if ($pipeline_com == 1 and $cluster != 1){
tie @samples, 'Tie::File', "${tag}_Sample_list.txt" or die "${tag}_Sample_list.txt: $!";
$num_samples;
print "There are ".(scalar @samples - 1)." samples to analyze\n";
if (scalar @samples <= 1 or $newlog) {
#Identify the samples present
print "Identifying FinalReports in the directory\n";
my ($fr_list, $hash_ref1, $hash_ref2, $hash_ref3) = &fr_list($data_dir);
my @fr_list = @$fr_list;
my %frtochip = %$hash_ref1;
my %chiptofr = %$hash_ref2;
my %chiptoline = %$hash_ref3;
@samples = join "\t",'SampleID','FinalReport','SNPs','Chip','Chip bpm';
push my @samples2, join "\t",'SampleID','FinalReport','SNPs','Chip','Chip bpm';
push @samples2, @fr_list;
open FROUT ,'>', 'Name_ID.txt' or die "Could not open Name_ID.txt\n$!";
my $frout = join "\n", @samples2;
print FROUT $frout;
close FROUT;
#Load the pedfile and check the samples are present
print "Looking for FinalReports for samples in pedfile\n";
open PED ,'<', $pedfile or die "Could not open $pedfile\n$!";
{ local $/= undef; our $input = <PED>; }
close PED;
(local $\) = (/(\r\n|\r|\n)/);
my @pedfile = split (/\r\n|\r|\n/, our $input); chomp @pedfile;
my (%chipspresent, %snpspresent);
foreach my $line (@pedfile){
$line =~ s/\n|\r|\n\r|\r\n//g;
my @tab = split /\s+/, $line;
#print $line.' Sample: '.$tab[1].' C2L: '.$chiptoline{$tab[1]}."\n";
if ($chiptoline{$tab[1]} =~ /$namematch/){
push @samples, $chiptoline{$tab[1]};
my @tab2 = split /\t/, $chiptoline{$tab[1]};
$chipspresent{$tab2[3]} = 0;
$snpspresent{$tab2[2]} = 0;
$prescount++;
}
else {
open PED ,'>>', "${tag}_Missing_files.txt" or die "Could not open ${tag}_Missing_files.txt\n$!";
print PED $tab[1]."\n";
$misscount++;
}
}
#Identify missing samples
unless ($misscount < 1 or $force){
print "There are $misscount samples missing FinalReports.\n";
print "Continue anyway? [y/n]\n";
chomp(my $resp = <STDIN>);
while ($resp !~ /^(y(es)?|no?)$/i) {
print "'$resp' is an invalid response.\n";
print "There are $misscount samples missing FinalReports.\n";
print "Continue anyway? [y/n]\n";
chomp($resp = <STDIN>);
}
if ($resp =~ /no/i) {
print "Canceling run; see ${tag}_Missing_files.txt for the list of missing files.\n";
exit;
}
}
else {
print "All $prescount samples are present\n";
}
#Identify chip types
my $chiptypes = keys %chipspresent;
if ($chiptypes != 1){
print "There are $chiptypes array types present.\n";
unless ($force){
print "Canceling run; see ${tag}_Sample_list.txt for the list of missing files.\n";
exit;
}
}
else {
print "All samples have been run on the ".(keys %chipspresent)[0]." array.\n";
$chip_type = (keys %chipspresent)[0];
$probe_num = (keys %snpspresent)[0];
}
}
%sample_cols = &parse_header($samples[0]);
#foreach my $sc (keys %sample_cols){print "$sc\t$sample_cols{$sc}\n";}
$num_samples = 0;
%sample_idx = map { m/^(.+?)\t/; $1 ? ($1 => ++$num_samples) : ("err$num_samples" => ++$num_samples) } @samples[1..$#samples];
@sample_files = map { my @row = split /\t/,$_,3; $row[1] } @samples[1..$#samples];
@sample_names = map { my @row = split /\t/,$_,3; $row[0] } @samples[1..$#samples];
%sample_build = map { my @row = split /\t/,$_; $row[0] => $row[$sample_cols{'Build'}] } @samples[1..$#samples];
#foreach my $samp (keys %sample_build){print "$samp\t$sample_build{$samp}\n";}
} elsif ($force or $simple_com) { #Skip this
} else {
my $sampin = "${tag}_Sample_list.txt";
open IN, '<', $sampin or print "Could not open $sampin file\n";
@samples = <IN>; close IN;
$num_samples;
print "There are ".(scalar @samples - 1)." samples to analyze\n";
%sample_cols = &parse_header($samples[0]);
$num_samples = 0;
%sample_idx = map { m/^(.+?)\t/; $1 ? ($1 => ++$num_samples) : ("err$num_samples" => ++$num_samples) } @samples[1..$#samples];
@sample_files = map { my @row = split /\t/,$_,3; $row[1] } @samples[1..$#samples];
@sample_names = map { my @row = split /\t/,$_,3; $row[0] } @samples[1..$#samples];
%sample_build = map { my @row = split /\t/,$_; $row[0] => $row[$sample_cols{'Build'}] } @samples[1..$#samples];
}
# Set processor / thread count. Should be equal to or less than total # of
# processors. Numbers greater than total processors will be largely ineffective
# and may slow down processing.
if (defined $threads_opt and $threads_opt =~ /^\d+|^clust/) {
$processors = $threads_opt;
} elsif ($processors) {
#print "Using default thread count: $processors\n";
} else {
print "What is the maximum number of threads you would like used? For greatest\n";
print "efficiency, choose the number of cores in the machine (e.g. 8); if using\n";
print "a unix-based cluster type 'clust' instead.\n";
chomp(my $resp = <>);
while ($resp =~ /^\d+|^clust/) {
print "'$resp' is not a valid entry. Select an integer value.\n";
print "What is the maximum number of threads you would like used? For greatest\n";
print "efficiency, choose the number of cores in the machine (e.g. 8); if using\n";
print "a unix-based cluster type 'clust' instead.\n";
chomp($resp = <>);
}
$processors = $resp;
}
#Create the logfile
if ($newlog){
if ($tag =~ /\w+/ and -d $data_dir and -e $pedfile and $processors =~ /^\d+|^clust/ and defined $chip_type) {
open LOG1, '>', "${tag}_Logfile.txt" or die "Could not open the logfile ${tag}_Logfile.txt: $!";
print LOG1 showtime(),"\tTag\tINFO\t$tag\n";
print LOG1 showtime(),"\tData Dir\tINFO\t$data_dir\n";
print LOG1 showtime(),"\tProcessors\tINFO\t$processors\n";
print LOG1 showtime(),"\tPedfile\tINFO\t$pedfile\n";
print LOG1 showtime(),"\tChip\tINFO\t$chip_type\n";
print LOG1 showtime(),"\tProbes\tINFO\t$probe_num\n";
print LOG1 showtime(),"\tSamplesPresent\tINFO\t$prescount\n";
print LOG1 showtime(),"\tSamplesMissing\tINFO\t$misscount\n";
} elsif ($force or $simple_com) { #Skip this
} else {
print "Incorrect input arguments, logfile not created\n";
print "Tag: $tag, Dir: $data_dir, Ped: $pedfile, Pro: $processors, Chip: $chip_type\n";
print "The data directory is:\t\t$data_dir\nThe pedfile is:\t\t\t$pedfile\nThe number of processors is:\t$processors\nThe chip type is:\t\t$chip_type\n\n";
}
}
else {
open LOG1, '>>', "${tag}_Logfile.txt" or die "Could not open the logfile ${tag}_Logfile.txt: $!";
}
# Create results directories if they do not exist already
if ($pipeline_com == 1 ){
foreach my $dir (qw(01_Raw_Results 02_Processed 03_Merged 04_Final_Results 05_Image_Data 06_Images 07_Plink 08_FRSum)) {
if (! -d $dir) {
system("mkdir $dir") == 0 or die "Unable to create $dir: $?\n";
}
}
}
print "=============================================================================\n";
print " CNVision: Automated CNV detection and analysis; www.cnvision.org\n";
print "=============================================================================\n";
###############################################################################
############### Primary Analysis Pipeline ###############
###############################################################################
# initialize ForkManager
my $forker = new Parallel::ForkManager($processors);
# Add pid tracking on finish to allow easier post-run log merging
# NOTE: make sure to undef @pids at the end of each init subroutine
$forker->run_on_finish(
sub {
my ($pid, $exit_code, $ident) = @_;
push @pids,$pid;
}
);
#################################################################################
# These are the main commands for pipelines:
if ($startall) {
&init_sexsift($forker) == 1 or die
"Failed to finish init_sexsift. Check the logs to determine the error.\n";
&init_chiperror($forker) == 1 or die
"Failed to finish init_chiperror. Check the logs to determine the error.\n";
my $sortedsnps = &snporder($sample_files[0]);
&init_convert($forker, $sortedsnps) == 1 or die
"Failed to finish init_convert. Check the logs to determine the error.\n";
&init_gnosis($forker, $sortedsnps) == 1 or die
"Failed to finish init_gnosis. Check the logs to determine the error.\n";
&init_penncnv($forker) == 1 or die
"Failed to finish init_penncnv. Check the logs to determine the error.\n";
&init_quantisnp2($forker) == 1 or die
"Failed to finish init_quantisnp2. Check the logs to determine the error.\n";
&qt2format();
&label_bad_chips();
&merge("$pro_dir$dir_sep${tag}_QT_Merge.txt", "$pro_dir$dir_sep${tag}_GN_Merge.txt", "$pro_dir$dir_sep${tag}_PN_Merge.txt");
&rarealg;
#&pedmodify();
&denovo("$merge_dir${dir_sep}Rare_${tag}_Merged.txt");
&inquire("$merge_dir${dir_sep}DN_Rare_${tag}_Merged.txt");
$headlinepres = 'y'; $sampcol = 6; $chromocol = 7; $startcol = 8; $stopcol = 9;
&denovo_raw("$merge_dir${dir_sep}${tag}_CNV_Results.txt", "$merge_dir${dir_sep}${tag}_CNV_Results_DN2.txt", $sortedsnps);
$headlinepres = 'y'; $sampcol = 6; $chromocol = 7; $startcol = 8; $stopcol = 9; $typecol = 12; $algoname = 17; $rarecol = 19; $onecol = 22; $snpcol = 23;
&ppv_estimate("$merge_dir${dir_sep}${tag}_CNV_Results_DN2.txt", "$merge_dir${dir_sep}${tag}_CNV_Results_DN2_PPV.txt");
# annotate("$merge_dir$dir_sep${tag}_CNV_Results.txt");
#&init_homodel($forker, $sortedsnps)== 1 or die "Failed to finish init_homodel. Check the logs to determine the error.\n";
#&peddetail("$pro_dir$dir_sep${tag}_HD_Merge.txt");
#&mark_samples("$merge_dir${dir_sep}Ped_${tag}_HD_Merge.txt", "$merge_dir$dir_sep${tag}_Badchips.txt");
# annotate("$merge_dir$dir_sep${tag}_HD_Results.txt");
&cleanup();
} elsif ($startquanton) {
my $sortedsnps = &snporder($sample_files[0]);
&qt2format();
&label_bad_chips();
&merge("$pro_dir$dir_sep${tag}_QT_Merge.txt", "$pro_dir$dir_sep${tag}_GN_Merge.txt", "$pro_dir$dir_sep${tag}_PN_Merge.txt");
&rarealg;
#&pedmodify();
&denovo("$merge_dir${dir_sep}Rare_${tag}_Merged.txt");
&inquire("$merge_dir${dir_sep}DN_Rare_${tag}_Merged.txt");
$headlinepres = 'y'; $sampcol = 6; $chromocol = 7; $startcol = 8; $stopcol = 9;
&denovo_raw("$merge_dir${dir_sep}${tag}_CNV_Results.txt", "$merge_dir${dir_sep}${tag}_CNV_Results_DN2.txt", $sortedsnps);
$headlinepres = 'y'; $sampcol = 6; $chromocol = 7; $startcol = 8; $stopcol = 9; $typecol = 12; $algoname = 17; $rarecol = 19; $onecol = 22; $snpcol = 23;
&ppv_estimate("$merge_dir${dir_sep}${tag}_CNV_Results_DN2.txt", "$merge_dir${dir_sep}${tag}_CNV_Results_DN2_PPV.txt");
# annotate("$merge_dir$dir_sep${tag}_CNV_Results.txt");
#&init_homodel($forker, $sortedsnps)== 1 or die "Failed to finish init_homodel. Check the logs to determine the error.\n";
#&peddetail("$pro_dir$dir_sep${tag}_HD_Merge.txt");
#&mark_samples("$merge_dir${dir_sep}Ped_${tag}_HD_Merge.txt", "$merge_dir$dir_sep${tag}_Badchips.txt");
# annotate("$merge_dir$dir_sep${tag}_HD_Results.txt");
&cleanup();
} elsif ($startmergeon) {
my $sortedsnps = &snporder($sample_files[0]);
&label_bad_chips();
&merge("$pro_dir$dir_sep${tag}_QT_Merge.txt", "$pro_dir$dir_sep${tag}_GN_Merge.txt", "$pro_dir$dir_sep${tag}_PN_Merge.txt");
&rarealg;
#&pedmodify();
&denovo("$merge_dir${dir_sep}Rare_${tag}_Merged.txt");
&inquire("$merge_dir${dir_sep}DN_Rare_${tag}_Merged.txt");
$headlinepres = 'y'; $sampcol = 6; $chromocol = 7; $startcol = 8; $stopcol = 9;
&denovo_raw("$merge_dir${dir_sep}${tag}_CNV_Results.txt", "$merge_dir${dir_sep}${tag}_CNV_Results_DN2.txt", $sortedsnps);
$headlinepres = 'y'; $sampcol = 6; $chromocol = 7; $startcol = 8; $stopcol = 9; $typecol = 12; $algoname = 17; $rarecol = 19; $onecol = 22; $snpcol = 23;
&ppv_estimate("$merge_dir${dir_sep}${tag}_CNV_Results_DN2.txt", "$merge_dir${dir_sep}${tag}_CNV_Results_DN2_PPV.txt");
# annotate("$merge_dir$dir_sep${tag}_CNV_Results.txt");
#&init_homodel($forker, $sortedsnps)== 1 or die "Failed to finish init_homodel. Check the logs to determine the error.\n";
#&peddetail("$pro_dir$dir_sep${tag}_HD_Merge.txt");
#&mark_samples("$merge_dir${dir_sep}Ped_${tag}_HD_Merge.txt", "$merge_dir$dir_sep${tag}_Badchips.txt");
# annotate("$merge_dir$dir_sep${tag}_HD_Results.txt");
&cleanup();
} elsif ($startjenni) {
&init_chiperror($forker) == 1 or die;
my $sortedsnps = &snporder($sample_files[0]);
#print 'SS: '.$sortedsnps."\n";
&init_convert($forker, $sortedsnps) == 1 or die;
&init_penncnv($forker) == 1 or die;
&label_bad_chips();
&merge("$pro_dir$dir_sep${tag}_QT_Merge.txt", "$pro_dir$dir_sep${tag}_GN_Merge.txt", "$pro_dir$dir_sep${tag}_PN_Merge.txt");
&rarealg;
#&pedmodify();
&denovo("$merge_dir${dir_sep}Rare_${tag}_Merged.txt");
&inquire("$merge_dir${dir_sep}DN_Rare_${tag}_Merged.txt");
$headlinepres = 'y'; $sampcol = 6; $chromocol = 7; $startcol = 8; $stopcol = 9;
&denovo_raw("$merge_dir${dir_sep}${tag}_CNV_Results.txt", "$merge_dir${dir_sep}${tag}_CNV_Results_DN2.txt", $sortedsnps);
$headlinepres = 'y'; $sampcol = 6; $chromocol = 7; $startcol = 8; $stopcol = 9; $typecol = 12; $algoname = 17; $rarecol = 19; $onecol = 22; $snpcol = 23;
&ppv_estimate("$merge_dir${dir_sep}${tag}_CNV_Results_DN2.txt", "$merge_dir${dir_sep}${tag}_CNV_Results_DN2_PPV.txt");
# annotate("$merge_dir$dir_sep${tag}_CNV_Results.txt");
#&init_homodel($forker, $sortedsnps)== 1 or die "Failed to finish init_homodel. Check the logs to determine the error.\n";
#&peddetail("$pro_dir$dir_sep${tag}_HD_Merge.txt");
#&mark_samples("$merge_dir${dir_sep}Ped_${tag}_HD_Merge.txt", "$merge_dir$dir_sep${tag}_Badchips.txt");
# annotate("$merge_dir$dir_sep${tag}_HD_Results.txt");
&cleanup();
} elsif ($sexsift) {
&init_sexsift($forker) == 1 or die
"Failed to finish init_sexsift. Check the logs to determine the error.\n";
} elsif ($chiperror) {
&init_chiperror($forker) == 1 or die
"Failed to finish init_chiperror. Check the logs to determine the error.\n";
} elsif ($convert) {
my $sortedsnps = &snporder($sample_files[0]);
&init_convert($forker, $sortedsnps) == 1 or die
} elsif ($run_gnosis) {
my $sortedsnps = &snporder($sample_files[0]);
&init_gnosis($forker, $sortedsnps) == 1 or die
"Failed to finish init_gnosis. Check the logs to determine the error.\n";
} elsif ($run_penncnv) {
&init_penncnv($forker) == 1 or die
"Failed to finish init_penncnv. Check the logs to determine the error.\n";
} elsif ($run_quantisnp) {
&init_quantisnp($forker) == 1 or die
"Failed to finish init_quantisnp. Check the logs to determine the error.\n";
} elsif ($run_quantisnp2) {
&init_quantisnp2($forker) == 1 or die
"Failed to finish init_quantisnp. Check the logs to determine the error.\n";
} elsif ($format_qt2) {
&qt2format();
} elsif ($merge_prog) {
&merge();
} elsif ($pedmodify) {
&pedmodify();
} elsif ($annotatefxn) {
&annotate("$merge_dir$dir_sep${tag}_CNV_Results.txt");
} elsif ($rarealg) {
&rarealg;
} elsif ($nastychip) {
&label_bad_chips();
} elsif ($denovoalg) {
&denovo("$merge_dir${dir_sep}Rare_${tag}_Merged.txt");
} elsif ($inquire) {
&inquire("$merge_dir${dir_sep}DN_Rare_${tag}_Merged.txt");
} elsif ($homodelfind) {
my $sortedsnps = snporder($sample_files[0]);
&init_homodel($forker, $sortedsnps);
} elsif ($ped_detail) {
&peddetail("$pro_dir$dir_sep${tag}_HD_Merge.txt");
} elsif ($mark_samples) {
&mark_samples("$merge_dir${dir_sep}Ped_${tag}_HD_Merge.txt", "$merge_dir$dir_sep${tag}_Badchips.txt");
} elsif ($clean) {
&cleanup();
} elsif ($show_version) {
print "CNVision v$version\n";
} elsif ($fr_name){
my $output = "Name_ID.txt";
open (OUT, ">$output")|| die "Could not open $output, may already be open\n";
print OUT "SampleID\tFinalReport\tSNPs\tChip\tChipBPM\n";
my ($fr_list, $hash_ref1, $hash_ref2, $hash_ref3) = &fr_list($data_dir);
my @output = join "\n", @$fr_list;
print OUT @output;
print "\nAll done!";
} elsif ($denovoalg2){
my $sortedsnps = &snporder($sample_files[0]);
my $input = "$merge_dir${dir_sep}${tag}_CNV_Results.txt";
my $output = "$merge_dir${dir_sep}${tag}_CNV_Results_DN2.txt";
if (scalar @ARGV == 1){
$input = $ARGV[0];
&headshow ($input) unless ($headlinepres =~ /[yn]/i and $sampcol =~ /\d+/ and $chromocol =~ /\d+/ and $startcol =~ /\d+/ and $stopcol =~ /\d+/);
&sampcol;&chrcol;&startcol;&stopcol;&header;
$output = 'DN2_'.$input;
}
elsif (scalar @ARGV > 1){
die "ERROR: Can only accept one input file; ".scalar @ARGV. "were detected\n$!";
}
else {
$headlinepres = 'y'; $sampcol = 6; $chromocol = 7; $startcol = 8; $stopcol = 9;
}
&denovo_raw($input, $output, $sortedsnps);
} elsif ($denovoalg3){
my $sortedsnps = &snporder($sample_files[0]);
my $input = "$merge_dir${dir_sep}${tag}_CNV_Results.txt";
my $output = "$merge_dir${dir_sep}${tag}_CNV_Results_DN3.txt";
if (scalar @ARGV == 1){
$input = $ARGV[0];
&headshow ($input) unless ($headlinepres =~ /[yn]/i and $sampcol =~ /\d+/ and $chromocol =~ /\d+/ and $startcol =~ /\d+/ and $stopcol =~ /\d+/);
&sampcol;&chrcol;&startcol;&stopcol;&header;
$output = 'DN3_'.$input;
}
elsif (scalar @ARGV > 1){
die "ERROR: Can only accept one input file; ".scalar @ARGV. "were detected\n$!";
}
else {
$headlinepres = 'y'; $sampcol = 6; $chromocol = 7; $startcol = 8; $stopcol = 9;
}
&denovo_raw_snp($input, $output, $sortedsnps);
} elsif ($plot){
my $sortedsnps = &snporder($sample_files[0]);
&headshow ($ARGV[0]) unless ($headlinepres =~ /[yn]/i and $sampcol =~ /\d+/ and $chromocol =~ /\d+/ and $startcol =~ /\d+/ and $stopcol =~ /\d+/);
&sampcol;&chrcol;&startcol;&stopcol;&header;
&plot_cnv($ARGV[0], $sortedsnps);
} elsif ($ppv_estimate){
my $input = "$merge_dir${dir_sep}${tag}_CNV_Results_DN2.txt";
my $output = "$merge_dir${dir_sep}${tag}_CNV_Results_DN2_PPV.txt";
$output =~ s/CNV_Results_DN2.txt/CNV_Results_DN2_PPV.txt/;
if (scalar @ARGV == 1){
$input = $ARGV[0];
&headshow ($ARGV[0]) unless ($headlinepres =~ /[yn]/i and $chromocol =~ /\d+/ and $startcol =~ /\d+/ and $stopcol =~ /\d+/ and $typecol =~ /\d+/ and $algoname =~ /\d+/ and $rarecol =~ /\d+/ and $onecol =~ /\d+/and $snpcol =~ /\d+/);
&gendercol; &sampcol; &chrcol; &startcol; &stopcol; &typecol; &algocol; &rarecol; &onecol; &snpcol; &header;
$output = 'PPV_'.$input;
}
elsif (scalar @ARGV > 1){
die "ERROR: Can only accept one input file; ".scalar @ARGV. "were detected\n$!";
}
else {
$headlinepres = 'y'; $sampcol = 6; $chromocol = 7; $startcol = 8; $stopcol = 9; $typecol = 12; $algoname = 17; $rarecol = 19; $onecol = 22; $snpcol = 23;
}
&ppv_estimate($input, $output);
} elsif ($second_hit){
&headshow ($ARGV[0]) unless ($headlinepres =~ /[yn]/i and $chromocol =~ /\d+/ and $startcol =~ /\d+/ and $stopcol =~ /\d+/ and $genecol =~ /\d+/);
&chrcol;&startcol;&stopcol;&genecol;
&second_hit ($ARGV[0], $ARGV[1]);
} elsif ($sort_snp) {
&init_sort_snp($forker) == 1 or die;
} elsif ($monitor_pbs) {
&monitor_pbs or die;
} elsif ($submit_batch) {
&submit_batch ($ARGV[0]) or die;
} elsif ($loci_find) {
&loci_find ($ARGV[0]) or die;
} elsif ($fr_sum_all) {
&init_fr_sum($forker) == 1 or die "Failed to finish init_fr_sum. Check the logs to determine the error.\n";
#&fr_sum_part_a or die "$!\n";
} elsif ($fr_sum_b) {
&fr_sum_part_b($ARGV[0]) or die "$!\n";
} elsif ($fr_sum_c) {
&fr_sum_part_c or die "$!\n";
} elsif ($fr_sum_d) {
&fr_sum_part_d or die "$!\n";
} else {
print "No recognised option\n";
}
###############################################################################
############### --frsum ###############
###############################################################################
#Summary of LogR and BAF metrics in Final Reports
sub init_fr_sum {
system("mkdir 08_FRSum") == 0 or die "Unable to create 08_FRSum: $?\n";
my $forker = shift;
# Stage 1 --chiperror
# Run the chiperror routine in cluster mode for specific sample
if ($cluster){
&fr_sum_guts($samplename);
}
# Submit all samples for analysis in cluster mode
elsif ($processors =~ /clust/){
print LOG1 showtime(),"\tFR_Summary\tINFO\tSummarizing FinalReport data across mutliple samples\n";
print showtime()," Summarizing FinalReport data across mutliple samples\n";
#Load pedfile
open my $ped_fh,'<',$pedfile or die "Cannot open pedfile $pedfile: $!";
my @peds;
while (<$ped_fh>) {
s/[\r\n]+$//;
push @peds, $_;
}
print "Loading pedfile data\n";
my ($pedfile, $family_member, $which_family, $which_mother, $which_father,
$which_child, $which_sibling, $which_gender, $gendername, $which_phenotype,
$namepheno) = &propedfile(@peds);
my %which_gender = %$which_gender;
#Load FinalReport names
print "Loading FinalReport names\n";
my ($fr_list, $hash_ref1, $hash_ref2, $hash_ref3) = &quick_fr_list($data_dir);
my @fr_list = @$fr_list;
my %frtochip = %$hash_ref1;
my %chiptofr = %$hash_ref2;
my %chiptoline = %$hash_ref3;
#Identify Final Reports
my (@frtosum, @filelist);
my $sampcount == 0;
my $outcount == 0;
print "Assigning FinalReport to batches of 50\n";
foreach my $samp (keys %which_gender){
$sampcount++;
my $fr = $chiptofr{$samp};
$fr =~ s/[\r\n]//g;
#print "Samp: $samp, FR: $chiptofr{$samp}, FR2: $fr, end\n";
push @frtosum, $fr;
if ($sampcount >= 50){
$outcount = sprintf("%04d", $outcount + 1);
my $output = $outcount.'_'.${tag}."_Summary_List.txt";
open OUT ,'>', $output or die "Could not open $output\n$!";
push @filelist, $output;
my $printout = join "\n", @frtosum;
print OUT $printout;
close OUT;
@frtosum = ();
$sampcount = 0;
}
}
$outcount = sprintf("%04d", $outcount + 1);
my $output = $outcount.'_'.${tag}."_Summary_List.txt";
open OUT ,'>', $output or die "Could not open $output\n$!";
push @filelist, $output;
my $printout = join "\n", @frtosum;
print OUT $printout;
print "There are $outcount batches\n";
my $mainshellname = $data_dir.$dir_sep."${tag}_FRSum.sh";
my (@submitme, $inputhere, @submitter);
my $sampcount = 0;
open SH, '>', $mainshellname or die "> file: $!\n";
foreach my $file (@filelist){
$sampcount++;
$inputhere = "source ~/.bashrc; cd $data_dir$dir_sep; perl $progname --frsum --tag $tag --clust --samp $file; ";
push @submitme, $inputhere;
print SH $inputhere."\n";
}
my $jobtag = 'FRSum_'.$tag;
print "Running a batch file of jobs: $timeanddate\n";
print LOG1 showtime(),"\t$jobtag\tINFO\tRunning the batch file $mainshellname\n";
my $shellname = "PBS_".$jobtag.".sh"; #Shell script name
my $jobname = $jobtag; #Job name
push (@submitter, $shellname, $jobname, 8, $jobtag);
push (@submitter, @submitme);
my $return = &submitter(@submitter);
print LOG1 showtime(),"\t$jobtag\t$return";
}
# Submit all samples for analysis to multiple processors on the same node/computer
elsif ($processors =~ /\d+/){
print LOG1 showtime(),"\tFR_Summary\tINFO\tSummarizing FinalReport data across mutliple samples\n";
print showtime()," Summarizing FinalReport data across mutliple samples\n";
#Load pedfile
open my $ped_fh,'<',$pedfile or die "Cannot open pedfile $pedfile: $!";
my @peds;
while (<$ped_fh>) {
s/[\r\n]+$//;
push @peds, $_;
}
print "Loading pedfile data\n";
my ($pedfile, $family_member, $which_family, $which_mother, $which_father,
$which_child, $which_sibling, $which_gender, $gendername, $which_phenotype,
$namepheno) = &propedfile(@peds);
my %which_gender = %$which_gender;
#Load FinalReport names
print "Loading FinalReport names\n";
my ($fr_list, $hash_ref1, $hash_ref2, $hash_ref3) = &quick_fr_list($data_dir);
my @fr_list = @$fr_list;
my %frtochip = %$hash_ref1;
my %chiptofr = %$hash_ref2;
my %chiptoline = %$hash_ref3;
#Identify Final Reports
my (@frtosum, @filelist);
my $sampcount == 0;
my $outcount == 0;
print "Assigning FinalReport to batches of 50\n";
foreach my $samp (keys %which_gender){
$sampcount++;
my $fr = $chiptofr{$samp};
$fr =~ s/[\r\n]//g;
#print "Samp: $samp, FR: $chiptofr{$samp}, FR2: $fr, end\n";
push @frtosum, $fr;
if ($sampcount >= 50){
$outcount = sprintf("%04d", $outcount + 1);
my $output = $outcount.'_'.${tag}."_Summary_List.txt";
open OUT ,'>', $output or die "Could not open $output\n$!";
push @filelist, $output;
my $printout = join "\n", @frtosum;
print OUT $printout;
close OUT;
@frtosum = ();
$sampcount = 0;
}
}
$outcount = sprintf("%04d", $outcount + 1);
my $output = $outcount.'_'.${tag}."_Summary_List.txt";
open OUT ,'>', $output or die "Could not open $output\n$!";
push @filelist, $output;
my $printout = join "\n", @frtosum;
print OUT $printout;
print "There are ".($outcount+0)." batches\n";
# start threads for batch of files assigned to a given proc
my @batches = &get_batches($processors, @filelist);
foreach my $batch (@batches) {
my $pid = $forker->start and next;
#print "$batch\n";
&fr_sum( @$batch );
$forker->finish;
}
# wait for all threads to complete
$forker->wait_all_children;
}
unless ($cluster){
print "Making master summary\n";
#Combine
&fr_sum_part_c;
#Summarize
&fr_sum_part_d;
}
}
sub fr_sum {
# List of files to process
my @files = @_;
# process each file for errors
foreach my $filename (@files) {
&fr_sum_guts($filename);
}
}
sub fr_sum_guts {
my ($input) = @_;
open IN, $input or die "Could not open $input\n$!";
$input =~ /(\d+)_\w+_Summary_List.txt/;
my $output1 = $1.'_'.${tag}."_Summary_Info.txt";
open OUT1, '>', $output1 or die "Could not open $output1\n$!";
print "Printing to $output1\n";
my @frtosum = <IN>; chomp @frtosum;
#Get data from FRs
my (%logr, %bafr, $frcount);
foreach my $fr (@frtosum){
$frcount++;
print "$frcount) Doing FR $fr\n";
open FR, '<', $fr or die "Could not open the $fr: $!";
while (($_ = <FR>) !~ /\[Data\]/) {}
chomp (my $colheader = <FR>);
# Update Final Report column numbers for this file
&fr_columns($colheader);
#Counts the number of SNPs per chromosome and the number that are 'bad'
while (<FR>) {
s/[\r\n]+$//g;
my @tabs = split /\t/, $_;
if ($tabs[$log2col] =~ /\d+/){
$logr{$tabs[$snpcol]} .= $tabs[$log2col].',';
} else {
$logr{$tabs[$snpcol]} .= 'NC,';
}
if ($tabs[$ballele] =~ /\d+/){
$bafr{$tabs[$snpcol]} .= $tabs[$ballele].',';
} else {
$bafr{$tabs[$snpcol]} .= 'NC,';
}
}
close FR;
}
print "Summarizing and printing output\n";
#Process and print out
foreach my $snp (keys %logr){
my $templogr = $logr{$snp};
my $tempbafr = $bafr{$snp};
print OUT1 $snp."\t".$templogr."\t".$tempbafr."\n";
}
close OUT1;
}
#Combine files
sub fr_sum_part_c {
my $search = '_'.${tag}."_Summary_Info.txt";
my @files = split /\n/, `ls *$search`;
my $filecount = @files;
my $output = $sum_dir.$dir_sep.'All_'.${tag}."_Summary_Data.txt";
open OUT, '>', $output or die "Could not open $output: $!\n";
print OUT "SNP\tLogR\tBAF\n";
#Get the number of lines
open IN, $files[0] or die "Could not open first file: $files[0]: $!\n";
my $counter = 0;
while (<IN>){
$counter++;
}
close IN;
print "Found $filecount files and $counter SNPs\n";
#Open the files
my %fh;
foreach my $file (@files){
open my $fh, $file or die "Could not open $file: $!\n";
$fh{$file} = $fh;
}
#Go through the lines
my $snpcount = 0;
foreach my $snp (1..$counter){
$snpcount++;
if ($snpcount % 100000 == 0){
print "Doing SNP $snpcount\n";
}
my $thissnp = 'FirstFileSNP';
my ($field1, $field2);
#go through the files
foreach my $file (@files){
my $fh = $fh{$file};
my $line = &read_file_line($fh);
#print "File: $file; Line: $line\n";
my @tab = split /\t/, $line;
if ($thissnp eq 'FirstFileSNP') {
$thissnp = $tab[0];
$field1 = $tab[1];
$field2 = $tab[2];
} elsif ($thissnp eq $tab[0]) {
$field1 .= $tab[1];
$field2 .= $tab[2];
} else {
print "Error: mismatch in SNPs for file $file: Observed: $thissnp, Expected: $tab[0]\n";
}
}
print OUT $thissnp."\t".$field1."\t".$field2."\n";
}
close OUT;
print "All data combined\n";
}
#Summarize files
sub fr_sum_part_d {
my $input = $sum_dir.$dir_sep.'All_'.${tag}."_Summary_Data.txt";
open IN, $input or die "Could not open $input\n$!";
my $ouput1 = $sum_dir.$dir_sep.'All_'.${tag}."_Summary_Results.txt";
open OUT1, '>', $ouput1 or die "Could not open $ouput1\n$!";
print OUT1 "SNP\tLogR_Mean\tLogR_StDev\tLogR_Median\tLogR_Max\tLogR_Min\tLogR_Conf\tLogR_NoCall\tLogR_Count\tAA\tAAB\tAB\tABB\tBB\tother\tNC\tBAF_Count\n";
print "Summarizing the data\n";
my %baf;
while (my $line = <IN>){
if ($. % 100000 == 0){
print "Doing SNP $.\n";
}
my @tab = split /\t/, $line;
my $snp = $tab[0];
#Remove the last comma
chop $tab[1];
chop $tab[2];
#LogR
my @logr = split /\,/, $tab[1];
my @logtemp = ();
my ($nccount, $lc, $bc) = (0,0,0);
foreach my $log (@logr){
if ($log !~ /\d+/){
$nccount++;
}else {
push @logtemp, $log;
}
$lc++;
}
my $logrref = \@logtemp;
my ($logrmean, $logrstdev, $logrmedian, $logrmax, $logrmin, $logrconf) = &meanmedianstdevconf($logrref);
#BAF
my @baf = split /\,/, $tab[2];
foreach my $baf (@baf){
if ($baf !~ /\d+/){
$baf{$snp}{'NC'} += 1;
} elsif ($baf <= 0.1 and $baf >= 0){
$baf{$snp}{'AA'} += 1;
} elsif ($baf >= 0.9 and $baf <= 1){
$baf{$snp}{'BB'} += 1;
} elsif ($baf >= 0.42 and $baf <= 0.58){
$baf{$snp}{'AB'} += 1;
} elsif ($baf >= 0.6 and $baf <= 0.75){
$baf{$snp}{'ABB'} += 1;
} elsif ($baf <= 0.4 and $baf >= 0.25){
$baf{$snp}{'AAB'} += 1;
} elsif ($baf =~ /\d+/){
$baf{$snp}{'other'} += 1;
} else {
print "New BAF output: $baf\n";
}
$bc++;
}
my $bafout = join "\t", ($baf{$snp}{'AA'}+0), ($baf{$snp}{'AAB'}+0), ($baf{$snp}{'AB'}+0), ($baf{$snp}{'ABB'}+0), ($baf{$snp}{'BB'}+0), ($baf{$snp}{'other'}+0), ($baf{$snp}{'NC'}+0), $bc;
my $out = join "\t", $snp, $logrmean, $logrstdev, $logrmedian, $logrmax, $logrmin, $logrconf, $nccount, $lc, $bafout;
print OUT1 $out."\n" if ($. > 1);
}
close OUT1;
print "Done!\n";
}
#Get next line from filehandle
sub read_file_line {
my ($fh) = @_;
#Get the next line
if ($fh and my $line = <$fh>){
$line =~ s/[\n\r\"]//g;
return ($line);
}
return;
}
#Converts genomic regions to non-overlapping loci
sub loci_find {
#open the reference input file
my ($input1) = @_;
print "Opening input file: $input1\n";
open LOCI, $input1 or die "Could not open file $input1: $!\n";
{ local $/= undef; our $input = <LOCI>; }
close LOCI;
(local $\) = (/(\r\n|\r|\n)/);
my @loci = split (/\r\n|\r|\n/, our $input); chomp @loci;
my @inputbits = split /$dir_sep/, $input1;
my $filename = pop @inputbits;
@inputbits = split /$dir_sep/, $data_dir if (scalar @inputbits < 1);
my $directory = (join "/", @inputbits).'/' if (scalar @inputbits >= 1);
#$output =~ s/$curr_dir//gi;
my $output = $directory.'Loci_'.$filename;
open OUT, '>', $output or die "Could not open file $output: $!\n";
my @lineshow = split /\t/, $loci[0];
my $linecount;
foreach my $line (@lineshow){
$linecount++;
print $linecount.') '.$line."\n";
}
########################################################
#Merge prog Output file
print "\nWhich column is the chromosome number in (0, 1, 2, etc)?\n";
my $user_chrome = <STDIN>; chomp $user_chrome; my $chromo = $user_chrome - 1;
print "\nWhich column is the region start co-ordinate in (0, 1, 2, etc)?\n";
my $user_start = <STDIN>; chomp $user_start; my $start = $user_start - 1;
print "\nWhich column is the region end co-ordinate in (0, 1, 2, etc)?\n";
my $user_stop = <STDIN>; chomp $user_stop; my $stop = $user_stop - 1;
#print "$lineshow[$chromo]\t$lineshow[$start]\t$lineshow[$stop]\n";
print "Sorting file by chromosome and number\n";
#Sort by Start (numbers)
@loci = sort { (split '\t', $a)[$start] <=> (split '\t', $b)[$start] } @loci;
#Sort by Chromosome (string)
@loci = sort { (split '\t', lc $a)[$chromo] cmp (split '\t', lc $b)[$chromo] } @loci;
#print @loci;
print "Looking for loci\n";
my ($tracker, $maxbase) = (0,0);
my (@match, $count);
foreach my $loci (@loci){
my @before = split /\t/, $loci[$tracker - 1];
my @now = split /\t/, $loci[$tracker];
my @after = split /\t/, $loci[$tracker + 1];
$tracker++;
#If this CNV is from a differet chromosome or if it does not overlap with the last CNV or maxbase then start a new set
if (lc $now[$chromo] ne lc $before[$chromo]
or ($now[$start] > $before[$stop]
and $now[$start] > $maxbase)){
$maxbase = 0;
@match = ();
push @match, $loci;
}
#If it is the same chromosome and this CNV overlaps with the last or with maxbase
elsif (lc $now[$chromo] eq lc $before[$chromo]
and ($now[$start] <= $before[$stop]
or $now[$start] <= $maxbase)){
#All matches get put into an array called @match
push @match, $loci;
}
#If this CNV does not overlap with the next CNV then @match is processed
if (lc $now[$chromo] ne lc $after[$chromo]
or ($now[$stop] < $after[$start]
and $maxbase < $after[$start])
or $after[$start] == ""){
#Process @match
$count++;
my (%bps, $chrm);
foreach my $match (@match){
my @bp = split /\t/, $match;
$bps{$bp[$start]} = 0;
$bps{$bp[$stop]} = 0;
$chrm = $bp[$chromo];
}
my @bps = sort {$a <=> $b} keys %bps;
print OUT $chrm."\t".$bps[0]."\t".$bps[-1]."\n";
}
#Makes Maxbase the highest it can be
if ($now[$stop] > $maxbase){
$maxbase = $now[$stop];
}
}
print "Found $count loci\n";
}
#Find overlapping transmitted variants from a list of de novo variants
sub second_hit {
my ($input1, $input2) = @_;
open IN1, '<', $input1 or die "Could not open file $input1: $!\n";
open IN2, '<', $input2 or die "Could not open file $input2: $!\n";
my $output = '2nd_'.$input1;
open OUTPUT, '>', $output or die "Could not open file $output: $!\n";
my $linecount = 0;
my (%chrplace, %gene);
#Load initial regions;
while (my $line = <IN1>){
$line =~ s/\n|\r|\n\r|\r\n//g;
$line =~ s/\"|^, //g;
my @tab = split /\t/, $line;
$linecount++;
my $chr_place_ref = $chrplace{$tab[$chromocol]};
#unless ( defined %$chr_place_ref ){
unless ( %$chr_place_ref ){
my %hash;
$chrplace{$tab[$chromocol]} = \%hash;
$chr_place_ref = $chrplace{$tab[$chromocol]};
}
$gene{$tab[$genecol]} .= $linecount.',';
$$chr_place_ref{$tab[$startcol]."\t".$tab[$stopcol]} .= $linecount.',';
}
($chromocol, $startcol, $stopcol, $genecol) = ('a','a','a','a');
our $loccol;
&headshow ($input2);
&chrcol;
&startcol;
&stopcol;
&genecol;
&loccol;
my $vcount = 0;
#Look for second hits in the next file
while (my $line = <IN2>){
$line =~ s/\n|\r|\n\r|\r\n//g;
$line =~ s/\"|^, //g;
if ($. == 1){
print OUTPUT "DN_line\t$line\n";
next;
}
my @tab = split /\t/, $line;
my $chrref = $chrplace{$tab[$chromocol]};
my $size = $tab[$stopcol] - $tab[$startcol];
#Look for match genes
if ($gene{$tab[$genecol]} =~ /\d+/ and $tab[$loccol] =~ /Exon/i){
print OUTPUT $gene{$tab[$genecol]}."\t".$line."\n";
$vcount++;
next;
}
#Look for 50% mutual overlap
foreach my $key (keys %$chrref){
my @tabdn = split /\t/, $key;
my $sizedn = $tabdn[1] - $tabdn[0];
#Before or after
unless ($tab[$startcol] > ($tabdn[1] - $sizedn/2) or $tab[$stopcol] < ($tabdn[0] + $sizedn/2)){
my @start = sort {$a <=> $b} ($tabdn[0], $tab[$startcol]);
my @stop = sort {$a <=> $b} ($tabdn[1], $tab[$stopcol]);
my $minsize = $stop[0] - $start[1];
if ($minsize >= $size/2 and $minsize >= $sizedn/2){
print OUTPUT $$chrref{$key}."\t".$line."\n";
$vcount++;
last;
}
}
#print "K: $key, V: $$chrref{$key}\n";
}
}
print "All done! Found $vcount matches\n";
}
###############################################################################
############### --ppv ###############
###############################################################################
#PPV estimate
sub ppv_estimate {
my ($input, $output) = @_;
print "Opening CNV file: $input\n";
open INPUT, '<', $input or die "Could not open file $input: $!\n";
print "Opening output file: $output\n";
open OUTPUT, '>', $output or die "Could not open file $output: $!\n";
my $headers = "PPV\tConfidence\tSNP_Density";
my (%locicount, %hclocicount, %locisize, %hclocisize);
$. = 0;
while (my $line=<INPUT>){
$line =~ s/\n|\r|\n\r|\r\n//g;
my @tab = split (/\t/, $line);
my ($ppv, $conf);
#print "Samp: $tab[$sampcol], Chr: $tab[$chromocol], St: $tab[$startcol], Sp: $tab[$stopcol], Type: $tab[$typecol], Alg: $tab[$algoname], %One: $tab[$onecol], SNP: $tab[$snpcol]\n";
if ($headlinepres =~ /y/i and $. == 1){
print OUTPUT $headers."\t".$line."\n";
}
else {
#Sort out the XTR region
if ($tab[$chromocol] =~ /X/i and $tab[$gendercol] eq 'Male' and $tab[$startcol] <= 92429752 and $tab[$stopcol] >= 88343459){
$ppv = '0%'; $conf = 'Low';
}
#three algo, one percent less than 50%
elsif ($tab[$algoname] =~ /GN/ and $tab[$algoname] =~ /PN/ and $tab[$algoname] =~ /QT/ and $tab[$onecol] < 50){
$ppv = '95%'; $conf = 'High';
}
#three algo, one percent >= 50%
elsif ($tab[$algoname] =~ /GN/ and $tab[$algoname] =~ /PN/ and $tab[$algoname] =~ /QT/ and $tab[$onecol] >= 50){
$ppv = 'untested (?45%)'; $conf = 'Low';
}
#two algo PNQT, one percent less than 50%
elsif ($tab[$algoname] =~ /PN/ and $tab[$algoname] =~ /QT/ and $tab[$onecol] < 50){
$ppv = '85%'; $conf = 'High';
}
#two algo PNQT, one percent >= 50%
elsif ($tab[$algoname] =~ /PN/ and $tab[$algoname] =~ /QT/ and $tab[$onecol] >= 50){
$ppv = 'untested (?40%)'; $conf = 'Low';
}
#two algo GNQT, one percent less than 50 and not a dup%
elsif ($tab[$algoname] =~ /GN/ and $tab[$algoname] =~ /QT/ and $tab[$onecol] < 50 and $tab[$typecol] !~ /3|4/){
$ppv = '60%'; $conf = 'Low';
}
#two algo GNQT, one percent >= 50% and not a dup
elsif ($tab[$algoname] =~ /GN/ and $tab[$algoname] =~ /QT/ and $tab[$onecol] >= 50 and $tab[$typecol] !~ /3|4/){
$ppv = 'untested (?30%)'; $conf = 'Low';
}
#two algo GNQT, dup
elsif ($tab[$algoname] =~ /GN/ and $tab[$algoname] =~ /QT/){
$ppv = '0%'; $conf = 'Low';
}
#two algo GNPN, one percent less than 50 and not a dup%
elsif ($tab[$algoname] =~ /GN/ and $tab[$algoname] =~ /PN/ and $tab[$onecol] < 50){
$ppv = '60%'; $conf = 'Low';
}
#two algo GNPN, one percent >= 50% and not a dup
elsif ($tab[$algoname] =~ /GN/ and $tab[$algoname] =~ /PN/ and $tab[$onecol] >= 50){
$ppv = 'untested (?30%)'; $conf = 'Low';
}
#one algo GN, and not a dup%
elsif ($tab[$algoname] =~ /GN/ and $tab[$typecol] !~ /3|4/){
$ppv = '25%'; $conf = 'Low';
}
#one algo GN, dup
elsif ($tab[$algoname] =~ /GN/){
$ppv = '0%'; $conf = 'Low';
}
#one algo QT, dup
elsif ($tab[$algoname] =~ /QT/ and $tab[$typecol] =~ /3|4/ and $tab[$typecol] !~ /0|1|2/){
$ppv = '60%'; $conf = 'Low';
}
#one algo QT, not a dup
elsif ($tab[$algoname] =~ /QT/){
$ppv = '30%'; $conf = 'Low';
}
#one algo PN
elsif ($tab[$algoname] =~ /PN/){
$ppv = '40%'; $conf = 'Low';
}
#All other scenarios...
else{
$ppv = 'Error'; $conf = 'Error';
print $tab[$algoname]."\t".$tab[$onecol]."\n";
}
my $size = $tab[$stopcol] - $tab[$startcol];
my $dense = sprintf ("%.0f", eval { $size / $tab[$snpcol] } + 0 );
#Final Correction
if ($conf eq 'High' and $tab[$snpcol] >= 100 and $dense < 7000 and $tab[$rarecol] > 80){
$ppv = "100%";
}
$locicount{$tab[$sampcol]}++;
$hclocicount{$tab[$sampcol]}++ if ($conf eq 'High');
$locisize{$tab[$sampcol]} += $size;
$hclocisize{$tab[$sampcol]} += $size if ($conf eq 'High');
print OUTPUT $ppv."\t".$conf."\t".$dense."\t".$line."\n";
}
}
&add_sample_col('PPV Loci');
my @result_cols = ('PPV Loci', 'PPV HC Loci', 'PPV Loci Size', 'PPV HC Loci Size' );
foreach my $col (@result_cols) {
&add_sample_col($col);
}
my $totalsamples = keys %locicount;
my $samplecounter = 0;
foreach my $samp (sort keys %sample_idx) {
my $lociout = $locicount{$samp} + 0;
my $hclociout = $hclocicount{$samp} + 0;
my $sizeout = $locisize{$samp} + 0;
my $hcsizeout = $hclocisize{$samp} + 0;
&set_sample_value($samp, 'PPV Loci', $lociout);
&set_sample_value($samp, 'PPV HC Loci', $hclociout);
&set_sample_value($samp, 'PPV Loci Size', $sizeout);
&set_sample_value($samp, 'PPV HC Loci Size', $hcsizeout);
if ($lociout){
$samplecounter++;
} else {
print LOG1 &showtime(),"\tPPV\tERROR\tNo loci present for $samp\n";
print "ERROR: No loci present for $samp\n";
}
}
if ($samplecounter == $totalsamples){
print LOG1 &showtime(),"\tPPV\tINFO\tSummary track complete for $totalsamples samples\n";
print "PPV complete for $totalsamples samples\n";
} else {
print LOG1 &showtime(),"\tPPV\tERROR\tSummary track complete, however loci were present for samples that were not listed in the Samplelist file\n";
print "ERROR: PPV complete, however loci were present for samples that were not listed in the Samplelist file, $totalsamples, $samplecounter\n";
}
}
###############################################################################
############### --plot ###############
###############################################################################
#Make images of CNVs
sub plot_cnv {
my ($input, $orderedsnps) = @_;
print "Opening co-ordinates file: $input\n";
open INPUT, '<', $input or die "Could not open file $input: $!\n";
my $output2 = $image_dir.$dir_sep.'R_input_'.$input;
open ROUT, '>', $output2 or die "Could not open file $output2: $!\n";
#Load pedfile
open PED,'<',$pedfile or die "Cannot open file $pedfile: $!";
{ local $/= undef; our $input = <PED>; }
close PED;
(local $\) = (/(\r\n|\r|\n)/);
my @peds = split (/\r\n|\r|\n/, our $input); chomp @peds;
print "Loading pedfile data\n";
my ($pedfile, $family_member, $which_family, $which_mother, $which_father,
$which_child, $which_sibling, $which_gender, $gendername, $which_phenotype,
$namepheno) = &propedfile(@peds);
my %which_gender = %$which_gender;
#Load chromosome arrays
print "Loading SNP arrays\n";
&snp_array("$working_dir$dir_sep${tag}_".$chip_type."_Sort_List.txt");
#Load FinalReport names
print "Loading FinalReport names\n";
my ($fr_list, $hash_ref1, $hash_ref2, $hash_ref3) = &fr_list($data_dir);
my ($counter, $sampcount) = (0,0);
my (@sample, $lastsamp);
#Splits the file into samples and sends an array per sample to the sampledeal subroutine
print "Generating input data for images\n";
while (my $region = <INPUT>){
#print $region;
$region =~ s/\n|\r|\n\r|\r\n//g;
if ($headlinepres =~ /y/i and $. == 1){
}
else {
my @thisone = split /\t/, $region;
#print "This: $thisone[$sampcol], Last: $lastsamp\n";
if (defined $lastsamp && $thisone[$sampcol] ne $lastsamp){
$sampcount++;
my $gender = $which_gender{$lastsamp};
print "Assessing sample $sampcount: $lastsamp \n";
&sampledeal_plot(\@sample, $lastsamp, $which_phenotype, $which_family, $which_mother, $which_father, $which_sibling, $hash_ref2, $gender);
@sample = $region;
}
else {
push (@sample, $region);
}
$lastsamp = $thisone[$sampcol];
}
}
my $gender = $which_gender{$lastsamp};
print "Assessing sample $sampcount: $lastsamp \n";
&sampledeal_plot(\@sample, $lastsamp, $which_phenotype, $which_family, $which_mother, $which_father, $which_sibling, $hash_ref2, $gender);
print "\nAll done\n";
}
#The sample may be either a child or a parent
sub sampledeal_plot{
my ($samparray, $sample, $which_phenotype, $which_family, $which_mother, $which_father, $which_sibling, $hash_ref2, $thegenderofsample) = @_;
#print "$samparray, $sample, $which_phenotype, $which_family, $which_mother, $which_father, $which_sibling, $hash_ref2, $thegenderofsample\n";
my $phenotype = $$which_phenotype{$sample};
my $family = $$which_family{$sample};
my $father = $$which_father{$sample};
my $mother = $$which_mother{$sample};
my @siblings = split /,/, $$which_sibling{$sample};
#print "Samp: $sample, Sibs: $$which_sibling{$sample}\n";
#print "S: ${sample}, P: ${phenotype}, F: ${family}, Fa: $father, Mo: $mother, Sib: $siblings[0]\n";
#Load FinalReport data for the family
my $case_fr_file = $$hash_ref2{$sample};
#print "opening $case_fr_file for $sample\n";
open FR1, '<', $case_fr_file or die "Could not open file $case_fr_file: X $!\n";
my @case_fr = <FR1>;
close FR1;
my (@fat_fr, @mot_fr, @sib_fr1, @sib_fr2, @sib_fr3);
my $fat_fr_file = $$hash_ref2{$father};
my $mot_fr_file = $$hash_ref2{$mother};
my $sib_fr1_file = $$hash_ref2{$siblings[0]};
my $sib_fr2_file = $$hash_ref2{$siblings[1]};
my $sib_fr3_file = $$hash_ref2{$siblings[2]};
#print "FRP: $case_fr_file, FRF: $fat_fr_file, FRM: $mot_fr_file, FRS: $sib_fr_file\n";
open FR2, '<', $fat_fr_file or die "A Could not open file $fat_fr_file: $!\n" unless ($father eq 0 or $father !~ /\w+/);
@fat_fr = <FR2>;
close FR2;
open FR3, '<', $mot_fr_file or die "B Could not open file $mot_fr_file: $!\n" unless ($mother eq 0 or $mother !~ /\w+/);
@mot_fr = <FR3>;
close FR3;
open FR4, '<', $sib_fr1_file or die "C Could not open file $sib_fr1_file: $!\n" unless ($siblings[0] eq 0 or $siblings[0] !~ /\w+/);
@sib_fr1 = <FR4>;
close FR4;
open FR5, '<', $sib_fr2_file or die "C Could not open file $sib_fr2_file: $!\n" unless ($siblings[1] eq 0 or $siblings[1] !~ /\w+/);
@sib_fr2 = <FR5>;
close FR5;
open FR6, '<', $sib_fr3_file or die "C Could not open file $sib_fr3_file: $!\n" unless ($siblings[2] eq 0 or $siblings[2] !~ /\w+/);
@sib_fr3 = <FR6>;
close FR6;
my ($sibpresent1, $sibpresent2, $sibpresent3, $motpresent, $fatpresent) = (0,0,0,0,0);
$sibpresent1 = 1 if ($siblings[0] =~ /\w+/ and $siblings[0] ne '0');
$sibpresent2 = 1 if ($siblings[1] =~ /\w+/ and $siblings[1] ne '0');
$sibpresent3 = 1 if ($siblings[2] =~ /\w+/ and $siblings[2] ne '0');
$motpresent = 1 if ($mother =~ /\w+/ and $mother ne '0');
$fatpresent = 1 if ($father =~ /\w+/ and $father ne '0');
#print "$sibpresent1, $sibpresent2, $sibpresent3, $motpresent, $fatpresent, F: $father\n";
my ($linecount, %lines, @output);
foreach my $line (@$samparray){
#print $line."\n";
my @tab = split /\t/, $line;
#Identify expanded region
my $margin = 35000 + ($tab[$stopcol] - $tab[$startcol])/3;
my ($snpcount, @lines) = &dandcdn ($tab[$chromocol], $tab[$startcol] - $margin, $tab[$stopcol] + $margin);
my $output;
#print "$tab[$chromocol]:$tab[$startcol]-$tab[$stopcol] has $snpcount SNPs\n";
my ($printout, $min, $max) = &getdata_plot ($fatpresent, $motpresent, $sibpresent1, $sibpresent2, $sibpresent3, \@lines, \@case_fr, \@fat_fr, \@mot_fr, \@sib_fr1, \@sib_fr2, \@sib_fr3);
my $output = $rin_dir.$dir_sep.$tab[$chromocol].'_'.$tab[$startcol].'_'.$tab[$stopcol].'_Fam_'.$family.'_'.$sample.'.txt';
my $routput = $image_dir.$dir_sep.$tab[$chromocol].'_'.$tab[$startcol].'_'.$tab[$stopcol].'_Fam_'.$family.'_'.$sample.'.pdf';
open OUTPUT, '>', $output or die "Could not open file $output: $!\n";
print OUTPUT "Pos\tCaB\tCaL\tFaB\tFaL\tMoB\tMoL\tS1B\tS1L\tS2B\tS2L\tS3B\tS3L\n";
my $lineout;
foreach my $outline (@$printout){
#print "Out: $outline\n";
print OUTPUT $outline."\n";
$lineout++;
}
#Set Y axis limits
my $ylimit;
if ($min == -5){$ylimit = -4.5;} else {$ylimit = $min - 0.25;}
#Set dot size
my $cex;
if ($lineout <= 40){$cex = 1;}
elsif ($lineout <= 250){$cex = 0.7;}
else {$cex = 0.4;}
#Extra horizontal lines
my $abextra = ',-4' if ($sibpresent2 == 1);
my $abextra = ',-5' if ($sibpresent3 == 1);
#Set X axis limits
my $xstart = ($tab[$startcol] - $margin) / 1000000;
my $xstop = ($tab[$stopcol] + $margin) / 1000000;
my $tstart = $tab[$startcol] / 1000000;
my $tstop = $tab[$stopcol] / 1000000;
#Correct dashes for 'R'
if ($operating_system eq 'Windows') {
#print "Dashing\n";
$data_dir =~ s/\\/\//g;
$output =~ s/\\/\//g;
$routput =~ s/\\/\//g;
}
#generate R code
print ROUT 'x <- read.delim("'.$data_dir.'/'.$output.'")'."\n";
print ROUT 'pdf("'.$data_dir.'/'.$routput.'")'."\n";
print ROUT 'plot(1,1,xlim=c('.$xstart.','.$xstop.'),ylim=range('.$ylimit.',1.5),type="n",xlab="Position (Mb) on '.$tab[$chromocol].'",ylab="Relative logR",axes=FALSE, main="Family: '.$family.', Sample: '.$sample.' LogR")'."\n"; #Start a new graph
print ROUT 'abline(h=c(0,-1,-2,-3'.$abextra.'),v=c('.$tstart.','.$tstop.'))'."\n";
#print ROUT 'axis(side=1,at=c('.$midplaces.'),labels=c('.$sevlabel.'),cex.axis=0.8, tcl=0.25)'."\n"; #X-axis
print ROUT 'axis(side=2,at=0:-3, labels=c("Case","Father","Mother","Sibling1"))'."\n"; #Y-axis
print ROUT 'par(new=T)'."\n";
print ROUT 'plot(x$CaL~x$Pos, ylim=range('.$ylimit.',1.5), xlim=c('.$xstart.','.$xstop.'), col="red", pch=20, cex='.$cex.', yaxt="n", xlab="", ylab="")'."\n";
print ROUT 'par(new=T)'."\n" if ($fatpresent == 1);
print ROUT 'plot(x$FaL~x$Pos, ylim=range('.$ylimit.',1.5), xlim=c('.$xstart.','.$xstop.'), col="blue", pch=20, cex='.$cex.', yaxt="n", xlab="", ylab="")'."\n" if ($fatpresent == 1);
print ROUT 'par(new=T)'."\n" if ($motpresent == 1);
print ROUT 'plot(x$MoL~x$Pos, ylim=range('.$ylimit.',1.5), xlim=c('.$xstart.','.$xstop.'), col="hotpink", pch=20, cex='.$cex.', yaxt="n", xlab="", ylab="")'."\n" if ($motpresent == 1);
print ROUT 'par(new=T)'."\n" if ($sibpresent1 == 1);
print ROUT 'plot(x$S1L~x$Pos, ylim=range('.$ylimit.',1.5), xlim=c('.$xstart.','.$xstop.'), col="darkgreen", pch=20, cex='.$cex.', yaxt="n", xlab="", ylab="")'."\n" if ($sibpresent1 == 1);
print ROUT 'par(new=T)'."\n" if ($sibpresent2 == 1);
print ROUT 'plot(x$S2L~x$Pos, ylim=range('.$ylimit.',1.5), xlim=c('.$xstart.','.$xstop.'), col="darkolivegreen", pch=20, cex='.$cex.', yaxt="n", xlab="", ylab="")'."\n" if ($sibpresent2 == 1);
print ROUT 'par(new=T)'."\n" if ($sibpresent3 == 1);
print ROUT 'plot(x$S3L~x$Pos, ylim=range('.$ylimit.',1.5), xlim=c('.$xstart.','.$xstop.'), col="forestgreen", pch=20, cex='.$cex.', yaxt="n", xlab="", ylab="")'."\n" if ($sibpresent3 == 1);
#BAF
#print ROUT 'mtext(header,side=3)'."\n";
print ROUT 'par(mfrow=c(3,2), oma=c(0,0,2,0))'."\n";
print ROUT 'plot(x$CaB~x$Pos,col="red",pch=20, cex='.$cex.',xlim=c('.$xstart.','.$xstop.'), ylim=range(0,1), xlab="Position (Mb) on '.$tab[$chromocol].'", ylab="Case", yaxp=c(0,1,2));abline(v=c('.$tstart.','.$tstop.'))'."\n";
print ROUT 'plot(x$FaB~x$Pos,col="blue",pch=20, cex='.$cex.',xlim=c('.$xstart.','.$xstop.'), ylim=range(0,1), xlab="Position (Mb) on '.$tab[$chromocol].'", ylab="Father", yaxp=c(0,1,2));abline(v=c('.$tstart.','.$tstop.'))'."\n" if ($fatpresent == 1);
print ROUT 'plot(x$MoB~x$Pos,col="hotpink",pch=20, cex='.$cex.',xlim=c('.$xstart.','.$xstop.'), ylim=range(0,1), xlab="Position (Mb) on '.$tab[$chromocol].'", ylab="Mother", yaxp=c(0,1,2));abline(v=c('.$tstart.','.$tstop.'))'."\n" if ($motpresent == 1);
print ROUT 'plot(x$S1B~x$Pos,col="darkgreen",pch=20, cex='.$cex.',xlim=c('.$xstart.','.$xstop.'), ylim=range(0,1), xlab="Position (Mb) on '.$tab[$chromocol].'", ylab="Sibling1", yaxp=c(0,1,2));abline(v=c('.$tstart.','.$tstop.'))'."\n" if ($sibpresent1 == 1);;
print ROUT 'plot(x$S2B~x$Pos,col="darkolivegreen",pch=20, cex='.$cex.',xlim=c('.$xstart.','.$xstop.'), ylim=range(0,1), xlab="Position (Mb) on '.$tab[$chromocol].'", ylab="Sibling2", yaxp=c(0,1,2));abline(v=c('.$tstart.','.$tstop.'))'."\n" if ($sibpresent2 == 1);;
print ROUT 'plot(x$S3B~x$Pos,col="forestgreen",pch=20, cex='.$cex.',xlim=c('.$xstart.','.$xstop.'), ylim=range(0,1), xlab="Position (Mb) on '.$tab[$chromocol].'", ylab="Sibling3", yaxp=c(0,1,2));abline(v=c('.$tstart.','.$tstop.'))'."\n" if ($sibpresent3 == 1);;
print ROUT 'mtext("Family: '.$family.', Sample: '.$sample.' BAF", outer=TRUE, line=0)'."\n";
print ROUT 'dev.off()'."\n\n";
}
return (\@output);
#my @proband = &getlines($sample, \%lines, $hash_ref2);
}
#Subroutine of plot, retrieves lines from FR
sub getdata_plot {
my ($fatpresent, $motpresent, $sibpresent1, $sibpresent2, $sibpresent3, $lineref, $caseref, $fatref, $motref, $sib1ref, $sib2ref, $sib3ref) = @_;
my @lines = @$lineref;
my (@return, $max, $min);
foreach my $frline (@lines){
#print "Line: $frline, Out: $$caseref[$frline-1]\n";
$$caseref[$frline-1] =~ s/\n|\r|\n\r|\r\n//g;
$$fatref[$frline-1] =~ s/\n|\r|\n\r|\r\n//g;
$$motref[$frline-1] =~ s/\n|\r|\n\r|\r\n//g;
$$sib1ref[$frline-1] =~ s/\n|\r|\n\r|\r\n//g;
$$sib2ref[$frline-1] =~ s/\n|\r|\n\r|\r\n//g;
$$sib3ref[$frline-1] =~ s/\n|\r|\n\r|\r\n//g;
my @out;
push @out, (split /\t/,$$caseref[$frline-1],10)[$chromodist,$ballele,$log2col];
push @out, (split /\t/,$$fatref[$frline-1],10)[$ballele,$log2col];
push @out, (split /\t/,$$motref[$frline-1],10)[$ballele,$log2col];
push @out, (split /\t/,$$sib1ref[$frline-1],10)[$ballele,$log2col];
push @out, (split /\t/,$$sib2ref[$frline-1],10)[$ballele,$log2col];
push @out, (split /\t/,$$sib3ref[$frline-1],10)[$ballele,$log2col];
chomp @out;
$out[0] = $out[0] / 1000000;
$out[4] -= 1;
$out[6] -= 2;
$out[8] -= 3;
$out[10] -= 4;
$out[12] -= 5;
$min = $out[12] if ($min > $out[12]);
$max = $out[12] if ($max < $out[2]);
my $out = join "\t", @out;
#print $out."\n";
push (@return, $out);
}
return (\@return, $min, $max);
}
###############################################################################
############### --denovo3 ##############
###############################################################################
#Finds de novo CNVs, or visualises CNVs or finds further CNVs in the same area for other CNVs
sub denovo_raw_snp {
my ($input, $output, $orderedsnps) = @_;
#print "H: $headlinepres, S: $sampcol, Chr: $chromocol, Start: $startcol, Stop: $stopcol\n";
print "Opening co-ordinates file: $input\n";
open INPUT, '<', $input or die "Could not open file $input: $!\n";
print "Opening output file: $output\n";
open OUTPUT, '>', $output or die "Could not open file $output: $!\n";
#Load pedfile
open PED ,'<', $pedfile or die "Could not open $pedfile\n$!";
{ local $/= undef; our $input = <PED>; }
close PED;
(local $\) = (/(\r\n|\r|\n)/);
my @peds = split (/\r\n|\r|\n/, our $input); chomp @peds;
print "Loading pedfile data\n";
my ($pedfile, $family_member, $which_family, $which_mother, $which_father,
$which_child, $which_sibling, $which_gender, $gendername, $which_phenotype,
$namepheno) = &propedfile(@peds);
my %which_gender = %$which_gender;
#Adds headers depending on the output to the user quesiton above
my $headers = "SNPs\tTrio/Quartet\tResult\tType\tPat_Type\tMat_Type\tSib_Type\t%Paternal\t%Maternal\tMedian_LogR\tHomo/Het/Dup/Other\tPat_Median_LogR\tPat_Homo/Het/Dup/Other\tMat_Median_LogR\tMat_Homo/Het/Dup/Other\tSib_Median_LogR\tSib_Homo/Het/Dup/Other\tDN3\tDN3\tp(CNV)\tp(Diff)\tp(DNCNV)\tp(ProDel)\tp(ProDup)\tp(FatDel)\tp(FatDup)\tp(MatDel)\tp(MatDup)\tp(FDiff)\tp(MDiff)";
#Load chromosome arrays
print "Loading SNP arrays\n";
&snp_array("$working_dir$dir_sep${tag}_".$chip_type."_Sort_List.txt");
#Load FinalReport names
print "Loading FinalReport names\n";
my ($fr_list, $hash_ref1, $hash_ref2, $hash_ref3) = &quick_fr_list($data_dir);
#Loading SNP summaries
print "Loading SNP summaries, this may take a couple of minutes\n";
my $snpin = $sum_dir.$dir_sep.'All_'.${tag}."_Summary_Results.txt";
open SNP, '<', $snpin or die "Could not open file $snpin: $!\n";
my $head = <SNP>;
my @header = split /\t/, $head;
$header[-1] =~ s/[\r\n]+$//;
#Assign Columns based on headers
my ($snplogmeancol, $snpnamecol, $snplogstdevcol, $snplognccol, $snplogcountcol, $snpaacol, $snpaabcol, $snpabcol, $snpabbcol, $snpbbcol, $snpothercol);
for (my $i = 0; $i < @header; $i++) {
if ($header[$i] eq 'LogR_Mean') {
$snplogmeancol = $i;
} elsif ($header[$i] eq 'SNP') {
$snpnamecol = $i;
} elsif ($header[$i] eq 'LogR_StDev') {
$snplogstdevcol = $i;
} elsif ($header[$i] eq 'LogR_NoCall') {
$snplognccol = $i;
} elsif ($header[$i] eq 'LogR_Count') {
$snplogcountcol = $i;
} elsif ($header[$i] eq 'AA') {
$snpaacol = $i;
} elsif ($header[$i] eq 'AAB') {
$snpaabcol = $i;
} elsif ($header[$i] eq 'AB') {
$snpabcol = $i;
} elsif ($header[$i] eq 'ABB') {
$snpabbcol = $i;
} elsif ($header[$i] eq 'BB') {
$snpbbcol = $i;
} elsif ($header[$i] eq 'other') {
$snpothercol = $i;
}
}
my %snphash;
#Make a hash of the SNPs
while (my $line = <SNP>){
$line =~ s/[\n\r]//g;
my @tab = split /\t/, $line;
$snphash{$tab[$snpnamecol]}{meanlogr} = $tab[$snplogmeancol];
$snphash{$tab[$snpnamecol]}{stdevlogr} = $tab[$snplogstdevcol];
$snphash{$tab[$snpnamecol]}{count} = $tab[$snplogcountcol];
$snphash{$tab[$snpnamecol]}{nocall} = eval {$tab[$snplognccol] / $tab[$snplogcountcol] * 100};
$snphash{$tab[$snpnamecol]}{aa} = $tab[$snpaacol];
$snphash{$tab[$snpnamecol]}{aab} = $tab[$snpaabcol];
$snphash{$tab[$snpnamecol]}{ab} = $tab[$snpabcol];
$snphash{$tab[$snpnamecol]}{abb} = $tab[$snpabbcol];
$snphash{$tab[$snpnamecol]}{bb} = $tab[$snpbbcol];
$snphash{$tab[$snpnamecol]}{other} = $tab[$snpothercol];
if ($line =~ /Overall/){
$snphash{metrics}{mean} = $tab[1] if ($tab[0] =~ /Overall_LogR_Mean/);
$snphash{metrics}{sd} = $tab[1] if ($tab[0] =~ /Overall_LogR_StDev/);
$snphash{metrics}{meanlogrsd} = $tab[1] if ($tab[0] =~ /Overall_LogRSD_Mean/);
$snphash{metrics}{sdlogrsd} = $tab[1] if ($tab[0] =~ /Overall_LogRSD_StDev/);
$snphash{metrics}{meannocall} = $tab[1] if ($tab[0] =~ /Overall_NC_Mean/);
$snphash{metrics}{sdnocall} = $tab[1] if ($tab[0] =~ /Overall_NC_StDev/);
}
}
my ($counter, $sampcount) = (0,0);
my (@sample, $lastsamp);
#Splits the file into samples and sends an array per sample to the sampledeal subroutine
print "Assessing inheritence\n";
my %locicount;
$. = 0;
while (my $region = <INPUT>){
#print $region."\n";
$region =~ s/\n|\r|\n\r|\r\n//g;
if ($headlinepres =~ /y/i and $. == 1){
print OUTPUT $region."\t".$headers."\n";
}
else {
my @thisone = split /\t/, $region;
#print "This: $thisone[$sampcol], Last: $lastsamp\n";
if (defined $lastsamp && $thisone[$sampcol] ne $lastsamp){
$sampcount++;
my $gender = $which_gender{$lastsamp};
print "Assessing sample $sampcount: $lastsamp \n";
my $outref = &sampledealdn3(\%snphash, \@sample, $lastsamp, $which_phenotype, $which_family, $which_mother, $which_father, $which_sibling, $hash_ref2, $gender);
foreach my $out (@$outref){
$locicount{$lastsamp}++;
print OUTPUT $out."\n";
}
@sample = $region;
}
else {
push (@sample, $region);
}
$lastsamp = $thisone[$sampcol];
}
}
print "Assessing sample $sampcount: $lastsamp \n";
my $gender = $which_gender{$lastsamp};
my $outref = &sampledealdn3(\%snphash, \@sample, $lastsamp, $which_phenotype, $which_family, $which_mother, $which_father, $which_sibling, $hash_ref2, $gender);
foreach my $out (@$outref){
#print "$out\n";
$locicount{$lastsamp}++;
print OUTPUT $out."\n";
}
&add_sample_col('DeNovo3 Loci');
my $totalsamples = keys %locicount;
my $samplecounter = 0;
foreach my $samp (sort keys %sample_idx) {
my $lociout = $locicount{$samp} + 0;
&set_sample_value($samp, 'DeNovo3 Loci', $lociout);
if ($lociout){
$samplecounter++;
} else {
print LOG1 &showtime(),"\tDeNovo3\tERROR\tNo loci present for $samp\n";
print "ERROR: No loci present for $samp\n";
}
}
if ($samplecounter == $totalsamples){
print LOG1 &showtime(),"\tDeNovo3\tINFO\tSummary track complete for $totalsamples samples\n";
print "DeNovo3 complete for $totalsamples samples\n";
} else {
print LOG1 &showtime(),"\tDeNovo3\tERROR\tSummary track complete, however loci were present for samples that were not listed in the Samplelist file\n";
print "ERROR: DeNovo3 complete, however loci were present for samples that were not listed in the Samplelist file, $totalsamples, $samplecounter\n";
}
}
#The sample may be either a child or a parent
sub sampledealdn3{
#print "SampDeal\n";
my ($snphashref, $samparray, $sample, $which_phenotype, $which_family, $which_mother, $which_father, $which_sibling, $hash_ref2, $thegenderofsample) = @_;
#print "$samparray, $sample, $which_phenotype, $which_family, $which_mother, $which_father, $which_sibling, $hash_ref2, $thegenderofsample\n";
my $phenotype = $$which_phenotype{$sample};
my $family = $$which_family{$sample};
my $father = $$which_father{$sample};
my $mother = $$which_mother{$sample};
my $sibling = (split /,/, $$which_sibling{$sample})[0];
my $noparentsib = 1 if ($father eq '0' and $mother eq '0' and $sibling !~ /w+/);
my $trioquart;
if ($noparentsib == 1){
$trioquart = 'No_Parents';
}
elsif ($father ne '0' and $mother ne '0' and $sibling =~ /\w+/ and $sibling ne '0'){
$trioquart = 'Quartet';
}
elsif($father ne '0' and $mother ne '0') {
$trioquart = 'Trio';
}
elsif ($father =~ /\w+/ and $father ne '0'){
$trioquart = 'Father_Only';
}
elsif ($mother =~ /\w+/ and $mother ne '0'){
$trioquart = 'Mother_Only';
}
#print "Samp: $sample, Sibs: $$which_sibling{$sample}\n";
#print "S: ${sample}, P: ${phenotype}, F: ${family}, Fa: $father, Mo: $mother, Sib: $sibling, TQ: $trioquart, Sex: $thegenderofsample\n";
#Load FinalReport data for the family
my $case_fr_file = $$hash_ref2{$sample};
open FR1, '<', $case_fr_file or die "P1 Could not open file $case_fr_file: $!\n";
#my @case_fr = map { chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col]."\t".$row[$chromocol]."\t".$row[$chromodist] } <FR1>;
my @case_fr = <FR1>;
close FR1;
#Modify Headers
my ($colheader, $mark, $frlinecount);
do {
my $line = $case_fr[$frlinecount];
$frlinecount++;
if ($line =~ /\[Data\]/) {
$colheader = $case_fr[$frlinecount];
$mark = 1;
}
} until ($mark == 1);
# Update Final Report column numbers for this file
chomp $colheader;
&fr_columns($colheader);
#print "NewSamp: LogR Col: $log2col, BAF: $ballele\n"; sleep 1;
my ($sibpresent, $motpresent, $fatpresent) = (0,0,0);
my (@fat_fr, @mot_fr, @sib_fr);
if ($noparentsib != 1){
my $fat_fr_file = $$hash_ref2{$father};
my $mot_fr_file = $$hash_ref2{$mother};
my $sib_fr_file = $$hash_ref2{$sibling};
#print "FRP: $case_fr_file, FRF: $fat_fr_file, FRM: $mot_fr_file, FRS: $sib_fr_file\n";
open FR2, '<', $fat_fr_file or die "Could not open file $fat_fr_file for father $father: $!\n" unless ($father eq 0 or $fat_fr_file !~ /\w+/);
print "Warning: no father final report for $father\n" if ($father ne 0 and $fat_fr_file !~ /\w+/);
print LOG1 &showtime(),"\tDeNovo2\tERROR\tWarning: no father final report for $father\n" if ($father ne 0 and $fat_fr_file !~ /\w+/);
#@fat_fr = map { chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col] } <FR2>;
@fat_fr = <FR2>;
close FR2;
open FR3, '<', $mot_fr_file or die "Could not open file $mot_fr_file for mother $mother: $!\n" unless ($mother eq 0 or $mot_fr_file !~ /\w+/);
print "Warning: no mother final report for $mother\n" if ($mother ne 0 and $mot_fr_file !~ /\w+/);
print LOG1 &showtime(),"\tDeNovo2\tERROR\tWarning: no mother final report for $mother\n" if ($mother ne 0 and $mot_fr_file !~ /\w+/);
#@mot_fr = map { chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col] } <FR3>;
@mot_fr = <FR3>;
close FR3;
open FR4, '<', $sib_fr_file or die "Could not open file $sib_fr_file for sibling $sibling: $!\n" unless ($sibling eq 0 or $sibling !~ /\w+/ or $sib_fr_file !~ /\w+/);
print "Warning: no sibling final report for $sibling\n" if ($sibling ne 0 and $sibling =~ /\w+/ and $sib_fr_file !~ /\w+/);
print LOG1 &showtime(),"\tDeNovo2\tERROR\tWarning: no sibling final report for $sibling\n" if ($sibling ne 0 and $sibling =~ /\w+/ and $sib_fr_file !~ /\w+/);
#@sib_fr = map { chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col] } <FR4>;
@sib_fr = <FR4>;
close FR4;
$sibpresent = 1 if ($sibling =~ /\w+/ and $sibling ne '0' and $sib_fr_file =~ /\w+/);
$motpresent = 1 if ($mother =~ /\w+/ and $mother ne '0' and $fat_fr_file =~ /\w+/);
$fatpresent = 1 if ($father =~ /\w+/ and $father ne '0' and $mot_fr_file =~ /\w+/);
}
#print "$sibpresent, $motpresent, $fatpresent\n";
my ($linecount, %lines, @output);
foreach my $line (@$samparray){
#print $line."\n";
my @tab = split /\t/, $line;
my ($snpcount, @lines) = &dandcdn ($tab[$chromocol], $tab[$startcol], $tab[$stopcol]);
my $output;
#print "$tab[$chromocol]:$tab[$startcol]-$tab[$stopcol] has $snpcount SNPs\n";
if ($noparentsib != 1){
$output = &getdatadn3 ($snphashref, $snpcount, $thegenderofsample, $tab[$chromocol], $sibpresent, $motpresent, $fatpresent, \@lines, \@case_fr, \@fat_fr, \@mot_fr, \@sib_fr);
}
else {
$output = &getdatadn3 ($snphashref, $snpcount, $thegenderofsample, $tab[$chromocol], $sibpresent, $motpresent, $fatpresent, \@lines, \@case_fr);
#print $output."\n";
}
push (@output, $line."\t".$snpcount."\t".$trioquart."\t".$output);
$linecount++;
}
return (\@output);
#my @proband = &getlines($sample, \%lines, $hash_ref2);
}
#Subroutine of de novo 2 alg, retrieves lines from FR
sub getdatadn3 {
my ($snphashref, $snpcount, $thegenderofsample, $chromohere, $sibpresent, $motpresent, $fatpresent, $lineref, @arrayref) = @_;
my @lines = @$lineref;
if (scalar @arrayref <= 1){
my $case_ref = $arrayref[0];
my @case;
foreach my $frline (@lines){
#print "Line: $frline, Out: $$case_ref[$frline-1]\n";
push @case, map {chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col] } $$case_ref[$frline-1];
}
my ($cmeanlogr, $csdlogr, $cmedlogr, $cmaxlogr, $cminlogr, $chet, $chomo, $cdup, $cother, $cthetype, $cuncertain) = &baflogr ($snpcount, \@case);
my $parout = 'No_parents';
$parout = 'No_CNV' if ($cthetype =~ /2/ and ($chromohere !~ /x/gi or $thegenderofsample =~ /Female/i));
my $return = join "\t", ($parout, $cthetype.$cuncertain, 'NA', 'NA', 'NA', 'NA', 'NA', $cmedlogr, $chet.'%/'.$chomo.'%/'.$cdup.'%/'.$cother.'%',
'NA', 'NA',
'NA', 'NA',
'NA', 'NA');
#print "LogR: $cmedlogr, Type: $cthetype, Inherit: No_parents\n";
return ($return);
}
else {
my $case_ref = $arrayref[0];
my $fat_ref = $arrayref[1];
my $mot_ref = $arrayref[2];
my $sib_ref = $arrayref[3];
my (@case, @fat, @mot, @sib);
foreach my $frline (@lines){
#print "Line: $frline, Out: $$case_ref[$frline-1]\n";
push @case, map {chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col]."\t".$row[$snpcol] } $$case_ref[$frline-1];
push @fat, map {chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col]."\t".$row[$snpcol] } $$fat_ref[$frline-1];
push @mot, map {chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col]."\t".$row[$snpcol] } $$mot_ref[$frline-1];
push @sib, map {chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col]."\t".$row[$snpcol] } $$sib_ref[$frline-1];
#push @case, $$case_ref[$frline-1];
#push @fat, $$fat_ref[$frline-1];
#push @mot, $$mot_ref[$frline-1];
#push @sib, $$sib_ref[$frline-1];
}
my ($cmeanlogr, $csdlogr, $cmedlogr, $cmaxlogr, $cminlogr, $chet, $chomo, $cdup, $cother, $cthetype, $cuncertain) = &baflogrdn3 ($snpcount, \@case);
my ($fmeanlogr, $fsdlogr, $fmedlogr, $fmaxlogr, $fminlogr, $fhet, $fhomo, $fdup, $fother, $fthetype, $funcertain) = &baflogrdn3 ($snpcount, \@fat);
my ($mmeanlogr, $msdlogr, $mmedlogr, $mmaxlogr, $mminlogr, $mhet, $mhomo, $mdup, $mother, $mthetype, $muncertain) = &baflogrdn3 ($snpcount, \@mot);
my ($smeanlogr, $ssdlogr, $smedlogr, $smaxlogr, $sminlogr, $shet, $shomo, $sdup, $sother, $sthetype, $suncertain) = &baflogrdn3 ($snpcount, \@sib);
my ($fmatch, $mmatch) = &parentmatchdn3 (\@case, \@fat, \@mot, $cthetype, $snpcount);
my ($cumpdel, $cumpdup, $cumfdel, $cumfdup, $cummdel, $cummdup, $cumpfdiff, $cumpmdiff) = &probdistdn3 (\@case, \@fat, \@mot, $cthetype, $snpcount, $snphashref);
my ($sreturn, $freturn, $mreturn, $fmatchout, $mmatchout);
#Correct if sibling data is missing
if ($sibpresent != 1){
#print "Correcting Sibling data\n";
$sthetype = 'NA';
$sreturn = 'NA'."\t".'NA';
}
else {
$sreturn = $smedlogr."\t".$shet.'%/'.$shomo.'%/'.$sdup.'%/'.$sother.'%';
}
#Correct if father data is missing
if ($fatpresent != 1){
$fthetype = 'NA';
$freturn = 'NA'."\t".'NA';
$fmatchout = 'NA';
$fmatch = 'NA';
}
else {
$freturn = $fmedlogr."\t".$fhet.'%/'.$fhomo.'%/'.$fdup.'%/'.$fother.'%';
$fmatchout = $fmatch.'%';
}
#Correct if mother data is missing
if ($motpresent != 1){
$mthetype = 'NA';
$mreturn = 'NA'."\t".'NA';
$mmatchout = 'NA';
$mmatch = 'NA';
}
else {
$mreturn = $mmedlogr."\t".$mhet.'%/'.$mhomo.'%/'.$mdup.'%/'.$mother.'%';
$mmatchout = $mmatch.'%'
}
#Work out the inheritence
my ($inherit) = &cnvinherit ($cthetype, $fthetype, $mthetype, $fmatch, $mmatch, $thegenderofsample, $chromohere);
my ($inherit2) = &cnvinheritdn3 ($cumpdel, $cumpdup, $cumfdel, $cumfdup, $cummdel, $cummdup, $cumpfdiff, $cumpmdiff);
#print "LogR: $cmedlogr, Type: $cthetype, Inherit: $inherit\n";
my $return = join "\t", ($inherit, $cthetype.$cuncertain, $fthetype.$funcertain, $mthetype.$muncertain, $sthetype.$suncertain, $fmatchout, $mmatchout, $cmedlogr, $chet.'%/'.$chomo.'%/'.$cdup.'%/'.$cother.'%',
$freturn,
$mreturn,
$sreturn,
$inherit2, $cumpdel, $cumpdup, $cumfdel, $cumfdup, $cummdel, $cummdup, $cumpfdiff, $cumpmdiff);
return ($return);
}
}
#Work out mean, median stdev logR
sub baflogrdn3 {
my ($snpcount, $baflogrref) = @_;
my @baflogdata = @$baflogrref;
my ($het, $homo, $dup, $other) = (0,0,0,0);
my ($thetype, $uncertain, @logr);
foreach my $datapoint (@baflogdata){
my @tab = split /\t/, $datapoint;
if ($tab[1] =~ /\d+/){
push (@logr, $tab[1]);
}
if ($tab[0] <= 0.1 or $tab[0] >= 0.9){$homo++;}
elsif ($tab[0] <= 0.58 and $tab[0] >= 0.42){$het++;}
elsif ($tab[0] >= 0.6 and $tab[0] <= 0.75){$dup++;}
elsif ($tab[0] <= 0.4 and $tab[0] >= 0.25){$dup++;}
else {$other++;}
}
#Calulate mean, stdev and median of logR
my ($meanlogr, $sdlogr, $medlogr, $maxlogr, $minlogr) = &meanmedianstdevconf(\@logr);
#Works out the type of CNV present
#Homozygous deletion
if($medlogr <= -1.5){
if ($homo < 0.5 or $medlogr <= -3.5){$thetype = 0;}
else {$thetype = 0; $uncertain = "?";}
}
#Heterozygous deletion
elsif($medlogr > -1.5 and $medlogr <= -0.25){
if ($homo >= 0.8){$thetype = 1;}
else {$thetype = 1; $uncertain = "?";}
}
#Normal
elsif($medlogr > -0.25 and $medlogr < 0.15){
if (($het + $homo) >= 0.8){$thetype = 2;}
else {$thetype = 2; $uncertain = "?";}
}
#Duplication
elsif($medlogr >= 0.15 and $medlogr < 0.4){
if ($dup >= $het){$thetype = 3;}
elsif ($het > 0.2 and $dup < 0.1){$thetype = 2;}
else {$thetype = 3; $uncertain = "?";}
}
#Duplication or Amplification
elsif($medlogr >= 0.4){
if ($het < 0.15){$thetype = 3;}
elsif ($het >= 0.15 and $other >= 0.1){$thetype = 4;}
else {$thetype = 4; $uncertain = "?";}
}
$homo = sprintf ("%.0f", eval {$homo / $snpcount}*100);
$het = sprintf ("%.0f", eval {$het / $snpcount}*100);
$dup = sprintf ("%.0f", eval {$dup / $snpcount}*100);
$other = sprintf ("%.0f", eval {$other / $snpcount}*100);
$meanlogr = sprintf ("%.2f", $meanlogr);
$sdlogr = sprintf ("%.2f", $sdlogr);
$medlogr = sprintf ("%.2f", $medlogr);
$maxlogr = sprintf ("%.2f", $maxlogr);
$minlogr = sprintf ("%.2f", $minlogr);
#print "$meanlogr, $sdlogr, $medlogr, $maxlogr, $minlogr, $het, $homo, $dup, $other, $thetype, $uncertain\n";
return ($meanlogr, $sdlogr, $medlogr, $maxlogr, $minlogr, $het, $homo, $dup, $other, $thetype, $uncertain);
}
#Identifies if parent LogR is in the range of the child LogR for each SNP
sub parentmatchdn3 {
my ($carrayref, $farrayref, $marrayref, $type, $snpcount) = @_;
my @casearray = @$carrayref;
my @fatarray = @$farrayref;
my @motarray = @$marrayref;
my ($arraycount, $fcount, $mcount) = (0,0,0);
foreach (@casearray){
my $clogr = (split /\t/, $casearray[$arraycount])[1];
my $flogr = (split /\t/, $fatarray[$arraycount])[1];
my $mlogr = (split /\t/, $motarray[$arraycount])[1];
#Looks if the logR for each SNP is the same as the proband
if ($type =~ /0|1/ and $flogr < ($clogr/2)){$fcount++;}
elsif ($type =~ /3|4/ and $flogr > ($clogr/2)){$fcount++;}
if ($type =~ /0|1/ and $mlogr < ($clogr/2)){$mcount++;}
elsif ($type =~ /3|4/ and $mlogr > ($clogr/2)){$mcount++;}
$arraycount++;
}
$fcount = sprintf ("%.0f", eval {$fcount / $snpcount}*100);
$mcount = sprintf ("%.0f", eval {$mcount / $snpcount}*100);
return ($fcount, $mcount);
}
#Identifies if parent LogR is in the range of the child LogR for each SNP
sub probdistdn3 {
my ($carrayref, $farrayref, $marrayref, $type, $snpcount, $snphashref) = @_;
my @casearray = @$carrayref;
my @fatarray = @$farrayref;
my @motarray = @$marrayref;
my %snphash = %$snphashref;
my ($arraycount, $fcount, $mcount) = (0,0,0);
my $meanlogrhighthres = $snphash{metrics}{mean} + 2*$snphash{metrics}{sd};
my $meanlogrlowthres = $snphash{metrics}{mean} - 2*$snphash{metrics}{sd};
my $meanlogrsdhighthres = $snphash{metrics}{meanlogrsd} + 2*$snphash{metrics}{sdlogrsd};
my $meanlogrsdlowthres = $snphash{metrics}{meanlogrsd} - 2*$snphash{metrics}{sdlogrsd};
my $meannocallhighthres = $snphash{metrics}{meannocall} + 2*$snphash{metrics}{sdnocall};
my $meannocalllowthres = $snphash{metrics}{meannocall} - 2*$snphash{metrics}{sdnocall};
my ($cumpdel, $cumpdup, $cumfdel, $cumfdup, $cummdel, $cummdup, $cumpfdiff, $cumpmdiff) = (0,0,0,0,0,0,0,0);
foreach (@casearray){
my ($cbaf, $xp, $csnp) = split /\t/, $casearray[$arraycount];
my $xf = (split /\t/, $fatarray[$arraycount])[1];
my $xm = (split /\t/, $motarray[$arraycount])[1];
#Estimates pdel and pdup
my $pi = 3.141593;
my $mean = $snphash{$csnp}{meanlogr};
my $sd = $snphash{$csnp}{stdevlogr};
my $nc = $snphash{$csnp}{nocall};
#Filter out bad SNPs
if ($mean > $meanlogrlowthres and $mean < $meanlogrhighthres and $sd > $meanlogrsdlowthres and $sd < $meanlogrsdhighthres and $nc > $meannocalllowthres and $nc < $meannocallhighthres){
#print "ProLogR: $xp, FatLogR: $xf, MotLogR: $xm, SNPLogR: $mean, SNPStdev: $sd\n";
#Probability distribution function
#my $pnormp = 1/(sqrt(2*$pi)*$sd) * exp(-($xp-$mean)**2/(2*$sd**2));
#my $pnormm = 1/(sqrt(2*$pi)*$sd) * exp(-($xm-$mean)**2/(2*$sd**2));
#my $pnormf = 1/(sqrt(2*$pi)*$sd) * exp(-($xf-$mean)**2/(2*$sd**2));
#print "P norm proband is $pnormp\n";
#print "P norm mother is $pnormm\n";
#print "P norm father is $pnormf\n";
my $zp = ($xp - $mean)/$sd;
my $zm = ($xm - $mean)/$sd;
my $zf = ($xf - $mean)/$sd;
my $ppdel = 1 - Statistics::Distributions::uprob($zp);
my $pmdel = 1 - Statistics::Distributions::uprob($zm);
my $pfdel = 1 - Statistics::Distributions::uprob($zf);
my $ppdup = Statistics::Distributions::uprob($zp);
my $pmdup = Statistics::Distributions::uprob($zm);
my $pfdup = Statistics::Distributions::uprob($zf);
#print "P (proband deletion) = $ppdel\n";
#print "P (mother deletion) = $pmdel\n";
#print "P (father deletion) = $pfdel\n\n";
#print "P (proband duplication) = $ppdup\n";
#print "P (mother duplication) = $pmdup\n";
#print "P (father duplication) = $pfdup\n\n";
my @pm = sort {$a <=> $b} ($ppdel, $pmdel);
my $ppm = 1 - ($pm[1] - $pm[0]);
my @pf = sort {$a <=> $b} ($ppdel, $pfdel);
my $ppf = 1 - ($pf[1] - $pf[0]);
#print "P (proband and mother different) = $ppm\n";
#print "P (proband and father different) = $ppf\n";
#Add minimum p-value (+0.001 sets the minimum value per SNP)
$cumpdel += log ($ppdel + 0.001);
$cumpdup += log ($ppdup + 0.001);
$cumfdel += log ($pfdel + 0.001);
$cumfdup += log ($pfdup + 0.001);
$cummdel += log ($pmdel + 0.001);
$cummdup += log ($pmdup + 0.001);
$cumpfdiff += log ($ppf + 0.001);
$cumpmdiff += log ($ppm + 0.001);
#print "P(del) = ".($cumpdel * $arraycount * 2)."\t";
#print "P(dup) = ".($cumpdup * $arraycount * 2)."\n";
#print "PF(del) = ".($cumfdel * $arraycount * 2)."\t";
#print "PF(dup) = ".($cumfdup * $arraycount * 2)."\n";
#print "PM(del) = ".($cummdel * $arraycount * 2)."\t";
#print "PM(dup) = ".($cummdup * $arraycount * 2)."\n";
#print "P(fdiff) = ".($cumpfdiff * $arraycount * 2)."\t";
#print "P(mdiff) = ".($cumpmdiff * $arraycount * 2)."\n\n";
#sleep 1;
$arraycount++;
}
#else {
# print "Reject SNP $csnp!!! Mean: $mean, StDev: $sd, NoCall: $nc\n";
#}
}
#Calculate Chi Squared
my $chipdel = -2 * $cumpdel;
my $chipdup = -2 * $cumpdup;
my $chifdel = -2 * $cumfdel;
my $chifdup = -2 * $cumfdup;
my $chimdel = -2 * $cummdel;
my $chimdup = -2 * $cummdup;
my $chipfdiff = -2 * $cumpfdiff;
my $chipmdiff = -2 * $cumpmdiff;
my $degoffree = 2 * $arraycount;
my ($allppdel, $allppdup, $allfpdel, $allfpdup, $allmpdel, $allmpdup, $allpfdiff, $allpmdiff) = (1,1,1,1,1,1,1,1);
if ($degoffree > 0){
$allppdel = Statistics::Distributions::chisqrprob ($degoffree, $chipdel);
$allppdup = Statistics::Distributions::chisqrprob ($degoffree, $chipdup);
$allfpdel = Statistics::Distributions::chisqrprob ($degoffree, $chifdel);
$allfpdup = Statistics::Distributions::chisqrprob ($degoffree, $chifdup);
$allmpdel = Statistics::Distributions::chisqrprob ($degoffree, $chimdel);
$allmpdup = Statistics::Distributions::chisqrprob ($degoffree, $chimdup);
$allpfdiff = Statistics::Distributions::chisqrprob ($degoffree, $chipfdiff);
$allpmdiff = Statistics::Distributions::chisqrprob ($degoffree, $chipmdiff);
}
#print "Final P(del) = $cumpdel\n";
#print "Final P(dup) = $cumpdup\n";
#print "Final PF(del) = $cumfdel\n";
#print "Final PF(dup) = $cumfdup\n";
#print "Final PM(del) = $cummdel\n";
#print "Final PM(dup) = $cummdup\n";
#print "Final P(fdiff) = $cumpfdiff\n";
#print "Final P(mdiff) = $cumpmdiff\n";
#print "Proband deletion; " if ($cumpdel <= 0.05);
#print "Proband duplication; " if ($cumpdup <= 0.05);
#print "de novo; " if ($cumpmdiff < 0.05 and $cumpfdiff < 0.05);
#print "\n\n";
#sleep 2;
return ($allppdel, $allppdup, $allfpdel, $allfpdup, $allmpdel, $allmpdup, $allpfdiff, $allpmdiff);
}
sub cnvinheritdn3 {
my ($cumpdel, $cumpdup, $cumfdel, $cumfdup, $cummdel, $cummdup, $cumpfdiff, $cumpmdiff) = @_;
my $procnv = "No_CNV";
my ($pcnv, $pdiff, $pdncnv);
if ($cumpdel <= 0.05){
$procnv = "Deletion";
$pcnv = $cumpdel;
} elsif ($cumpdup <= 0.05){
$procnv = "Duplication";
$pcnv = $cumpdup;
}
my $pdiff = (sort {$b <=> $a} ($cumpmdiff, $cumpfdiff))[0];
my $inherit = "Inherited";
if ($cumpmdiff < 0.05 and $cumpfdiff < 0.05){
$inherit = "DeNovo";
}
my $pdncnv = $pcnv * $pdiff;
return ($procnv."\t".$inherit."\t".$pcnv."\t".$pdiff."\t".$pdncnv);
}
###############################################################################
############### --denovo2 ##############
###############################################################################
#Finds de novo CNVs, or visualises CNVs or finds further CNVs in the same area for other CNVs
sub denovo_raw {
my ($input, $output, $orderedsnps) = @_;
#print "H: $headlinepres, S: $sampcol, Chr: $chromocol, Start: $startcol, Stop: $stopcol\n";
print "Opening co-ordinates file: $input\n";
open INPUT, '<', $input or die "Could not open file $input: $!\n";
print "Opening output file: $output\n";
open OUTPUT, '>', $output or die "Could not open file $output: $!\n";
#Load pedfile
open PED ,'<', $pedfile or die "Could not open $pedfile\n$!";
{ local $/= undef; our $input = <PED>; }
close PED;
(local $\) = (/(\r\n|\r|\n)/);
my @peds = split (/\r\n|\r|\n/, our $input); chomp @peds;
print "Loading pedfile data\n";
my ($pedfile, $family_member, $which_family, $which_mother, $which_father,
$which_child, $which_sibling, $which_gender, $gendername, $which_phenotype,
$namepheno) = &propedfile(@peds);
my %which_gender = %$which_gender;
#Adds headers depending on the output to the user quesiton above
my $headers = "SNPs\tTrio/Quartet\tResult\tType\tPat_Type\tMat_Type\tSib_Type\t%Paternal\t%Maternal\tMedian_LogR\tHomo/Het/Dup/Other\tPat_Median_LogR\tPat_Homo/Het/Dup/Other\tMat_Median_LogR\tMat_Homo/Het/Dup/Other\tSib_Median_LogR\tSib_Homo/Het/Dup/Other";
#Load chromosome arrays
print "Loading SNP arrays\n";
&snp_array("$working_dir$dir_sep${tag}_".$chip_type."_Sort_List.txt");
#Load FinalReport names
print "Loading FinalReport names\n";
my ($fr_list, $hash_ref1, $hash_ref2, $hash_ref3) = &fr_list($data_dir);
my ($counter, $sampcount) = (0,0);
my (@sample, $lastsamp);
#Splits the file into samples and sends an array per sample to the sampledeal subroutine
print "Assessing inheritence\n";
my %locicount;
$. = 0;
while (my $region = <INPUT>){
#print $region."\n";
$region =~ s/\n|\r|\n\r|\r\n//g;
if ($headlinepres =~ /y/i and $. == 1){
print OUTPUT $region."\t".$headers."\n";
}
else {
my @thisone = split /\t/, $region;
#print "This: $thisone[$sampcol], Last: $lastsamp\n";
if (defined $lastsamp && $thisone[$sampcol] ne $lastsamp){
$sampcount++;
my $gender = $which_gender{$lastsamp};
print "Assessing sample $sampcount: $lastsamp \n";
my $outref = &sampledeal(\@sample, $lastsamp, $which_phenotype, $which_family, $which_mother, $which_father, $which_sibling, $hash_ref2, $gender);
foreach my $out (@$outref){
$locicount{$lastsamp}++;
print OUTPUT $out."\n";
}
@sample = $region;
}
else {
push (@sample, $region);
}
$lastsamp = $thisone[$sampcol];
}
}
print "Assessing sample $sampcount: $lastsamp \n";
my $gender = $which_gender{$lastsamp};
my $outref = &sampledeal(\@sample, $lastsamp, $which_phenotype, $which_family, $which_mother, $which_father, $which_sibling, $hash_ref2, $gender);
foreach my $out (@$outref){
#print "$out\n";
$locicount{$lastsamp}++;
print OUTPUT $out."\n";
}
&add_sample_col('DeNovo2 Loci');
my $totalsamples = keys %locicount;
my $samplecounter = 0;
foreach my $samp (sort keys %sample_idx) {
my $lociout = $locicount{$samp} + 0;
&set_sample_value($samp, 'DeNovo2 Loci', $lociout);
if ($lociout){
$samplecounter++;
} else {
print LOG1 &showtime(),"\tDeNovo2\tERROR\tNo loci present for $samp\n";
print "ERROR: No loci present for $samp\n";
}
}
if ($samplecounter == $totalsamples){
print LOG1 &showtime(),"\tDeNovo2\tINFO\tSummary track complete for $totalsamples samples\n";
print "DeNovo2 complete for $totalsamples samples\n";
} else {
print LOG1 &showtime(),"\tDeNovo2\tERROR\tSummary track complete, however loci were present for samples that were not listed in the Samplelist file\n";
print "ERROR: DeNovo2 complete, however loci were present for samples that were not listed in the Samplelist file, $totalsamples, $samplecounter\n";
}
}
#The sample may be either a child or a parent
sub sampledeal{
#print "SampDeal\n";
my ($samparray, $sample, $which_phenotype, $which_family, $which_mother, $which_father, $which_sibling, $hash_ref2, $thegenderofsample) = @_;
#print "$samparray, $sample, $which_phenotype, $which_family, $which_mother, $which_father, $which_sibling, $hash_ref2, $thegenderofsample\n";
my $phenotype = $$which_phenotype{$sample};
my $family = $$which_family{$sample};
my $father = $$which_father{$sample};
my $mother = $$which_mother{$sample};
my $sibling = (split /,/, $$which_sibling{$sample})[0];
my $noparentsib = 1 if ($father eq '0' and $mother eq '0' and $sibling !~ /w+/);
my $trioquart;
if ($noparentsib == 1){
$trioquart = 'No_Parents';
}
elsif ($father ne '0' and $mother ne '0' and $sibling =~ /\w+/ and $sibling ne '0'){
$trioquart = 'Quartet';
}
elsif($father ne '0' and $mother ne '0') {
$trioquart = 'Trio';
}
elsif ($father =~ /\w+/ and $father ne '0'){
$trioquart = 'Father_Only';
}
elsif ($mother =~ /\w+/ and $mother ne '0'){
$trioquart = 'Mother_Only';
}
#print "Samp: $sample, Sibs: $$which_sibling{$sample}\n";
#print "S: ${sample}, P: ${phenotype}, F: ${family}, Fa: $father, Mo: $mother, Sib: $sibling, TQ: $trioquart, Sex: $thegenderofsample\n";
#Load FinalReport data for the family
my $case_fr_file = $$hash_ref2{$sample};
open FR1, '<', $case_fr_file or die "Could not open file $case_fr_file for proband $sample: $!\n";
#my @case_fr = map { chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col]."\t".$row[$chromocol]."\t".$row[$chromodist] } <FR1>;
my @case_fr = <FR1>;
close FR1;
#Modify Headers
my ($colheader, $mark, $frlinecount);
do {
my $line = $case_fr[$frlinecount];
$frlinecount++;
if ($line =~ /\[Data\]/) {
$colheader = $case_fr[$frlinecount];
$mark = 1;
}
} until ($mark == 1);
# Update Final Report column numbers for this file
chomp $colheader;
&fr_columns($colheader);
#print "NewSamp: LogR Col: $log2col, BAF: $ballele\n"; sleep 1;
my ($sibpresent, $motpresent, $fatpresent) = (0,0,0);
my (@fat_fr, @mot_fr, @sib_fr);
if ($noparentsib != 1){
my $fat_fr_file = $$hash_ref2{$father};
my $mot_fr_file = $$hash_ref2{$mother};
my $sib_fr_file = $$hash_ref2{$sibling};
#print "FRP: $case_fr_file, FRF: $fat_fr_file, FRM: $mot_fr_file, FRS: $sib_fr_file\n";
open FR2, '<', $fat_fr_file or die "Could not open file $fat_fr_file for father $father: $!\n" unless ($father eq 0 or $fat_fr_file !~ /\w+/);
print "Warning: no father final report for $father\n" if ($father ne 0 and $fat_fr_file !~ /\w+/);
print LOG1 &showtime(),"\tDeNovo2\tERROR\tWarning: no father final report for $father\n" if ($father ne 0 and $fat_fr_file !~ /\w+/);
#@fat_fr = map { chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col] } <FR2>;
@fat_fr = <FR2>;
close FR2;
open FR3, '<', $mot_fr_file or die "Could not open file $mot_fr_file for mother $mother: $!\n" unless ($mother eq 0 or $mot_fr_file !~ /\w+/);
print "Warning: no mother final report for $mother\n" if ($mother ne 0 and $mot_fr_file !~ /\w+/);
print LOG1 &showtime(),"\tDeNovo2\tERROR\tWarning: no mother final report for $mother\n" if ($mother ne 0 and $mot_fr_file !~ /\w+/);
#@mot_fr = map { chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col] } <FR3>;
@mot_fr = <FR3>;
close FR3;
open FR4, '<', $sib_fr_file or die "Could not open file $sib_fr_file for sibling $sibling: $!\n" unless ($sibling eq 0 or $sibling !~ /\w+/ or $sib_fr_file !~ /\w+/);
print "Warning: no sibling final report for $sibling\n" if ($sibling ne 0 and $sibling =~ /\w+/ and $sib_fr_file !~ /\w+/);
print LOG1 &showtime(),"\tDeNovo2\tERROR\tWarning: no sibling final report for $sibling\n" if ($sibling ne 0 and $sibling =~ /\w+/ and $sib_fr_file !~ /\w+/);
#@sib_fr = map { chomp $_; my @row = split /\t/,$_,10; $row[$ballele]."\t".$row[$log2col] } <FR4>;
@sib_fr = <FR4>;
close FR4;
$sibpresent = 1 if ($sibling =~ /\w+/ and $sibling ne '0' and $sib_fr_file =~ /\w+/);
$motpresent = 1 if ($mother =~ /\w+/ and $mother ne '0' and $fat_fr_file =~ /\w+/);
$fatpresent = 1 if ($father =~ /\w+/ and $father ne '0' and $mot_fr_file =~ /\w+/);
}
#print "$sibpresent, $motpresent, $fatpresent\n";
my ($linecount, %lines, @output);
foreach my $line (@$samparray){
#print $line."\n";
my @tab = split /\t/, $line;
my ($snpcount, @lines) = &dandcdn ($tab[$chromocol], $tab[$startcol], $tab[$stopcol]);
my $output;
#print "$tab[$chromocol]:$tab[$startcol]-$tab[$stopcol] has $snpcount SNPs\n";
if ($noparentsib != 1){
$output = &getdata ($snpcount, $thegenderofsample, $tab[$chromocol], $sibpresent, $motpresent, $fatpresent, \@lines, \@case_fr, \@fat_fr, \@mot_fr, \@sib_fr);
}
else {
$output = &getdata ($snpcount, $thegenderofsample, $tab[$chromocol], $sibpresent, $motpresent, $fatpresent, \@lines, \@case_fr);
#print $output."\n";
}
push (@output, $line."\t".$snpcount."\t".$trioquart."\t".$output);
$linecount++;
}
return (\@output);
#my @proband = &getlines($sample, \%lines, $hash_ref2);
}
#Subroutine of de novo 2 alg, retrieves lines from FR
sub getdata {
my ($snpcount, $thegenderofsample, $chromohere, $sibpresent, $motpresent, $fatpresent, $lineref, @arrayref) = @_;
#print "GetData: LogR Col: $log2col, BAF: $ballele\n";
my @lines = @$lineref;
if (scalar @arrayref <= 1){
my $case_ref = $arrayref[0];
my @case;
foreach my $frline (@lines){
#print "Line: $frline, In: $$case_ref[$frline-1]";
push @case, map {chomp $_; my @row = split /\t/,$_; $row[$ballele]."\t".$row[$log2col] } $$case_ref[$frline-1];
#print "Line: $frline, Out: $case[-1]\n";
}
#print "Data case:\n$case[0]\n$case[4]\n$case[8]\n";
my ($cmeanlogr, $csdlogr, $cmedlogr, $cmaxlogr, $cminlogr, $chet, $chomo, $cdup, $cother, $cthetype, $cuncertain) = &baflogr ($snpcount, \@case);
my $parout = 'No_parents';
$parout = 'No_CNV' if ($cthetype =~ /2/ and ($chromohere !~ /x/gi or $thegenderofsample =~ /Female/i));
my $return = join "\t", ($parout, $cthetype.$cuncertain, 'NA', 'NA', 'NA', 'NA', 'NA', $cmedlogr, $chet.'%/'.$chomo.'%/'.$cdup.'%/'.$cother.'%',
'NA', 'NA',
'NA', 'NA',
'NA', 'NA');
#print "LogR: $cmedlogr, Type: $cthetype, Inherit: No_parents\n";
return ($return);
}
else {
my $case_ref = $arrayref[0];
my $fat_ref = $arrayref[1];
my $mot_ref = $arrayref[2];
my $sib_ref = $arrayref[3];
my (@case, @fat, @mot, @sib);
foreach my $frline (@lines){
#print "Line2: $frline, Out: $$case_ref[$frline-1]\n";
push @case, map {chomp $_; my @row = split /\t/,$_; $row[$ballele]."\t".$row[$log2col] } $$case_ref[$frline-1];
push @fat, map {chomp $_; my @row = split /\t/,$_; $row[$ballele]."\t".$row[$log2col] } $$fat_ref[$frline-1];
push @mot, map {chomp $_; my @row = split /\t/,$_; $row[$ballele]."\t".$row[$log2col] } $$mot_ref[$frline-1];
push @sib, map {chomp $_; my @row = split /\t/,$_; $row[$ballele]."\t".$row[$log2col] } $$sib_ref[$frline-1];
#push @case, $$case_ref[$frline-1];
#push @fat, $$fat_ref[$frline-1];
#push @mot, $$mot_ref[$frline-1];
#push @sib, $$sib_ref[$frline-1];
}
#print "Data case2:\n$case[0]\n$case[4]\n$case[8]\n";
my ($cmeanlogr, $csdlogr, $cmedlogr, $cmaxlogr, $cminlogr, $chet, $chomo, $cdup, $cother, $cthetype, $cuncertain) = &baflogr ($snpcount, \@case);
my ($fmeanlogr, $fsdlogr, $fmedlogr, $fmaxlogr, $fminlogr, $fhet, $fhomo, $fdup, $fother, $fthetype, $funcertain) = &baflogr ($snpcount, \@fat);
my ($mmeanlogr, $msdlogr, $mmedlogr, $mmaxlogr, $mminlogr, $mhet, $mhomo, $mdup, $mother, $mthetype, $muncertain) = &baflogr ($snpcount, \@mot);
my ($smeanlogr, $ssdlogr, $smedlogr, $smaxlogr, $sminlogr, $shet, $shomo, $sdup, $sother, $sthetype, $suncertain) = &baflogr ($snpcount, \@sib);
my ($fmatch, $mmatch) = &parentmatch (\@case, \@fat, \@mot, $cthetype, $snpcount);
my ($sreturn, $freturn, $mreturn, $fmatchout, $mmatchout);
#Correct if sibling data is missing
if ($sibpresent != 1){
#print "Correcting Sibling data\n";
$sthetype = 'NA';
$sreturn = 'NA'."\t".'NA';
}
else {
$sreturn = $smedlogr."\t".$shet.'%/'.$shomo.'%/'.$sdup.'%/'.$sother.'%';
}
#Correct if father data is missing
if ($fatpresent != 1){
$fthetype = 'NA';
$freturn = 'NA'."\t".'NA';
$fmatchout = 'NA';
$fmatch = 'NA';
}
else {
$freturn = $fmedlogr."\t".$fhet.'%/'.$fhomo.'%/'.$fdup.'%/'.$fother.'%';
$fmatchout = $fmatch.'%';
}
#Correct if mother data is missing
if ($motpresent != 1){
$mthetype = 'NA';
$mreturn = 'NA'."\t".'NA';
$mmatchout = 'NA';
$mmatch = 'NA';
}
else {
$mreturn = $mmedlogr."\t".$mhet.'%/'.$mhomo.'%/'.$mdup.'%/'.$mother.'%';
$mmatchout = $mmatch.'%'
}
#Work out the inheritence
my ($inherit) = &cnvinherit ($cthetype, $fthetype, $mthetype, $fmatch, $mmatch, $thegenderofsample, $chromohere);
#print "LogR: $cmedlogr, Type: $cthetype, Inherit: $inherit\n";
my $return = join "\t", ($inherit, $cthetype.$cuncertain, $fthetype.$funcertain, $mthetype.$muncertain, $sthetype.$suncertain, $fmatchout, $mmatchout, $cmedlogr, $chet.'%/'.$chomo.'%/'.$cdup.'%/'.$cother.'%',
$freturn,
$mreturn,
$sreturn);
return ($return);
}
}
#Identifies if parent LogR is in the range of the child LogR for each SNP
sub parentmatch {
my ($carrayref, $farrayref, $marrayref, $type, $snpcount) = @_;
my @casearray = @$carrayref;
my @fatarray = @$farrayref;
my @motarray = @$marrayref;
my ($arraycount, $fcount, $mcount) = (0,0,0);
foreach (@casearray){
my $clogr = (split /\t/, $casearray[$arraycount])[1];
my $flogr = (split /\t/, $fatarray[$arraycount])[1];
my $mlogr = (split /\t/, $motarray[$arraycount])[1];
#Looks if the logR for each SNP is the same as the proband
if ($type =~ /0|1/ and $flogr < ($clogr/2)){$fcount++;}
elsif ($type =~ /3|4/ and $flogr > ($clogr/2)){$fcount++;}
if ($type =~ /0|1/ and $mlogr < ($clogr/2)){$mcount++;}
elsif ($type =~ /3|4/ and $mlogr > ($clogr/2)){$mcount++;}
$arraycount++;
}
$fcount = sprintf ("%.0f", eval {$fcount / $snpcount}*100);
$mcount = sprintf ("%.0f", eval {$mcount / $snpcount}*100);
return ($fcount, $mcount);
}
#This section determines whether a CNV is de novo or inherited
sub cnvinherit {
my ($cthetype, $fthetype, $mthetype, $fmatch, $mmatch, $thegenderofsample, $chromohere) = @_;
my $inherit;
#print "Gender: $thegenderofsample\n";
#Male ChrX Duplication
if ($cthetype =~ /2/ and $chromohere =~ /x/gi and $thegenderofsample eq "Male") {
if ($mthetype =~ /3/ or $mthetype =~ /4/){$inherit = "Maternal";}
elsif ($mthetype =~ /2/){$inherit = "De_Novo";}
elsif ($mthetype =~ /NA/){$inherit = "No_Mother";}
else {$inherit = "?De_Novo";}
#print "I'm here: $inherit\n";
}
#No CNV
elsif ($cthetype =~ /2/) {$inherit = "No_CNV";}
#Homozygous deletion
elsif ($cthetype =~ /0/) {
if ($chromohere =~ /x/gi and ($mthetype =~ /1/ or $mthetype =~ /0/)){$inherit = "Hemi_X";}
elsif ($fthetype =~ /0|1/ and $mthetype =~ /0|1/){$inherit = "Homo_Both";}
elsif ($fthetype =~ /[234]/ and $mthetype =~ /[234]/){$inherit = "De_Novo";}
else {$inherit = "Unclear";}
}
#Likely inherited
elsif ($fmatch >= 75 or $mmatch >= 75){
if ($fthetype =~ /$cthetype/ and $mthetype =~ /$cthetype/){$inherit = "Both";}
elsif ($fthetype =~ /$cthetype/ and $mthetype !~ /$cthetype/){$inherit = "Paternal";}
elsif ($fthetype !~ /$cthetype/ and $mthetype =~ /$cthetype/){$inherit = "Maternal";}
elsif ($fthetype =~ /[01234]/ and $mthetype =~ /[01234]/){$inherit = "?Both";}
else {$inherit = "Unclear";}
}
elsif ($fmatch >= 50 and $mmatch >= 50){
if ($fthetype =~ /$cthetype/ and $mthetype =~ /$cthetype/){$inherit = "Both";}
elsif ($fthetype =~ /$cthetype/ and $mthetype !~ /$cthetype/){$inherit = "Paternal";}
elsif ($fthetype !~ /$cthetype/ and $mthetype =~ /$cthetype/){$inherit = "Maternal";}
elsif ($fthetype =~ /[01234]/ and $mthetype =~ /[01234]/){$inherit = "?Both";}
else {$inherit = "Unclear";}
}
elsif ($fmatch >= 50 and $mmatch < 50){
if ($fthetype =~ /$cthetype/){$inherit = "Paternal";}
else {$inherit = "?Paternal";}
}
elsif ($fmatch < 50 and $mmatch >= 50){
if ($mthetype =~ /$cthetype/){$inherit = "Maternal";}
else {$inherit = "?Maternal";}
}
#Possibly inherited
elsif ($fmatch < 50 and $mmatch < 50 and ($fmatch >= 25 or $mmatch >= 25)){
if ($fthetype =~ /$cthetype/ and $mthetype =~ /$cthetype/){$inherit = "?Both";}
elsif ($fthetype =~ /$cthetype/){$inherit = "?Paternal";}
elsif ($mthetype =~ /$cthetype/){$inherit = "?Maternal";}
elsif ($fthetype =~ /[01234]/ and $mthetype =~ /[01234]/){$inherit = "?De_Novo";}
else {$inherit = "Unclear";}
}
#Probably not inherited
elsif ($fmatch < 25 and $mmatch < 25){
if ($fthetype =~ /$cthetype/ and $mthetype =~ /$cthetype/){$inherit = "?Both";}
elsif ($fthetype =~ /$cthetype/){$inherit = "?Paternal";}
elsif ($mthetype =~ /$cthetype/){$inherit = "?Maternal";}
elsif ($fthetype =~ /[01234]/ and $mthetype =~ /[01234]/){$inherit = "De_Novo";}
else {$inherit = "Unclear";}
}
else {$inherit = "Unclear";}
return ($inherit);
}
#Work out mean, median stdev logR
sub baflogr {
my ($snpcount, $baflogrref) = @_;
my @baflogdata = @$baflogrref;
my ($het, $homo, $dup, $other) = (0,0,0,0);
my ($thetype, $uncertain, @logr);
foreach my $datapoint (@baflogdata){
#print "Data: $datapoint\n";
my @tab = split /\t/, $datapoint;
if ($tab[1] =~ /\d+/){
push (@logr, $tab[1]);
}
if ($tab[0] <= 0.1 or $tab[0] >= 0.9){$homo++;}
elsif ($tab[0] <= 0.58 and $tab[0] >= 0.42){$het++;}
elsif ($tab[0] >= 0.6 and $tab[0] <= 0.75){$dup++;}
elsif ($tab[0] <= 0.4 and $tab[0] >= 0.25){$dup++;}
else {$other++;}
}
#Calulate mean, stdev and median of logR
my ($meanlogr, $sdlogr, $medlogr, $maxlogr, $minlogr) = &meanmedianstdevconf(\@logr);
#Works out the type of CNV present
#Homozygous deletion
if($medlogr <= -1.5){
if ($homo < 0.5 or $medlogr <= -3.5){$thetype = 0;}
else {$thetype = 0; $uncertain = "?";}
}
#Heterozygous deletion
elsif($medlogr > -1.5 and $medlogr <= -0.25){
if ($homo >= 0.8){$thetype = 1;}
else {$thetype = 1; $uncertain = "?";}
}
#Normal
elsif($medlogr > -0.25 and $medlogr < 0.15){
if (($het + $homo) >= 0.8){$thetype = 2;}
else {$thetype = 2; $uncertain = "?";}
}
#Duplication
elsif($medlogr >= 0.15 and $medlogr < 0.4){
if ($dup >= $het){$thetype = 3;}
elsif ($het > 0.2 and $dup < 0.1){$thetype = 2;}
else {$thetype = 3; $uncertain = "?";}
}
#Duplication or Amplification
elsif($medlogr >= 0.4){
if ($het < 0.15){$thetype = 3;}
elsif ($het >= 0.15 and $other >= 0.1){$thetype = 4;}
else {$thetype = 4; $uncertain = "?";}
}
$homo = sprintf ("%.0f", eval {$homo / $snpcount}*100);
$het = sprintf ("%.0f", eval {$het / $snpcount}*100);
$dup = sprintf ("%.0f", eval {$dup / $snpcount}*100);
$other = sprintf ("%.0f", eval {$other / $snpcount}*100);
$meanlogr = sprintf ("%.2f", $meanlogr);
$sdlogr = sprintf ("%.2f", $sdlogr);
$medlogr = sprintf ("%.2f", $medlogr);
$maxlogr = sprintf ("%.2f", $maxlogr);
$minlogr = sprintf ("%.2f", $minlogr);
#print "$meanlogr, $sdlogr, $medlogr, $maxlogr, $minlogr, $het, $homo, $dup, $other, $thetype, $uncertain\n";
return ($meanlogr, $sdlogr, $medlogr, $maxlogr, $minlogr, $het, $homo, $dup, $other, $thetype, $uncertain);
}
#Subroutine returns mean, median, stdev and confidence intervals for an array
sub meanmedianstdevconf {
my ($arrayref) = @_;
#print $arrayref."\n";
my @array = @$arrayref;
@array = sort {$a <=> $b} @array;
my $arraysize = @array;
my ($arraytotal, $arraystdevsum, $outmean, $outmedian, $outstdev, $outconf, $outmin, $outmax) = 0;
#Mean
foreach my $data (@array){
$arraytotal += $data;
}
$outmean = eval {$arraytotal / $arraysize} + 0;
#Median
my $half = $arraysize / 2;
if ($half == int($half)){
$outmedian = $array[$half];
}
else {
$outmedian = ($array[$half - 0.5] + $array[$half + 0.5])/2;
}
#StDev
foreach my $data (@array){
$arraystdevsum += ($data - $outmean)**2;
}
$outstdev = eval {$arraystdevsum / $arraysize}**0.5 + 0;
$outmax = $array[-1];
$outmin = $array[0];
#Confidence
$outconf = eval {1.96 * ($outstdev / ($arraysize**0.5))} + 0;
return ($outmean, $outstdev, $outmedian, $outmax, $outmin, $outconf);
}
#This subroutine returns the position and arrayline of every probe within a chr/start/stop term; it needs the dividedn and conquerdn parts to work
sub dandcdn{
my ($chrm, $starth, $stoph) = @_;
our %chrtoarray;
#print "Term: $term\n";
my $arrayref = $chrtoarray{$chrm};
#print "Chr: $chrm, Ref: $arrayref\n";
my $arraysize = @$arrayref if (defined @$arrayref);
my $newspot = sprintf ("%.f",($arraysize / 2));
my $halfspot = $newspot;
my ($zero, $round, $conquerdn) = (0,0,0);
#If the chromosome does not have any SNPs it is picked up here
if ($arraysize == 0){$zero = 1;}
my @first = split ("\t", $$arrayref[0]);
my @laster = split ("\t", $$arrayref[-1]);
#print "Array size: $arraysize, Round: $round\n";
do {
$round++;
my $divison = 2**$round;
#print "Chr: $chrm, Array location: $newspot, Round: $round, Divison: $divison\n";
if ($round == 30) {sleep(5)};
#The numbers below are minus one to allow the first position in the array to be reached
my @here = split ("\t", $$arrayref[$newspot - 1]);
my @above = split ("\t", $$arrayref[$newspot]);
my @below = split ("\t", $$arrayref[$newspot - 2]);
my $herespot = $here[0];
#If the region is has no SNPs within it then it is picked up here
if ($herespot < $starth and $above[0] > $stoph){$zero = 1};
if ($herespot > $stoph and $below[0] < $starth){$zero = 1};
#If the region starts after the last SNP on the chromosome or before the first one it is picked up here
if ($laster[0] < $starth){$zero = 1};
if ($first[0] > $stoph){$zero = 1};
#Otherwise newspot is adjusted depending on whether it is above or below the region of interest
if ($herespot < $starth){$newspot = sprintf ("%.f",($newspot + ($halfspot/$divison)));};
if ($herespot >= $starth and $herespot <= $stoph){$conquerdn = 1};
if ($herespot > $stoph){$newspot = sprintf ("%.f",($newspot - ($halfspot/$divison)));};
#Check that there is no infinite loop
if ($round > 30){
#Last position of the array
if ($laster[0] == $starth or $laster[0] == $stoph){
$newspot = $arraysize;
$conquerdn = 1;
}
else {
print "Error: dandcdn subroutine over 30 iterations for $chrm:$starth-$stoph\n";
$zero = 1;
}
}
} until ($conquerdn == 1 or $zero == 1);
#print "Hey I'm back here\n";
if ($zero == 1){
my @returner;
my $snpcount = 0;
return ($snpcount, @returner);
}
elsif ($conquerdn == 1) {
my $snpcount = 0;
my $upspot = $newspot - 1;
my $downspot = $newspot;
my ($marker1, $marker2) = (0,0);
my $arrayref = $chrtoarray{$chrm};
my @returner;
#Here the algorithm moves towards the start of the chromosome counting SNPs as it goes
do{
my @upspot = split ("\t", $$arrayref[$upspot]);
if ($upspot < 0){$marker1 = 1;}
elsif ($upspot[0] >= $starth){
push (@returner, (split /\t/, $$arrayref[$upspot])[1] );
$snpcount++;
#print "$linecount2) Spot: Up: $upspot, SNP position: $$arrayref[$upspot], SNP count: $snpcount\n";
$upspot--;
}
elsif ($upspot[0] < $starth){
$marker1 = 1;
}
}until ($marker1 == 1);
#Here the algorithm moves towards the end of the chromosome counting SNPs as it goes
do{
my @downspot = split ("\t", $$arrayref[$downspot]);
if ($downspot > $#$arrayref){$marker2 = 1;}
elsif ($downspot[0] <= $stoph){
push (@returner, (split /\t/, $$arrayref[$downspot])[1] );
$snpcount++;
#print "$linecount2) Down: SNP position: $$arrayref[$downspot], SNP count: $snpcount\n";
$downspot++;
}
elsif ($downspot[0] > $stoph){
$marker2 = 1;
}
}until ($marker2 == 1);
#@returner = sort { $a <=> $b } @returner;
#my $here = join "\t", @returner;
#print "Return: $here\n";
return ($snpcount, @returner);
}
}
###############################################################################
############### --denovo ###############
###############################################################################
#Finds de novo CNVs by looking for CNVs in the parents
sub denovo {
print LOG1 showtime(),"\tDenovo\tINFO\tStarting DeNovo indentification\n";
# Input file: "$merge_dir${dir_sep}Rare_${tag}_Merged.txt"
# Output file: "$merge_dir${dir_sep}DN_Rare_${tag}_Merged.txt"
my $input = shift;
print "Opening CNV file: $input\n";
my $output = $input;
if ($dir_sep =~ /\//){
$output =~ s/^(.+$dir_sep)(.+)$/${1}DN_$2/;
}
elsif ($dir_sep eq '\\'){
my @output = split /\\/, $input;
$output = $output[0].$dir_sep.'DN_'.$output[1];
}
########################################################
#Merge prog Output file
open my $infile,'<',$input or die "Cannot open file $input: $!";
my @CNValls;
while (<$infile>) {
s/[\r\n]+$//;
push @CNValls, $_;
}
close $infile;
my @lineshow = split ("\t", $CNValls[0]);
#open output file
print "Opening output CNV file: $output\n";
open my $denovo_out,'>',$output or die "Cannot open the file $output: $!";
print $denovo_out "Gender\tPhenotype\tFamily Size\tDe Novo\t$CNValls[0]\n";
shift @CNValls;
print "Opening pedfile: $pedfile\n";
open PED,'<',$pedfile or die "Cannot open file $pedfile: $!";
{ local $/= undef; our $input = <PED>; }
close PED;
(local $\) = (/(\r\n|\r|\n)/);
my @peds = split (/\r\n|\r|\n/, our $input); chomp @peds;
########################################################
#Merge prog Output file
# set variable offset for column numbering
my $extra = 1;
my $famID = 0 + $extra;
my $sampleID = 1 + $extra;
my $chromo = 2 + $extra;
my $lstart = 3 + $extra;
my $lstop = 4 + $extra;
my $cnvtype= 5 + $extra;
my $maxsize = 6 + $extra;
my $maxsnp = 7 + $extra;
my $lsize = 8 + $extra;
my $start = 10 + $extra;
my $stop = 11 + $extra;
my $size = 12 + $extra;
############################################################################
#pedfile - key: sampleID, value: all 6 columns of pedfile
#family_member - key: familyID, value: list of samples in that family
#which_family - key: sampleID, value: familyID
#which_mother - key: sampleID, value: mother's sampleID
#which_father - key: sampleID, value: father's sampleID
#which_child - key: either parent's sampleID, value: list of children's sampleID
#which_sibling - key: sampleID, value: list of sibling sampleIDs
#gender - key: sampleID, value: gender (0, 1, 2)
#gendername - key: sampleID, value: gender (Unknown, Male, Female)
#phenotype - key: sampleID, value: phenotype (0, 1, 2)
#namepheno - key: sampleID, value: Proband, Sibling, Unaffected child, Control, Father, Mother, Unknown
my ($pedfile, $family_member, $which_family, $which_mother, $which_father,
$which_child, $which_sibling, $gender, $gendername, $phenotype,
$namepheno) = &propedfile(@peds);
############################################################################
#Correct Family IDs in samples using the pedfile
my @CNVall;
foreach (@CNValls){
my @here = split ("\t", $_);
$here[$famID] = $which_family->{$here[$sampleID]};
push (@CNVall, join ("\t", @here)) if ($which_family->{$here[$sampleID]});
}
print "Sorting CNV file by Family\n";
#Sort by FamID (string)
@CNVall = sort { (split '\t', lc $a, 20)[$famID] cmp (split '\t', lc $b, 20)[$famID] } @CNVall;
print "There are ",scalar @CNVall," sorted CNV segments\n";
# Split CNV list into families with an array dedicated to each sample and
# then process each family as it ends
my $tracker2 = 0;
my $familiespres = 0;
my $setcount = 0;
my $error = 0;
my (%samp_cnv, %samplelog, %fammembers, %rare_loci, %com_loci, %dn_check);
foreach (@CNVall) {
my @now = split ("\t", $CNVall[$tracker2]);
my @after = split ("\t", $CNVall[$tracker2 + 1]) if ($tracker2 < $#CNVall);
$tracker2++;
#Each CNV is put into an array named after the sample ID
my $samphere = $now[$sampleID];
push (@{$samp_cnv{$samphere}}, $_);
$fammembers{$now[$sampleID]}++;
my ($themother, $thefather, $mothersize, $fathersize);
if (!$after[$famID] or $now[$famID] ne $after[$famID]) {
$familiespres++;
my $famnow = $now[$famID];
my @family = keys %fammembers;
%fammembers = ();
# BEGIN familyprod
my $famsize = @family;
#If the sample is not identified as a parent it must be a 'child'
foreach my $member (@family) {
my @commonarray;
my ($fathersize, $mothersize) = (0, 0);
if ($which_father->{$member} ne 0 and $which_mother->{$member} ne 0){
$thefather = $which_father->{$member};
$themother = $which_mother->{$member};
if (exists $samp_cnv{$thefather}){
$fathersize = @{$samp_cnv{$thefather}};
} else {
$fathersize = 0;
}
if (exists $samp_cnv{$themother}){
$mothersize = @{$samp_cnv{$themother}};
} else {
$fathersize = 0;
}
if ($samp_cnv{$thefather} and $samp_cnv{$themother}) {
#print "Calculating: Samp: $member, Fat: $thefather, Mot: $themother, ArrayF: $samp_cnv{$thefather}, ArrayM: $samp_cnv{$themother}\n"; sleep 2;
# BEGIN locimakerd
my @others;
push (@others, @{$samp_cnv{$thefather}});
push (@others, @{$samp_cnv{$themother}});
#Sort by Chromosome, then starting position
@others = sort {
(split '\t', lc $a)[$chromo] cmp (split '\t', lc $b)[$chromo]
|| (split '\t', $a)[$start] <=> (split '\t', $b)[$start]
} @others;
#Make the reference input file into loci
my $tracker = 0;
my $maxbase = 0;
my (@parent_match, @input);
foreach (@others){
my @before = split (/\t/, $others[$tracker - 1]) if ($tracker);
my @now = split (/\t/, $others[$tracker]);
my @after = split (/\t/, $others[$tracker + 1]) if ($tracker < $#others);
$tracker++;
# If this CNV is from a different chromosome or
# if it does not overlap with the last CNV or maxbase
# then start a new set
if ($tracker == 1
or lc $now[$chromo] ne lc $before[$chromo]
or ($now[$start] > $before[$stop]
and $now[$start] > $maxbase)) {
$maxbase = 0;
@parent_match = ($_);
} elsif (lc $now[$chromo] eq lc $before[$chromo]
and ($now[$start] <= $before[$stop]
or $now[$start] <= $maxbase)) {
# If it is the same chromosome and this CNV overlaps
# with the last or with maxbase
push (@parent_match, $_);
} else {
# If the CNV does not fit into either of the above groups then there is an error
print LOG1 showtime(),"\tDenovo\tERROR\tThe status of this CNV could not be determined:\t$_\n";
print "Error with the following CNV, its status could not be determined:\n$_\n";
$error++;
}
#If this CNV does not overlap with the next CNV then @parent_match is processed
if (!@after
or lc $now[$chromo] ne lc $after[$chromo]
or ($now[$stop] < $after[$start]
and $maxbase < $after[$start])) {
#Process @parent_match
my %bps;
my $chrm;
foreach (@parent_match) {
my @bp = split ("\t", $_);
$bps{$bp[$start]} = 0;
$bps{$bp[$stop]} = 0;
$chrm = $bp[$chromo];
}
my @bps = sort {$a <=> $b} keys %bps;
my $st = $bps[0];
my $en = $bps[-1];
my $arrayin = $chrm."\t".$st."\t".$en."\n";
push (@input, $arrayin);
undef @parent_match;
}
#Makes Maxbase the highest it can be
$maxbase = $now[$stop] if ($now[$stop] > $maxbase);
}
# Modify commonarray to same format as CNV file and make unique sampleID
my $dcounter = 0;
foreach my $line (@input){
my @essex = split ("\t", $line);
$dcounter++;
my @newarray;
$newarray[$sampleID] = "Common$dcounter";
$newarray[$chromo] = $essex[0];
$newarray[$start] = $essex[1];
$newarray[$stop] = $essex[2];
push @commonarray, join ("\t", map { defined $_ ? $_ : '' } @newarray);
}
# END locimakerd
my $commonsize1 = @commonarray;
push (@commonarray, @{$samp_cnv{$member}});
my $commonsize2 = @commonarray;
# BEGIN samplepro2d
$setcount++;
print "$setcount: $member) Family $famnow, $famsize members, $commonsize1 parent loci, $commonsize2 child CNVs\n";
#Sort by Chromosome, then starting position
@commonarray = sort {
(split '\t', lc $a)[$chromo] cmp (split '\t', lc $b)[$chromo]
|| (split '\t', $a)[$start] <=> (split '\t', $b)[$start]
} @commonarray;
my $track = 0;
#Does each CNV line up with the one below?
my @match;
$maxbase = 0;
foreach my $line (@commonarray){
my @before = split ("\t", $commonarray[$track - 1]) if ($track);
my @now = split ("\t", $commonarray[$track]);
my @after = split ("\t",$commonarray[$track + 1]) if ($track < $#commonarray);
$track++;
# If this CNV is from a differet sample or chromosome or
# if it does not overlap with the last CNV or maxbase
# then start a new set
if ($track == 1
or lc $now[$chromo] ne lc $before[$chromo]
or ($now[$start] > $before[$stop]
and $now[$start] > $maxbase)){
$maxbase = 0;
@match = ($line);
} elsif (lc $now[$chromo] eq lc $before[$chromo]
and ($now[$start] <= $before[$stop]
or $now[$start] <= $maxbase)) {
# If it is the same sample and chromosome and this
# CNV overlaps with the last or with maxbase
push (@match, $line);
} else {
# If the CNV does not fit into either of the above groups then there is an error
print LOG1 showtime(),"\tDenovo\tERROR\tThe status of this CNV could not be determined:\t$line\n";
print "Error with the following CNV, its status could not be determined:\n$line\n";
$error++;
}
#If this CNV does not overlap with the next CNV then @match is processed
if (!@after
or lc $now[$chromo] ne lc $after[$chromo]
or ($now[$stop] < $after[$start]
and $maxbase < $after[$start])) {
#Process @match
# BEGIN setexamined
# Put the start and stop positions into a new
# array and determine the characteristics of
# this group of matches
my ($sample, $chrm);
my %coord;
foreach (@match) {
my @temp = split (/\t/, $_);
$temp[$start] =~ s/^\s*(.+?)\s*$/$1/;
$temp[$stop] =~ s/^\s*(.+?)\s*$/$1/;
$coord{$temp[$start]} = 0;
$coord{$temp[$stop]} = 0;
if ($temp[$sampleID] !~ /Common/){
$sample = $temp[$sampleID];
$chrm = $temp[$chromo];
}
}
#Sort and determine the loci start and end
my @coord = sort {$a <=> $b} keys %coord;
my $algocount = 0;
my %uid;
################################################
#Look for matches at each line of the co-ord
my $counter = 0;
foreach my $bp (@coord) {
my $lastone = $coord[$counter - 1] if ($counter);
my $thisone = $coord[$counter];
my $nextone = $coord[$counter + 1] if ($counter < $#coord);
$counter++;
############################################
# For each coord look for matches in the start and stop coords
foreach my $line4 (@match){
my @cnvm = split ("\t", $line4);
# If the coord matches the start of a cnv the uid
# and features are added to hashes as the key and value
if ($thisone == $cnvm[$start]){
$algocount++;
chomp $cnvm[$sampleID];
$uid{$cnvm[$sampleID]} = $line4;
}
#If the coord matches the end of a CNV the uid and algo are removed from the hashes
if ($thisone == $cnvm[$stop]){
$algocount--;
chomp $cnvm[$sampleID];
delete ($uid{$cnvm[$sampleID]});
}
}
# Work out the size of this section
my $musize = $nextone - $thisone if ($nextone);
my @uidkeys = keys %uid;
my $commie = 0;
my $interest = 0;
my $samplepoint;
my @resize;
foreach my $key (@uidkeys){
if ($key =~ /Common/) {
$commie = 1;
} else {
@resize = split ("\t", $uid{$key});
$resize[$start] = $thisone;
$resize[$stop] = $nextone;
$resize[$size] = $musize;
$samplepoint = $key;
$interest = 1;
}
}
my $hashin = $resize[$sampleID].'_'.$resize[$chromo].'_'.$resize[$lstart].'_'.$resize[$lstop];
#print "Hash: $hashin\n"; sleep 1;
unless ($dn_check{$hashin} =~ /r|c/){
$dn_check{$hashin} = 'r';
$rare_loci{$resize[$sampleID]}++;
#print "Samp: $thissamp, Loci: $rare_loci{$thissamp}\n";sleep 1;
}
unless ($dn_check{$hashin} =~ /c/ or $commie != 1){
$dn_check{$hashin} = 'c';
$com_loci{$resize[$sampleID]}++;
}
# Printout this section of the match
if ($nextone and $interest) {
my $printout = join ("\t", map { defined $_ ? $_ : '' } @resize);
print $denovo_out "$gendername->{$samplepoint}\t$namepheno->{$samplepoint}\t$famsize\t$commie\t$printout\n";
#print "A This is $samplepoint\n" if ($samplepoint =~ /AU0613301_HI2119/);
$samplelog{$samplepoint} = {
'Phenotype' => $namepheno->{$samplepoint} ,
'Family Size' => $famsize ,
'De Novo Calculated' => 'Yes' ,
'De Novo: Loci' => $rare_loci{$samplepoint} ,
'De Novo: Inherited' => $com_loci{$samplepoint} ,
'De Novo: %Inherited' => sprintf ("%.2f", eval {$com_loci{$samplepoint} / $rare_loci{$samplepoint} * 100 } + 0 ).'%'
};
}
} # END setexamined
undef @match;
}
#Makes Maxbase the highest it can be
if ($now[$stop] > $maxbase){
$maxbase = $now[$stop];
}
} # END samplepro2d
} else {
print "Warning parental CNVs not found on both parents for $member. Father: $fathersize CNVs, Mother: $mothersize CNVs\n";
print LOG1 &showtime(),"\tDenovo\tERROR\tNo parental CNVs found for $member. Father: $fathersize CNVs, Mother: $mothersize CNVs\n";
foreach my $line (@{$samp_cnv{$member}}) {
my @tab = split /\t/, $line, $lstop+2;
my $hashin = $tab[$sampleID].'_'.$tab[$chromo].'_'.$tab[$lstart].'_'.$tab[$lstop];
unless ($dn_check{$hashin} =~ /r/){
$dn_check{$hashin} = 'r';
$rare_loci{$member}++;
}
print $denovo_out "$gendername->{$member}\t$namepheno->{$member}\t$famsize\t1\t$line\n";
#print "B This is $member\n" if ($member =~ /AU0613301_HI2119/);
$samplelog{$member} = {
'Phenotype' => $namepheno->{$member} ,
'Family Size' => $famsize ,
'De Novo Calculated' => 'No' ,
'De Novo: Loci' => $rare_loci{$member} ,
'De Novo: Inherited' => 0 ,
'De Novo: %Inherited' => '0%'
};
}
}
} else {
#This is a parental sample
foreach my $line (@{$samp_cnv{$member}}){
my @tab = split /\t/, $line, $lstop+2;
my $hashin = $tab[$sampleID].'_'.$tab[$chromo].'_'.$tab[$lstart].'_'.$tab[$lstop];
unless ($dn_check{$hashin} =~ /r/){
$dn_check{$hashin} = 'r';
$rare_loci{$member}++;
}
print $denovo_out "$gendername->{$member}\t$namepheno->{$member}\t$famsize\t1\t$line\n";
#print "C This is $member\n" if ($member =~ /AU0613301_HI2119/);
}
$samplelog{$member} = {
'Phenotype' => $namepheno->{$member} ,
'Family Size' => $famsize ,
'De Novo Calculated' => 'No' ,
'De Novo: Loci' => $rare_loci{$member} ,
'De Novo: Inherited' => 0 ,
'De Novo: %Inherited' => '0%'
};
}
}
}
}
close $denovo_out;
print "Finished processing $tracker2 CNVs\n";
##################################################################################################################
my @result_cols = ('Phenotype', 'Family Size', 'De Novo Calculated', 'De Novo: Loci', 'De Novo: Inherited', 'De Novo: %Inherited');
foreach my $col (@result_cols) {
&add_sample_col($col);
}
my $totalsamples = keys %samplelog;
my $samplecounter = 0;
foreach my $samp (sort keys %sample_idx) {
if ($samplelog{$samp}) {
$samplecounter++;
#print "Doing sample $samplecounter) $samp\n";
foreach my $col (@result_cols) {
#print $samplelog{$samp}->{$col}."\n";
&set_sample_value($samp, $col, $samplelog{$samp}->{$col});
}
} else {
foreach my $col (@result_cols) {
&set_sample_value($samp, $col, 0);
}
print LOG1 &showtime(),"\tDenovo\tERROR\tNo loci present for $samp\n";
print "ERROR: No loci present for $samp\n";
}
}
if ($samplecounter == $totalsamples){
print LOG1 &showtime(),"\tDenovo\tINFO\tDe Novo comparison complete for $totalsamples samples from $familiespres families\n";
print "De Novo comparison complete for $totalsamples samples from $familiespres families\n";
} else {
print LOG1 &showtime(),"\tDenovo\tERROR\tDe Novo comparison complete, however loci were present for samples that were not listed in the Samplelist file\n";
print "ERROR: De Novo comparison complete, however loci were present for samples that were not listed in the Samplelist file, $totalsamples, $samplecounter\n";
}
print "All done!\n";
}
# Convert FinalReport files to QuantiSNP and PennCNV format before processing -- This is redundant
sub init_sort_snp {
my $forker = shift;
my (%snptype, %snpcount);
my @output = &fr_list;
foreach my $file (@output){
my @tab = split /\t/, $file;
unless (-e $tab[3].'_Sorted.txt'){
$snptype{$tab[3]} = $tab[0];
$snpcount{$tab[0]} = $tab[3];
}
}
my @frtosort = (values %snptype);
# Stage 1 --sortsnp, Processing
if ($processors == 1) {
#sort_snp( \@frtosort );
} else {
my @batches = get_batches($processors, @frtosort);
foreach my $batch (@batches) {
print "Batch: $batch\n";
my $pid = $forker->start and next;
sort_snp( $batch );
$forker->finish;
}
#wait for all threads to complete
$forker->wait_all_children;
# Stage 2 --convert, Merging
# no merging necessary
}
}
###############################################################################
############### --annotate ###############
###############################################################################
# This is the annotation programe, the first bit lists the files that will be
# used for annotation using a custom annotation file if present
sub annotate {
my $cnv_results = shift;
my $custfile = "$working_dir${dir_sep}Custom_annotation.txt";
my $custfile2 = "$ANloc${dir_sep}Custom_annotation.txt";
my ($genesfile1, $tdgvfile);
my (@inputfiles, %files, %firstcolhash, %perhash, %disthash);
if (-e $custfile or -e $custfile2) {
print "Loading custom annotation file\n";
my $custom;
if (-e $custfile) {
open $custom,'<',$custfile or die "Could not open custom annotation file $custfile: $!\n";
} elsif (-e $custfile2) {
open $custom,'<',$custfile2 or die "Could not open custom annotation file $custfile2: $!\n";
}
# Load the custom file, remove the header line
my @custom;
while (<$custom>) {
s/[\r\n]+$//;
push @custom, $_;
}
close $custom;
shift @custom;
my $inputcounter = 1;
foreach my $line (@custom) {
my @tab = split (/\t/, $line);
if ($tab[1] =~ /Gene_list/) {
$genesfile1 = $tab[0];
$inputfiles[0] = $genesfile1;
$firstcolhash{$genesfile1} = 'Y';
$perhash{$genesfile1} = $tab[2];
$disthash{$genesfile1} = $tab[3];
} elsif ($tab[1] =~ /DGV_file/) {
$tdgvfile = $tab[0];
$inputfiles[1] = $tdgvfile;
$firstcolhash{$tdgvfile} = 'Y';
$perhash{$tdgvfile} = $tab[2];
$disthash{$tdgvfile} = $tab[3];
} else {
$inputcounter++;
my $firstcolhashinput = "N";
my $perhashinput = "N";
my $disthashinput = "N";
my $keepcount = 0;
for (my $tabcount = 0; $tabcount < @tab; $tabcount++) {
my $tab = $tab[$tabcount];
$keepcount++ if (defined $tab or uc $tab ne 'N');
if (uc $tab eq "Y" and $tabcount == 2) {
$firstcolhashinput = "Y";
} elsif (uc $tab eq "Y" and $tabcount == 3) {
$perhashinput = "Y";
} elsif (uc $tab eq "Y" and $tabcount == 4) {
$disthashinput = "Y";
} elsif ($tabcount >= 5){
# 'N' or '' means do not include
# 'Y' or 'Name' means return unique names
# 'Num' means return number of unique names
# 'Total' means return total of all calls (not reliable if there are duplicates)
# 'Max' means return highest number
# 'Min' means return lowest number
$files{$tab[0]}->{$tabcount} = $tab;
}
}
#This is where the files are put into the array to be loaded
$inputfiles[$inputcounter] = $tab[0] unless ($keepcount == 0);
$disthash{$tab[0]} = $disthashinput;
$perhash{$tab[0]} = $perhashinput;
$firstcolhash{$tab[0]} = $firstcolhashinput;
}
}
} else {
$genesfile1 = "hg18_UCSC_genes_merged_no_duplicate.txt";
push (@inputfiles, $genesfile1);
my %exclude = ( "Genome" => 1 ,
"AN_setup.txt" => 1 ,
"AN_custom_annotation.txt" => 1 ,
"hg18_cnvsnps.txt" => 1 ,
"Annotation.zip" => 1 ,
"hg18_AIMs.txt" => 1 ,
"tempanno" => 1 ,
"Custom_annotation.txt" => 1 ,
"plink.exe" => 1 ,
"Hapmap_LD.prune.in" => 1 ,
"dbSNP_build130.txt" => 1 ,
"dbSNP_build130.zip" => 1 ,
"Annotation_v1.0" => 1 );
my @tempfiles = <$ANloc$dir_sep*>;
# If there is no custom annotation file in the working directory then all
# the files in the annotation folder are loaded
#Checks file is not in exclude list
foreach my $foundfile (@tempfiles){
if (-f $foundfile){
if ($foundfile ne $genesfile1 and !$exclude{$foundfile} and $foundfile !~ /PreMerged_/){
push (@inputfiles, $foundfile);
if ($foundfile =~ /variation.hg18/ && $foundfile !~ /McC/){
$tdgvfile = $foundfile;
}
}
#If in this hash with N do not give percent
$perhash{$foundfile} = "N";
$firstcolhash{$foundfile} = "Y";
}
}
}
print "Genes: $genesfile1\n";
print "DGV: $tdgvfile\n";
my $newfile = $cnv_results;
$newfile =~ s/^.+$dir_sep//;
$newfile = "$fin_dir${dir_sep}Annot_$newfile";
open my $anno_out,'>',$newfile or die "Could not open the results file $newfile: $!";
my @finaldata;
print "Loading input file for $cnv_results\n";
open my $finaldata,'<',$cnv_results or die "Could not open the results file $cnv_results: $!";
while (<$finaldata>) {
s/[\r\n]+$//;
push @finaldata, $_;
}
close $finaldata;
my ($chromocol, $upchromodist, $downchromodist, $headme);
my $hereonly = $tag . "_HD";
if ($cnv_results =~ /$hereonly/){
$chromocol = 5;
$upchromodist = 6;
$downchromodist = 7;
$headme = "y";
} else {
$chromocol = 7;
$upchromodist = 8;
$downchromodist = 9;
$headme = "y";
}
######################################################
# Now we filter for known variants and add annotation
######################################################
print "\nChecking Toronto Database of Genomic Variants for latest file...\n";
my $fail = 0;
get("http://www.google.com") or do { $fail = 1};
if ($fail) {
print "Could not connect to the access server, as you appear to be offline.\n";
print "We will not check the site\n";
} else {
my $content = get('http://projects.tcag.ca/variation/tableview.asp?table=DGV_Content_Summary.txt');
my @page = split("\n", $content);
my $uptodate;
foreach my $guy (@page){
if ($guy =~ /current/i){
$uptodate = "yes";
} elsif ($guy =~ /older/i){
$uptodate = "no";
}
if ($guy =~ /variation.hg18/ and $uptodate eq "yes"){
my @bits = split("'>", $guy);
$bits[1] =~ s|</a>\&nbsp;</font\>\</td>||;
print "Current version is $bits[1]\n";
if ($bits[1] eq $tdgvfile){
print "We are up to date\n";
} else {
print "ERROR: You're version is $tdgvfile\nYou need to download the latest version and place it into this directory\n";
print LOG1 showtime(),"\tAnnotation\tERROR\tCurrent DGV file is $bits[1] and we are using $tdgvfile\n";
}
}
}
}
# Overlap > 0 not currently supported, but may be at some point
my ($overlap, $sampleoverlap) = 0;
if ($overlap) {
$sampleoverlap = $overlap / 100;
} else {
$sampleoverlap = 0;
}
my $bigguy = $sampleoverlap * 100;
if ($bigguy > 0){
print "Checking for regions $bigguy% overlap with known CNVs ($sampleoverlap)\n";
}
my $genome = "hg18";
my @chrs = qw(CHR1 CHR2 CHR3 CHR4 CHR5 CHR6 CHR7 CHR8 CHR9 CHR10
CHR11 CHR12 CHR13 CHR14 CHR15 CHR16 CHR17 CHR18 CHR19 CHR20
CHR21 CHR22 CHRX CHRY);
my $premerged_file = $genesfile1;
if ($genesfile1 =~ /$ANloc/) {
$premerged_file =~ s/$dir_sep([^$dir_sep]+)$/${dir_sep}PreMerged_$1/;
} else {
$genesfile1 = $ANloc.$dir_sep.$genesfile1;
$premerged_file = "$ANloc${dir_sep}PreMerged_$premerged_file";
}
print "\nLoading genes and exons from $genesfile1";
my @premerge;
if (-e $premerged_file){
open my $in,'<',$premerged_file or die "Could not open $premerged_file: $!";
while (<$in>) {
s/[\r\n]+$//;
push @premerge, $_;
}
}
open my $genes,'<',$genesfile1 or die "Could not the genes file $genesfile1: $!";
my @genesfile;
while (<$genes>) {
s/[\r\n]+$//;
push @genesfile, $_;
}
close $genes;
# The gene files are loaded into a hash of chromosome specific arrays named
# CHR#. e.g., @{$chr{'CHR1'}}
my $tracker = 0;
my (%phanlist, %chr);
for (my $z = 0; $z < @genesfile; $z++) {
my ($ENSG, $chromo, $start_gene, $stop_gene, $gene_start, $gene_stop,
$name, $exon, $size) = split("\t", $genesfile[$z]);
if ($z >= $tracker and !$javamethod) {
print "\rLoading genes and exons from $genesfile1... $z";
$tracker += 50;
}
#This submits the gene positions to a hash that will become the first file in @inputfiles
my $phangene = "$ENSG\t$chromo\t$start_gene\t$stop_gene";
$phanlist{$phangene}++;
#This is the original that makes an array of exon starts and stops
my $newexon = "$ENSG\t$chromo\t$gene_start\t$gene_stop\t$name\t$exon\t$size";
$chromo = "CHR" . $chromo;
push @{$chr{$chromo}}, $newexon;
}
my @gene_pos_list = keys %phanlist;
# Here the annotation files are loaded into chromosome specific arrays called
# $ct.CHR.chr number eg 0CHR1
my %fileheaders;
for (my $ct = 0; $ct < @inputfiles; $ct++) {
my $countah = 0;
my @input;
my $premerged = 0;
my $inputhere = $inputfiles[$ct];
if ($ct == 0){
if ($#premerge > $#gene_pos_list){
@input = @premerge;
} else {
@input = @gene_pos_list;
}
} else {
print "Loading file $inputfiles[$ct]";
if ($inputfiles[$ct] =~ /$ANloc/) {
($premerged_file = $inputfiles[$ct]) =~ s/$dir_sep([^$dir_sep]+)$/${dir_sep}PreMerged_$1/;
} else {
$inputhere = "$ANloc$dir_sep$inputfiles[$ct]";
$premerged_file = "$ANloc${dir_sep}PreMerged_$inputfiles[$ct]";
}
if (-e $premerged_file) {
open my $in,'<',$premerged_file or die "Could not open $premerged_file: $!";
while (<$in>) {
s/[\r\n]+$//;
push @input, $_;
}
$premerged = 1;
} else {
open my $in,'<',$inputhere or die "Could not open $inputhere: $!";
while (<$in>) {
s/[\r\n]+$//;
push @input, $_;
}
}
}
#This makes a hash of fileheaders
$fileheaders{$inputfiles[$ct]} = $input[0];
#Now sort the custom file
if ($inputhere =~ /variation.hg/ and $inputhere !~ /McC/ and !$premerged) {
my @dgvcorrect;
foreach (@input){
my @tab = split (/\t/,$_);
#DGV will become: Name, Chr, Start, Stop, Papers, Gain, Loss, Total
my $dgvcorrect = "$tab[0]\t$tab[2]\t$tab[3]\t$tab[4]\t$tab[9]\t$tab[12]\t$tab[13]\t$tab[14]";
push (@dgvcorrect, $dgvcorrect);
}
@input = @dgvcorrect;
}
@input = sort {
(split '\t', $a, 4)[1] cmp (split '\t', $b, 4)[1]
|| (split '\t', $a, 4)[2] <=> (split '\t', $b, 4)[2]
} @input;
# set column indexes
my ($sampleID, $chromo, $start, $stop) = 0..3;
#This looks for overlap in the reference file; if found flag = 1
my ($pchromo, $pstop, $flag) = ( '', 0 , 0 );
foreach my $piece (@input){
my @pnow = split (/\t/, $piece);
if ($pnow[$chromo] eq $pchromo && $pnow[$start] <= $pstop) {
$flag = 1;
last;
}
$pchromo = $pnow[$chromo];
$pstop = $pnow[$stop];
}
if ($flag) {
print "\nOverlapping regions detected, merging regions to correct\n";
############################################
## Start of Merge Function for Custom Files
############################################
@input = MergeAnnotation();
##########################################
## End of Merge Function for Custom Files
##########################################
}
my $input_counter = 0;
foreach (@input) {
#This is the dgv file - note numpaps vs nums
my $pusher;
if ($inputfiles[$ct] eq $tdgvfile){
my ($name, $chromo, $gene_start, $gene_stop, $na, $g1, $l1, $t, $freq) = split /\t/, $_;
$chromo = uc $chromo;
my $g12 = 0;
$g12 += (/\d/ ? $_ : 0) for split (/, /, $g1);
my $l12 = 0;
$l12 += (/\d/ ? $_ : 0) for split (/, /,$l1);
my $t2 = 0;
$t2 += (/\d/ ? $_ : 0) for split (/, /,$t);
$pusher = "$name\t$chromo\t$gene_start\t$gene_stop\t$na\t$g12\t$l12\t$t2\t";
} else {
my ($name, $chromo, $gene_start, $gene_stop, $na, $g1, $l1, $t, $freq, $nums) = split ("\t", $_);
$chromo = uc $chromo;
my @temp = ($name, $chromo, $gene_start, $gene_stop, $na, $g1, $l1, $t, $freq);
$pusher = join("\t",map { defined $_ ? $_ : '' } @temp,'');
#$pusher = "$name\t$chromo\t$gene_start\t$gene_stop\t$na\t$g1\t$l1\t$t\t$freq\t";
}
$input_counter++;
if ($input_counter >= $tracker and $javamethod == 0){
print "\rLoading file $inputfiles[$ct]... $input_counter";
$tracker += 25;
}
$chromo =~ s/chr//i;
$chromo = "${ct}CHR$chromo";
push(@{$chr{$chromo}}, $pusher);
}
print "\n";
}
my @headtemp = split("\t", $finaldata[0]);
if ($headme =~ /N/i) {
print $anno_out join "\t", @headtemp;
} else {
print $anno_out "$finaldata[0]\t";shift @finaldata;
}
my $dtotal = @finaldata;
print "\nNow annotating your $dtotal lines\n";
print LOG1 showtime(),"\tAnnotation\tINFO\t$dtotal lines to be annotated\n";
print $anno_out "Gene\tLocation\t#Genes\t#Exons\t5'gene\t5'dist(kb)\t3'gene\t3'dist(kb)\t";
#This is for the headers of the custom files
for (my $ct=1; $ct <= $#inputfiles; $ct++) {
if ($inputfiles[$ct] =~ /variation.hg18/ && $inputfiles[$ct] !~ /McC/i){
print $anno_out "dups(DGV)\tdels(DGV)\ttotal_known_CNVs(DGV)\tnum_papers(DGV)\tpapers\t";
} elsif ($inputfiles[$ct] =~ /McCarroll/i) {
print $anno_out "CNP_dups(McCarroll)\tCNP_dels(McCarroll)\tCNPsall(McCarroll)\t";
} else {
my $filehere = $inputfiles[$ct];
print $anno_out "$filehere\t" if ($firstcolhash{$filehere} =~ /y/i);
print $anno_out "$filehere %overlap\t" if ($perhash{$filehere} !~ /n/i);
print $anno_out "$filehere 5'feature\t$filehere 5'dist(kb)\t$filehere 3'feature\t$filehere 3'dist(kb)\t" if ($disthash{$filehere} !~ /n/i);
my @extracolumns;
@extracolumns = sort {$a <=> $b} keys %{$files{$filehere}};
my @newhead = split (/\t/, $fileheaders{$filehere});
foreach my $edge (@extracolumns) {
# the user puts a column, but Perl starts counting at zero, so
my $newedge = ($edge - 1);
if ($files{$filehere}->{$edge} =~ /y/i or $files{$filehere}->{$edge} =~ /Name/i){
print $anno_out "${filehere}_$newhead[$newedge]\t";
} elsif ($files{$filehere}->{$edge} =~ /Num/i) {
print $anno_out "${filehere}_$newhead[$newedge]_Number\t";
} elsif ($files{$filehere}->{$edge} =~ /Total/i) {
print $anno_out "${filehere}_$newhead[$newedge]_Total\t";
} elsif ($files{$filehere}->{$edge} =~ /Max/i) {
print $anno_out "${filehere}_$newhead[$newedge]_Max\t";
} elsif ($files{$filehere}->{$edge} =~ /Min/i) {
print $anno_out "${filehere}_$newhead[$newedge]_Min\t";
}
}
}
}
print $anno_out "\n";
print "Finished\n";
my $countah = 0;
my $found = 0;
my (%allthrees, %allfives, %allhits);
# Here the input file is processed, each line is a region in @finaldata
foreach (@finaldata) {
$countah++;
if ($countah >= $tracker and $javamethod == 0){
$tracker += 50;
print "\r$tracker completed...";
} elsif ($countah >= $tracker and $javamethod == 1){
$tracker += 5000;
print "\r$tracker completed...";
}
my @fornow = split("\t", $_);
my $chrom = $fornow[$chromocol];
my $head = $fornow[$upchromodist];
my $tail = $fornow[$downchromodist];
$head =~ s/[,"]//g;
$tail =~ s/[,"]//g;
my $headtotail= ($tail - $head +1);
$chrom =~ s/chr//i;
$chrom = "CHR" . uc $chrom;
my $endspot = $#{$chr{$chrom}};
my $begspot = 0;
my $size = $#{$chr{$chrom}};
# Of note the $newspot is rounded using a subroutine here
my $newspot = round($size / 2);
my $found = 0;
my (@genes, @exons, @introns, @names);
my ($type, $oldspot);
my ($fivegene, $threegene) = qw(in in);
my ($fivedist, $threedist) = (0, 0);
print $anno_out "$_\t";
# Check for empty chromosome
if ($#{$chr{$chrom}} == 0) {
$found = 1;
}
# Here it deals with genes and exons from the genes file that was loaded
# spearately (format CHR.chr number)
my ($oldgene, $inspot, $incheck, @intergenic) = '';
do {
my ($ENSG0, $chromo0, $prev_gene_start, $prev_gene_stop, $name0, $exon0, $size0) = split("\t", $chr{$chrom}->[$newspot - 1]) if ($newspot > 0);
my ($ENSG, $chromo, $gene_start, $gene_stop, $name, $exon, $size) = split("\t", $chr{$chrom}->[$newspot]);
my ($ENSG2, $chromo2, $next_gene_start, $next_gene_stop, $name2, $exon2, $size2) = split("\t", $chr{$chrom}->[$newspot + 1]) if ($newspot < $#{$chr{$chrom}});
# If the head and tail lie within an exon then the region is fully
# within an exon
# Elsif the head and tail lie either side of an exon then there is
# an exon inside
# Elsif newspot has hit a region where the exon extends in the 5'
# direction
# Elsif newspot has hit a region where the exon extends in the 3'
# direction
# Elsif The region is between two exons (before and current) without
# touching either 5'
# Elsif the region is between two exons (current and next) without
# touching either 3'
# Elsif the region is before the first exon at the 5' end of the
# chromosome
# Elsif the region is after the last exon at the 3' end of the
# chromosome
# Else newspot is not hitting any of the scenarios, repeat
my $oldguy = '';
if ($gene_start <= $head && $tail <= $gene_stop){ #region inside of exon
my $found = 1;
$type = "Exon";
push (@genes, $name);
push (@exons, $exon);
} elsif ($gene_start >= $head && $tail >= $gene_stop) {
# exon inside of region
$found = 1;
$type = "Exon";
push (@genes, $name);
push (@exons, $exon);
#Here the algorithm looks in the 5' direction to find other
# exons that might be in the region
my $inspot = $newspot;
$incheck = 0;
$oldgene = '';
do {
if ($inspot > 0) {
$inspot--;
my ($ENSG, $chromo, $gene_start, $gene_stop, $name, $exon, $size) = split("\t", $chr{$chrom}->[$inspot]);
if ($head < $gene_start) {
push (@genes, $name);
push (@exons, $exon);
push (@introns, $exon);
} elsif ($head >= $gene_start && $head <= $gene_stop) {
$incheck = 1;
push (@genes, $name);
push (@exons, $exon);
push (@introns, $exon);
} else {
$incheck = 1;
push (@introns, $ENSG) if ($ENSG eq $oldgene);
}
$oldgene = $ENSG;
}
} until ($incheck || !$inspot);
$inspot = $newspot;
$incheck = 0;
# Here the algorithm looks in the 3' direction to find other
# exons that might be in the region
do {
if ($inspot < $#{$chr{$chrom}}) {
$inspot++;
($ENSG, $chromo, $gene_start, $gene_stop, $name, $exon, $size) = split("\t", $chr{$chrom}->[$inspot]);
if ($tail > $gene_stop) {
push (@genes, $name);
push (@exons, $exon);
push (@introns, $exon);
} elsif ($tail >= $gene_start && $tail <= $gene_stop) {
$incheck = 1;
push (@genes, $name);
push (@exons, $exon);
push (@introns, $exon);
} else {
$incheck = 1;
push (@introns, $exon) if ($ENSG eq $oldgene);
}
$oldgene = $ENSG;
}
} until ($incheck || $inspot >= $#{$chr{$chrom}});
$found = 1;
} elsif ($gene_start <= $tail && $tail <= $gene_stop){
#exon 5' overlap
push (@genes, $name);
push (@exons, $exon);
$type = "Exon";
$inspot = $newspot;
$incheck = 0;
#Here the algorithm looks in the 5' direction to find other exons that might be in the region
do {
$inspot-- unless ($newspot <= 0);
my ($ENSG, $chromo, $gene_start, $gene_stop, $name, $exon, $size) = split("\t", $chr{$chrom}->[$inspot]);
if ($head < $gene_start){
push (@genes, $name);
push (@exons, $exon);
push (@introns, $exon);
} elsif ($head >= $gene_start && $head <= $gene_stop) {
$incheck = 1;
push (@genes, $name);
push (@exons, $exon);
push (@introns, $exon);
} else {
$incheck = 1;
push (@introns, $ENSG) if ($ENSG eq $oldgene);
}
$oldgene = $ENSG;
} until($incheck==1 or $inspot<=0);
$found = 1;
} elsif ($gene_start <= $head && $gene_stop >= $head){
#exon 3' overlap
push (@genes, $name);
push (@exons, $exon);
$type = "Exon";
$inspot = $newspot;
$incheck = 0;
# Here the algorithm looks in the 3' direction to find other
# exons that might be in the region
do {
$inspot++;
my ($ENSG, $chromo, $gene_start, $gene_stop, $name, $exon, $size) = split("\t", $chr{$chrom}->[$inspot]);
if ($tail > $gene_stop) {
push (@genes, $name);
push (@exons, $exon);
push (@introns, $exon);
} elsif ($tail >= $gene_start && $tail <= $gene_stop) {
$incheck = 1;
push (@genes, $name);
push (@exons, $exon);
push (@introns, $exon);
} else{
$incheck=1;
push (@introns, $exon) if ($ENSG eq $oldgene);
}
$oldgene = $ENSG;
} until ($incheck || $inspot >= $#{$chr{$chrom}});
$found = 1;
} elsif ($head > $prev_gene_stop && $tail< $gene_start) {
push (@intergenic, $_);
$type = "Intergenic";
$fivegene = $name0;
$threegene = $name;
$fivedist = ($head - $prev_gene_stop) / 1000;
$threedist = ($gene_start - $tail) / 1000;
$found = 1;
} elsif ($head > $gene_stop && $tail< $next_gene_start ) {
push (@intergenic, $_);
$type = "Intergenic";
$fivegene = $name;
$threegene = $name2;
$fivedist = ($head - $gene_stop) / 1000;
$threedist = ($next_gene_start - $tail) / 1000;
$found = 1;
} elsif ($tail < $gene_start && $tail< $gene_stop && $newspot==0) {
push (@intergenic, $_);
$type = "Intergenic";
$fivegene = $name;
$threegene = "StartChr";
$fivedist = ($gene_start - $tail) / 1000;
$threedist = "StartChr";
$found = 1;
} elsif ($head > $gene_start && $head > $gene_stop && $newspot>=$#{$chr{$chrom}}) {
$type="Intergenic";
$fivegene = $name;
$threegene = "EndChr";
$fivedist = ($head - $gene_stop) / 1000;
$threedist = "EndChr";
$found=1;
} else {
if ($tail < $gene_start) {
#then we want the first half
$oldspot = $newspot;
$endspot = $newspot;
$newspot = $begspot + ($endspot - $begspot) / 2;
$newspot = round($newspot);
} else {
my $oldspot = $newspot;
$begspot = $newspot;
$newspot = $begspot + ($endspot - $begspot) / 2;
if ($newspot > $#{$chr{$chrom}}){$newspot=$#{$chr{$chrom}}; }
$newspot = round($newspot);
}
}
$newspot = 0 if ($oldguy);
$oldguy = $newspot;
} until ($found);
my @ordered_genes = sort @genes;
my @hitgenes;
my $old = '';
# find out how many unique functions are involved
foreach (@ordered_genes) {
push (@hitgenes, $_) unless ($_ eq $old);
$old = $_;
}
shift(@hitgenes);
my $genecount = @hitgenes;
my $genelist = join ', ', @hitgenes;
%allhits = map { $_ => 1 } @hitgenes;
$genelist = 'NA' if ($type eq 'Intergenic');
shift(@exons);
my $numgenes = @hitgenes;
my $numexons = @exons;
$allthrees{$threegene}++;
$allfives{$fivegene}++;
my $exonlistouttype = $type;
my $exonlistout = "$numexons\t$fivegene\t$fivedist\t$threegene\t$threedist";
my $ogchrom = $chrom;
#This is where the inputfiles are used (ie after the genes)
for (my $ct = 0; $ct < @inputfiles; $ct++) {
$chrom = $ct . $ogchrom;
my ($totaldups, $totaldels, $totalcnvs, $begspot, $found) = (0,0,0,0,0);
my (@known, @names, @dups, @dels, @tots, @covers, @nibs, @dist3, @dist5);
$endspot = $#{$chr{$chrom}};
$begspot = 0;
$size = $#{$chr{$chrom}};
my $truesize = @{$chr{$chrom}};
$newspot = ($size / 2);
#Again a rounding subroutine
$newspot = round($newspot);
# All this is if there is only one term in the chromosome specific
# array relating to that input file
my $percover;
if ($truesize == 0) {
$found = 1;
} else {
do {
my ($name0, $chromo0, $prev_gene_start, $prev_gene_stop, $na0, $g0, $l0, $t0, $nib0) = split(/\t/, $chr{$chrom}->[$newspot - 1]) if ($newspot);
my ($name, $chromo, $gene_start, $gene_stop, $na, $ga, $la, $ta, $nib) = split(/\t/, $chr{$chrom}->[$newspot]);
my ($name2, $chromo2, $next_gene_start, $next_gene_stop, $na2, $g2, $l2, $t2, $nib2) = split(/\t/, $chr{$chrom}->[$newspot + 1]) if ($newspot < $#{$chr{$chrom}});
if ($gene_start <= $head && $tail <= $gene_stop) {
#region inside of exon
$percover = 1;
} elsif ($gene_start >= $head && $tail >= $gene_stop) {
# exon inside of region
$percover = ($gene_stop - $gene_start) / $headtotail;
} elsif ($gene_start <= $tail && $tail <= $gene_stop) {
# exon 5' overlap
$percover = ($tail - $gene_start) / $headtotail;
} elsif ($gene_start <= $head && $head <= $gene_stop) {
# exon 3' overlap
$percover = ($gene_stop - $head) / $headtotail;
} else {
$percover = 0;
}
#Exon start is less than or equal to the region start and exon end is greater than or equal to the region end
# -------------------------- exon
# ---------------- region
if ($gene_start <= $head && $tail <= $gene_stop) { #region inside of exon
$found = 1;
push (@names, $name);
push (@known, $na);
push (@dups,$ga);
push (@dels,$la);
push (@tots,$ta);
push (@nibs, $nib);
push (@covers, $percover);
$inspot = $newspot;
$incheck = 0;
do {
unless (!$newspot) {
$inspot--;
my ($name, $chromo, $gene_start, $gene_stop, $na, $ga, $la, $ta, $nib) = split("\t", $chr{$chrom}->[$inspot]);
#let's figure out the overlap
if ($gene_start <= $head && $tail <= $gene_stop) {
# region inside of exon
$percover = 1;
} elsif ($gene_start >= $head && $tail >= $gene_stop) {
# exon inside of region
$percover = ($gene_stop - $gene_start) / $headtotail;
} elsif ($gene_start <= $tail && $tail <= $gene_stop) {
# exon 5' overlap
$percover = ($tail - $gene_start) / $headtotail;
} elsif ($gene_start <= $head && $head <= $gene_stop) {
# exon 3' overlap
$percover = ($gene_stop - $head) / $headtotail;
} elsif ($head > $prev_gene_stop && $tail < $gene_start) {
# Not in an exon
$percover = 0;
} elsif ($head > $gene_stop && $tail > $gene_start && $newspot == $#{$chr{$chrom}}) {
# Not in an exon, end chr
$percover = 0;
} elsif ($head < $gene_stop && $tail < $gene_start && $newspot == 0) {
# Not in an exon, start chr
$percover = 0;
} elsif ($head > $gene_stop && $tail< $next_gene_start ){
# Not in an exon
$percover = 0;
} else {
# Need to go through binary search to find this one
$percover = 0;
}
if (($gene_start <= $head && $tail <= $gene_stop)
or ($head < $gene_start && $tail > $gene_stop)) {
push (@names, $name);
push (@known, $na);
push (@dups,$ga);
push (@dels,$la);
push (@tots,$ta);
push (@nibs, $nib);
push (@covers, $percover);
} elsif($head >= $gene_start && $head <= $gene_stop) {
$incheck = 1;
if($percover >= $sampleoverlap) {
push (@names, $name);
push (@known, $na);
push (@dups,$ga);
push (@dels,$la);
push (@tots,$ta);
push (@nibs, $nib);
push (@covers, $percover);
}
$inspot--;
} else {
$incheck = 1;
}
}
} until ($incheck || !$inspot);
($name, $chromo, $gene_start, $gene_stop, $na, $ga, $la, $ta, $nib) = split("\t", $chr{$chrom}->[$inspot]);
my $dist5in;
if ($inspot <= 0) {
$dist5in = "StartChr\tStartChr";
} else {
my $dist5 = ($head - $gene_stop)/1000;
$dist5in = "$name\t$dist5";
}
push (@dist5, $dist5in);
$inspot = $newspot;
$incheck = 0;
do {
unless ($newspot >= $#{$chr{$chrom}}) {
$inspot++;
($name, $chromo, $gene_start, $gene_stop, $na, $ga, $la, $ta, $nib) = split("\t", $chr{$chrom}->[$inspot]);
if ($gene_start <= $head && $tail <= $gene_stop) {
# region inside of exon
$percover = 1;
} elsif ($gene_start >= $head && $tail >= $gene_stop) {
# exon inside of region
$percover = ( ($gene_stop - $gene_start) / $headtotail );
} elsif ($gene_start <= $tail && $tail <= $gene_stop) {
# exon 5' overlap
$percover = ( ($tail - $gene_start) / $headtotail );
} elsif ($gene_start <= $head && $head <= $gene_stop) {
# exon 3' overlap
$percover = ( ($gene_stop - $head) / $headtotail );
} elsif ($head > $prev_gene_stop && $tail < $gene_start) {
# Not in an exon
$percover = 0;
} elsif ($head > $gene_stop && $tail > $gene_start && $newspot==$#{$chr{$chrom}}) {
# Not in an exon, end chr
$percover = 0;
} elsif ($head < $gene_stop && $tail < $gene_start && $newspot == 0) {
# Not in an exon, start chr
$percover = 0;
} elsif ($head > $gene_stop && $tail< $next_gene_start ) {
# Not in an exon
$percover = 0;
} else {
# Need to go through binary search to find this one
$percover = 0;
}
if (($gene_start <= $head && $tail <= $gene_stop)
or ($tail > $gene_stop)) {
push (@names, $name);
push (@known, $na);
push (@dups,$ga);
push (@dels,$la);
push (@tots,$ta);
push (@nibs, $nib);
push (@covers, $percover);
} elsif ($tail >= $gene_start && $tail <= $gene_stop) {
$incheck = 1;
if ($percover >= $sampleoverlap) {
push (@names, $name);
push (@known, $na);
push (@dups,$ga);
push (@dels,$la);
push (@tots,$ta);
push (@nibs, $nib);
push (@covers, $percover);
}
$inspot++;
} else {
$incheck=1;
}
}
} until ($incheck || $inspot >= $#{$chr{$chrom}});
($name, $chromo, $gene_start, $gene_stop, $na, $ga, $la, $ta, $nib) = split("\t", $chr{$chrom}->[$inspot]);
my $dist3in;
if ($inspot >=<