view rapsodyn/mpileupfilter.pl @ 17:9435ccd4e0c4 draft

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#!/usr/bin/perl
use strict;
use Getopt::Long;

#
# Filter a pileup file on forward/reverse presence and %read having the variant
# The error code 
#  1 : multiple variant type detected insertion/deletion/mutation
#  1i : inconsistency in insertion
#  1d : inconsistency in deletion
#  1m : inconsistency in mutation
#  2 : insufficient depth	
#  3 : insufficient variant frequency 
#  4 : variant position not covered by forward and reverse reads
#  5 : variant with other variant in neighbourhood
#  6 : too much depth
#  8 : parsing error (couldn't parse the mpileup line correctly)
#  9 : parsing error (couldn't parse the readbase string correctly)


my $inputfile;
my $logfile;
my $MIN_DISTANCE=0;
my $MIN_VARIANTFREQUENCY=0;
my $MIN_FORWARDREVERSE=0;
my $MIN_DEPTH=0;
my $MAX_DEPTH=500;
my $VERBOSE=0;
my $ONLY_UNFILTERED_VARIANT="OFF";

if ($#ARGV<0){
	print "\n";
	print "perl 020_FilterPileupv6 -input_file <mpileup_file> [OPTION]\n";
	print "-input_file \tinputfile in mpileup format\n";
	print "-log_file \tlogfile containing discarded mpileup lines and the errorcode associated\n";
	print "-min_depth \tminimum depth required [1]\n";
	print "-max_depth \tmaximim depth (position with more coverage will be discarded) [100]\n";
	print "-min_frequency \tminimum variant frequency (0->1) [1] (default 1 => 100% reads show the variant at this position)\n";
	print "-min_distance \tminimum distance between variant [0]\n";
	print "-min_forward_and_reverse \tminimum number of reads in forward and reverse covering the variant required [0]\n";
	print "\n";
	exit(0);
}

GetOptions (
"input_file=s" => \$inputfile,
"log_file=s" => \$logfile,
"min_depth=i" => \$MIN_DEPTH,
"max_depth=i" => \$MAX_DEPTH,
"min_frequency=f" => \$MIN_VARIANTFREQUENCY,
"min_distance=i" => \$MIN_DISTANCE,
"min_forward_and_reverse=i" => \$MIN_FORWARDREVERSE,
"variant_only=s" => \$ONLY_UNFILTERED_VARIANT,
"v=i" => \$VERBOSE
) or die("Error in command line arguments\n");


open(IF, $inputfile)  or die("Can't open $inputfile\n");

my @tbl_line;
my @tbl_variant_position;
my @tbl_variant_chr;
my @tbl_variant_refbase;
my @tbl_variant_coverage;
my @tbl_variant_readbase_string;
my @tbl_variant_quality_string;

#Extraction des variants
my $nb_line=0;
while (my $line=<IF>){
	$nb_line++;
	if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){
		print "$nb_line\n";
	}
	my $error_code=0;
	if ($line=~/(.*?)\s+(\d+)\s+([ATGCN])\s+(\d+)\s+(.*?)\s+(.*?)$/){
		my $current_chromosome = $1;
		my $current_position = $2;
		my $current_refbase = $3;
		my $current_coverage = $4;
		my $current_readbase_string = $5;
		my $current_quality_string = $6;
		
		#Suppression of mPileUp special character
		$current_readbase_string =~ s/\$//g; #the read start at this position
		$current_readbase_string =~ s/\^.//g; #the read end at this position followed by quality char
		
		if ($current_readbase_string =~ /[ATGCNatgcn\d]/){
			push(@tbl_line,$line);
			push(@tbl_variant_chr,$current_chromosome);
			push(@tbl_variant_position,$current_position);
			push(@tbl_variant_refbase,$current_refbase);
			push(@tbl_variant_coverage,$current_coverage);
			push(@tbl_variant_readbase_string,$current_readbase_string);
			push(@tbl_variant_quality_string,$current_quality_string);
			if ($ONLY_UNFILTERED_VARIANT eq "ON"){
				print $line;
			}
			
		}
		else {
			#Position with no variant
		}
		
	}
	else {
		#Error Parsing
		print STDERR "$line #8";
	}
}
close(IF);

if ($ONLY_UNFILTERED_VARIANT eq "ON"){
	exit(0);
}

####Checking the distance between variant and other filter

if ($logfile){
	open(LF,">$logfile") or die ("Cant't open $logfile\n");
}

for (my $i=0;$i<=$#tbl_line;$i++){
	# print "ligne : $tbl_line[$i]\n";
				
	my $error_code=0;
	if ($i==0){
		#Comparing $i and $i+1 for neighbourhood filter;
		if ($#tbl_line>0){
			if (($tbl_variant_chr[$i+1] eq $tbl_variant_chr[$i])&&($tbl_variant_position[$i]+$MIN_DISTANCE>=$tbl_variant_position[$i+1])){
				$error_code=5;
				chomp($tbl_line[$i]);
				if ($logfile){
					print LF "$tbl_line[$i]\tcode:$error_code\n";
				}
				next;
			}
		}

		#Additionnal filters
		$error_code = check_error($tbl_variant_chr[$i],$tbl_variant_position[$i],$tbl_variant_refbase[$i],$tbl_variant_coverage[$i],$tbl_variant_readbase_string[$i]);

	}
	else {
		#Compairing $i and $i-1 for neighbourhood filter
		if (($tbl_variant_chr[$i-1] eq $tbl_variant_chr[$i])&&($tbl_variant_position[$i-1]+$MIN_DISTANCE>=$tbl_variant_position[$i])){
			$error_code=5;
			chomp($tbl_line[$i]);
			if ($logfile){
				print LF "$tbl_line[$i]\tcode:$error_code\n";
			}
			next;
		}
		else {
			#Additionnal filters
			$error_code = check_error($tbl_variant_chr[$i],$tbl_variant_position[$i],$tbl_variant_refbase[$i],$tbl_variant_coverage[$i],$tbl_variant_readbase_string[$i]);
		}
	}
	if ($error_code == 0){
		print $tbl_line[$i];
	}
	else {
		chomp($tbl_line[$i]);
		if ($logfile){
			print LF "$tbl_line[$i]\tcode:$error_code\n";
		}
	}
}

if ($logfile){
	close (LF);
}

sub check_error{
	my $current_chromosome = shift;
	my $current_position = shift;
	my $current_refbase = shift;
	my $current_coverage = shift;
	my $current_readbase_string = shift;
	
	# print "test : $current_readbase_string\n";
	

	
	#Extraction of insertions
	
	##################################################################
	# my @IN = $current_readbase_string =~ m/\+[0-9]+[ACGTNacgtn]+/g;
	# my @DEL = $current_readbase_string =~ m/\-[0-9]+[ACGTNacgtn]+/g;
	# print "IN : @IN\n";
	# print "DEL :@DEL\n";
	#$current_readbase_string=~s/[\+\-][0-9]+[ACGTNacgtn]+//g; 
	##################################################################
	#!!! marche pas : exemple .+1Ct. correspond a . / +1C / t /. mais le match de l'expression vire +1Ct
	##################################################################
	
	# => parcours de boucle
	my @readbase = split(//,$current_readbase_string);
	my $cleaned_readbase_string="";
	my @IN;
	my @DEL;
	my $current_IN="";
	my $current_DEL="";
	my $current_size=0;
	
	for (my $i=0;$i<=$#readbase;$i++){
		if ($readbase[$i] eq "+"){
			#Ouverture de IN
			$current_IN="+";
			
			#Recuperation de la taille
			my $sub = substr $current_readbase_string,$i;
			if ($sub=~/^\+(\d+)/){
				$current_size = $1;
			}
			my $remaining_size = $current_size;
			while (($remaining_size>0)&&($i<=$#readbase)){
				$i++;
				$current_IN.=$readbase[$i];
				if ($readbase[$i]=~ /[ATGCNatgcn]/){
					$remaining_size--;
				}
			}
			push(@IN,$current_IN);
		}
		elsif ($readbase[$i] eq "-"){
			#Ouverture de DEL
			$current_DEL="-";
			
			#Recuperation de la taille
			my $sub = substr $current_readbase_string,$i;
			if ($sub=~/^\-(\d+)/){
				$current_size = $1;
			}
			my $remaining_size = $current_size;
			while (($remaining_size>0)&&($i<=$#readbase)){
				$i++;
				$current_DEL.=$readbase[$i];
				if ($readbase[$i]=~ /[ATGCNatgcn]/){
					$remaining_size--;
				}
			}
			push(@DEL,$current_DEL);
			
		}
		else {
			#Ajout a la string
			$cleaned_readbase_string .= $readbase[$i];
		}
	}

	
	# print "IN : @IN\n";
	# print "DEL :@DEL\n";
	# print "$cleaned_readbase_string\n";	
	
	my @current_readbase_array = split(//,$cleaned_readbase_string);

	#Filtering : error detection

	if ($#current_readbase_array+1 != $current_coverage){
		return 9;
		#parsing error (couldn't parse the readbase string correctly)
	}
	elsif ($current_coverage<$MIN_DEPTH){
		return 2;
		#  2 : insufficient depth
	}
	elsif ($current_coverage>$MAX_DEPTH){
		return 6;
		#  6 : too much depth
	}
	else {
		if ($#IN>=0){
			if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){
				return 1;
				#  1 : variant type overload (multiple variant type detected insertion/deletion/mutation)
			}
			else {
				########## TEST de coherence des insertions ################
				# for (my $i=0;$i<=$#IN;$i++){
					# if (uc($IN[0]) ne uc($IN[$i])){
						# print uc($IN[0]),"\n";
						# print uc($IN[$i]),"\n";
						# return "1i";
					# }
				# }		
				###########################################################

				if($#IN+1 < $current_coverage*$MIN_VARIANTFREQUENCY){
					return 3;
					#  3 : insufficient variant frequency 
				}
			}
		}
		elsif ($#DEL>=0){
			if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){
				return 1;
				#  1 : variant type overload (multiple variant type detected insertion/deletion/mutation)
			}
			else {
				########## TEST de coherence des deletions ################
				# for (my $i=0;$i<=$#DEL;$i++){
					# if (uc($DEL[0]) ne uc($DEL[$i])){
						# print uc($DEL[0]),"\n";
						# print uc($DEL[$i]),"\n";
						# return "1d";
					# }
				# }
				###########################################################

				if($#DEL+1 < $current_coverage*$MIN_VARIANTFREQUENCY){
					return 3;
					#  3 : insufficient variant frequency 
				}
			}
		}
		else {
			my $nbA=0;
			$nbA++ while ($current_readbase_string =~ m/A/g);
			my $nbC=0;
			$nbC++ while ($current_readbase_string =~ m/C/g);
			my $nbT=0;
			$nbT++ while ($current_readbase_string =~ m/T/g);
			my $nbG=0;
			$nbG++ while ($current_readbase_string =~ m/G/g);
			my $nbN=0;
			$nbN++ while ($current_readbase_string =~ m/N/g);
			my $nba=0;
			$nba++ while ($current_readbase_string =~ m/a/g);
			my $nbc=0;
			$nbc++ while ($current_readbase_string =~ m/c/g);
			my $nbt=0;
			$nbt++ while ($current_readbase_string =~ m/t/g);
			my $nbg=0;
			$nbg++ while ($current_readbase_string =~ m/g/g);
			my $nbn=0;
			$nbn++ while ($current_readbase_string =~ m/n/g);

			if (($nbA+$nba>0)&&($nbT+$nbt+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){
				return "1m";
			}
			if (($nbT+$nbt>0)&&($nbA+$nba+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){
				return "1m";
			}
			if (($nbG+$nbg>0)&&($nbA+$nba+$nbT+$nbt+$nbC+$nbc+$nbN+$nbn>0)){
				return "1m";
			}
			if (($nbC+$nbc>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbN+$nbn>0)){
				return "1m";
			}
			if (($nbN+$nbn>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbC+$nbc>0)){
				return "1m";
			}

			if ($nbA+$nba >= $current_coverage*$MIN_VARIANTFREQUENCY){
				if (($nbA<$MIN_FORWARDREVERSE)||($nba<$MIN_FORWARDREVERSE)){
					return 4;
					#  4 : variant position not covered by forward and reverse reads
				}
			}
			elsif ($nbT+$nbt >= $current_coverage*$MIN_VARIANTFREQUENCY){
				if (($nbT<$MIN_FORWARDREVERSE)||($nbt<$MIN_FORWARDREVERSE)){
					return 4;
					#  4 : variant position not covered by forward and reverse reads
				}
			}	 
			elsif ($nbG+$nbg >= $current_coverage*$MIN_VARIANTFREQUENCY){
				if (($nbG<$MIN_FORWARDREVERSE)||($nbg<$MIN_FORWARDREVERSE)){
					return 4;
					#  4 : variant position not covered by forward and reverse reads
				}
			}
			elsif ($nbC+$nbc >= $current_coverage*$MIN_VARIANTFREQUENCY){
				if (($nbC<$MIN_FORWARDREVERSE)||($nbc<$MIN_FORWARDREVERSE)){
					return 4;
					#  4 : variant position not covered by forward and reverse reads
				}
			}
			elsif ($nbN+$nbn >= $current_coverage*$MIN_VARIANTFREQUENCY){
				if (($nbN<$MIN_FORWARDREVERSE)||($nbn<$MIN_FORWARDREVERSE)){
					return 4;
					#  4 : variant position not covered by forward and reverse reads
				}
			}
			else {
				return 3;
				#  3 : insufficient variant frequency 
			}	
		}
	}
	
	return 0;
}