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0
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1 #!/usr/bin/perl
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2 use strict;
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3 use Getopt::Long;
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4
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5 #
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6 # Filter a pileup file on forward/reverse presence and %read having the variant
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7 # The error code
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8 # 1 : multiple variant type detected insertion/deletion/mutation
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9 # 1i : inconsistency in insertion
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10 # 1d : inconsistency in deletion
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11 # 1m : inconsistency in mutation
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12 # 2 : insufficient depth
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13 # 3 : insufficient variant frequency
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14 # 4 : variant position not covered by forward and reverse reads
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15 # 5 : variant with other variant in neighbourhood
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16 # 6 : too much depth
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17 # 8 : parsing error (couldn't parse the mpileup line correctly)
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18 # 9 : parsing error (couldn't parse the readbase string correctly)
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19
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20
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21 my $inputfile;
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22 my $logfile;
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23 my $MIN_DISTANCE=0;
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24 my $MIN_VARIANTFREQUENCY=0;
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25 my $MIN_FORWARDREVERSE=0;
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26 my $MIN_DEPTH=0;
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27 my $MAX_DEPTH=500;
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28 my $VERBOSE=0;
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29 my $ONLY_UNFILTERED_VARIANT="OFF";
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30 my $DO_STAT="NO";
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31
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32
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33 my $STAT_MIN_DEPTH_MIN = 2;
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34 my $STAT_MIN_DEPTH_MAX = 10;
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35 my $STAT_MIN_DEPTH_STEP = 2;
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36 my $STAT_MAX_DEPTH_MIN = 100;
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37 my $STAT_MAX_DEPTH_MAX = 200;
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38 my $STAT_MAX_DEPTH_STEP = 100;
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39 my $STAT_FREQ_MIN = 0.8;
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40 my $STAT_FREQ_MAX = 1;
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41 my $STAT_FREQ_STEP = 0.1;
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42 my $STAT_DIST_MIN = 0;
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43 my $STAT_DIST_MAX = 50;
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44 my $STAT_DIST_STEP = 50;
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45
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46 GetOptions (
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47 "input_file=s" => \$inputfile,
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48 "log_file=s" => \$logfile,
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49 "min_depth=i" => \$MIN_DEPTH,
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50 "max_depth=i" => \$MAX_DEPTH,
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51 "min_frequency=f" => \$MIN_VARIANTFREQUENCY,
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52 "min_distance=i" => \$MIN_DISTANCE,
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53 "min_forward_and_reverse=i" => \$MIN_FORWARDREVERSE,
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54 "variant_only=s" => \$ONLY_UNFILTERED_VARIANT,
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55 "v=i" => \$VERBOSE,
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56 "do_stat=s" => \$DO_STAT,
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57 "stat_min_depth_min=i" => \$STAT_MIN_DEPTH_MIN,
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58 "stat_min_depth_max=i" => \$STAT_MIN_DEPTH_MAX,
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59 "stat_min_depth_step=i" => \$STAT_MIN_DEPTH_STEP,
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60 "stat_max_depth_min=i" => \$STAT_MAX_DEPTH_MIN,
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61 "stat_max_depth_max=i" => \$STAT_MAX_DEPTH_MAX,
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62 "stat_max_depth_step=i" => \$STAT_MAX_DEPTH_STEP,
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63 "stat_freq_min=f" => \$STAT_FREQ_MIN,
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64 "stat_freq_max=f" => \$STAT_FREQ_MAX,
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65 "stat_freq_step=f" => \$STAT_FREQ_STEP,
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66 "stat_dist_min=i" => \$STAT_DIST_MIN,
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67 "stat_dist_max=i" => \$STAT_DIST_MAX,
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68 "stat_dist_step=i" => \$STAT_DIST_STEP
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69 ) or die("Error in command line arguments\n");
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70
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71 open(IF, $inputfile) or die("Can't open $inputfile\n");
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72
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73 my @tbl_line;
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74 my %USR_PARAM;
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75 $USR_PARAM{"min_depth"} = $MIN_DEPTH;
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76 $USR_PARAM{"max_depth"} = $MAX_DEPTH;
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77 $USR_PARAM{"min_freq"} = $MIN_VARIANTFREQUENCY;
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78 $USR_PARAM{"min_dist"} = $MIN_DISTANCE;
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79 $USR_PARAM{"min_fr"} = $MIN_FORWARDREVERSE;
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80
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81
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82
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83 #Extraction des variants
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84 my $nb_line=0;
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85 while (my $line=<IF>){
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86 $nb_line++;
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87 if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){
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88 print "$nb_line\n";
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89 }
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90 my $error_code=0;
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91 if ($line=~/(.*?)\s+(\d+)\s+([ATGCN])\s+(\d+)\s+(.*?)\s+(.*?)$/){
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92 my $current_chromosome = $1;
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93 my $current_position = $2;
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94 my $current_refbase = $3;
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95 my $current_coverage = $4;
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96 my $current_readbase_string = $5;
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97 my $current_quality_string = $6;
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98
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99 #Suppression of mPileUp special character
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100 $current_readbase_string =~ s/\$//g; #the read start at this position
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101 $current_readbase_string =~ s/\^.//g; #the read end at this position followed by quality char
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102
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103 if ($current_readbase_string =~ /[ATGCNatgcn\d]/){
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104 my %variant;
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105 $variant{"line"} = $line;
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106 $variant{"chr"} = $current_chromosome;
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107 $variant{"pos"} = $current_position;
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108 $variant{"refbase"} = $current_refbase;
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109 $variant{"coverage"} = $current_coverage;
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110 $variant{"readbase"} = $current_readbase_string;
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111 $variant{"quality"} = $current_quality_string;
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112 push(@tbl_line,\%variant);
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113
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114 if ($ONLY_UNFILTERED_VARIANT eq "ON"){
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115 print $line;
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116 }
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117
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118 }
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119 else {
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120 #Position with no variant
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121 }
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122
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123 }
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124 else {
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125 #Error Parsing
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126 print STDERR "$line #8";
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127 }
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128 }
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129 close(IF);
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130
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131 if ($ONLY_UNFILTERED_VARIANT eq "ON"){
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132 exit(0);
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133 }
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134
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135 ####Checking the distance between variant and other filter
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136
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137
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138 my @error;
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139 for (my $i=0;$i<=$#tbl_line;$i++){
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140 # print "ligne : $tbl_line[$i]\n";
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141 my $before="";
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142 my $after="";
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143 my %line = %{$tbl_line[$i]};
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144
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145 if ($tbl_line[$i-1]){
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146 $before = $tbl_line[$i-1];
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147 }
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148 if ($tbl_line[$i+1]){
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149 $after = $tbl_line[$i+1];
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150 }
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151 my $error_code = check_error($tbl_line[$i],$before,$after,\%USR_PARAM);
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152 if ($error_code == 0){
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153 print $line{"line"};
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154 }
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155 else {
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156 push(@error,$error_code,"\t",$line{"line"});
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157 }
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158 }
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159
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160 ### LOG
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161 open(LF,">$logfile") or die ("Can't open $logfile\n");
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162
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163 if ($DO_STAT eq "YES"){
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164 for (my $idx_min_depth=$STAT_MIN_DEPTH_MIN;$idx_min_depth<=$STAT_MIN_DEPTH_MAX;$idx_min_depth = $idx_min_depth + $STAT_MIN_DEPTH_STEP ){
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165 for (my $idx_max_depth=$STAT_MAX_DEPTH_MIN;$idx_max_depth<=$STAT_MAX_DEPTH_MAX;$idx_max_depth = $idx_max_depth + $STAT_MAX_DEPTH_STEP ){
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166 for (my $idx_freq = $STAT_FREQ_MIN;$idx_freq<=$STAT_FREQ_MAX;$idx_freq= $idx_freq+$STAT_FREQ_STEP){
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167 for (my $idx_dist=$STAT_DIST_MIN;$idx_dist<=$STAT_DIST_MAX;$idx_dist = $idx_dist + $STAT_DIST_STEP){
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168 for (my $idx_fr=0;$idx_fr<=1;$idx_fr++){
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169 my %stat_param;
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170 $stat_param{"min_depth"}=$idx_min_depth;
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171 $stat_param{"max_depth"}=$idx_max_depth;
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172 $stat_param{"min_freq"}=$idx_freq;
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173 $stat_param{"min_fr"}=$idx_fr;
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174 $stat_param{"min_dist"}=$idx_dist;
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175
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176 print LF "#SNP = ",&test_check(\@tbl_line,\%stat_param),"\tdepth (min/max) = ",$stat_param{"min_depth"}," / ",$stat_param{"max_depth"},"\tmin_dist=",$stat_param{"min_dist"},"\tmin_freq=",$stat_param{"min_freq"},"\tmin_forwardreverse = ",$stat_param{"min_fr"},"\n";
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177 }
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178 }
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179 }
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180 print "\n";
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181 }
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182 }
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183 }
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184
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185
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186 for (my $i=0;$i<=$#error;$i++){
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187 print LF $error[$i];
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188 }
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189 close (LF);
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190
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191
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192
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193
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194 sub test_check{
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195 my $ref_tbl_line = shift;
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196 my $ref_param = shift;
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197 my @tbl_line = @$ref_tbl_line;
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198 my %param = %$ref_param;
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199 my $nb=0;
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200
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201 for (my $i=0;$i<=$#tbl_line;$i++){
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202 my $before="";
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203 my $after="";
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204 my %line = %{$tbl_line[$i]};
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205
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206 if ($tbl_line[$i-1]){
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207 $before = $tbl_line[$i-1];
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208 }
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209 if ($tbl_line[$i+1]){
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210 $after = $tbl_line[$i+1];
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211 }
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212 my $error_code = check_error($tbl_line[$i],$before,$after,\%param);
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213 if ($error_code == 0){
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214 $nb++;
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215 }
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216 }
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217
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218 return $nb;
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219 }
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220
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221 sub check_error{
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222 my $refline = shift;
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223 my %line = %$refline;
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224 my $refbefore = shift;
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225 my $refafter = shift;
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226 my $refparam = shift;
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227 my %param = %$refparam;
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228
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229
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230 my $current_chromosome = $line{"chr"};
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231 my $current_position = $line{"pos"};
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232 my $current_refbase = $line{"refbase"};
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233 my $current_coverage = $line{"coverage"};
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234 my $current_readbase_string = $line{"readbase"};
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235
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236
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237 my $min_depth = $param{"min_depth"};
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238 my $max_depth = $param{"max_depth"};
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239 my $min_variant_frequency = $param{"min_freq"};
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240 my $min_forward_reverse = $param{"min_fr"};
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241 my $min_dist = $param{"min_dist"};
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242
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243 #Verification of neightbourhood
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244 if ($refbefore){
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245 my %compareline = %$refbefore;
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246 my $compare_chromosome = $compareline{"chr"};
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247 my $compare_position = $compareline{"pos"};
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248 my $compare_refbase = $compareline{"refbase"};
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249 my $compare_coverage = $compareline{"coverage"};
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250 my $compare_readbase_string = $compareline{"readbase"};
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251
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252 if (($current_chromosome eq $compare_chromosome )&&($compare_position + $min_dist >= $current_position)){
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253 return 5;
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254 }
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255 }
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256
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257 if ($refafter){
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258 my %compareline = %$refafter;
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259 my $compare_chromosome = $compareline{"chr"};
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260 my $compare_position = $compareline{"pos"};
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261 my $compare_refbase = $compareline{"refbase"};
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262 my $compare_coverage = $compareline{"coverage"};
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263 my $compare_readbase_string = $compareline{"readbase"};
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264
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265 if (($current_chromosome eq $compare_chromosome )&&($current_position + $min_dist >= $compare_position)){
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266 return 5;
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267 }
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268 }
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269
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270
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271
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272
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273 #Extraction of insertions
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274
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275 ##################################################################
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276 # my @IN = $current_readbase_string =~ m/\+[0-9]+[ACGTNacgtn]+/g;
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277 # my @DEL = $current_readbase_string =~ m/\-[0-9]+[ACGTNacgtn]+/g;
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278 # print "IN : @IN\n";
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279 # print "DEL :@DEL\n";
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280 #$current_readbase_string=~s/[\+\-][0-9]+[ACGTNacgtn]+//g;
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281 ##################################################################
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282 #!!! marche pas : exemple .+1Ct. correspond a . / +1C / t /. mais le match de l'expression vire +1Ct
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283 ##################################################################
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284
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285 # => parcours de boucle
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286 my @readbase = split(//,$current_readbase_string);
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287 my $cleaned_readbase_string="";
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288 my @IN;
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289 my @DEL;
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290 my $current_IN="";
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291 my $current_DEL="";
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292 my $current_size=0;
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293
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294 for (my $i=0;$i<=$#readbase;$i++){
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295 if ($readbase[$i] eq "+"){
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296 #Ouverture de IN
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297 $current_IN="+";
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298
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299 #Recuperation de la taille
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300 my $sub = substr $current_readbase_string,$i;
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301 if ($sub=~/^\+(\d+)/){
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302 $current_size = $1;
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303 }
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304 my $remaining_size = $current_size;
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305 while (($remaining_size>0)&&($i<=$#readbase)){
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306 $i++;
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307 $current_IN.=$readbase[$i];
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308 if ($readbase[$i]=~ /[ATGCNatgcn]/){
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309 $remaining_size--;
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310 }
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311 }
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312 push(@IN,$current_IN);
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313 }
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314 elsif ($readbase[$i] eq "-"){
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315 #Ouverture de DEL
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316 $current_DEL="-";
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317
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318 #Recuperation de la taille
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319 my $sub = substr $current_readbase_string,$i;
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320 if ($sub=~/^\-(\d+)/){
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321 $current_size = $1;
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322 }
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323 my $remaining_size = $current_size;
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324 while (($remaining_size>0)&&($i<=$#readbase)){
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325 $i++;
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326 $current_DEL.=$readbase[$i];
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327 if ($readbase[$i]=~ /[ATGCNatgcn]/){
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328 $remaining_size--;
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329 }
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330 }
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331 push(@DEL,$current_DEL);
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332
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333 }
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334 else {
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335 #Ajout a la string
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336 $cleaned_readbase_string .= $readbase[$i];
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337 }
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338 }
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339
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340
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341 # print "IN : @IN\n";
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342 # print "DEL :@DEL\n";
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343 # print "$cleaned_readbase_string\n";
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344
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345 my @current_readbase_array = split(//,$cleaned_readbase_string);
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346
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347 #Filtering : error detection
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348
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349 if ($#current_readbase_array+1 != $current_coverage){
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350 return 9;
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351 #parsing error (couldn't parse the readbase string correctly)
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352 }
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353 elsif ($current_coverage<$min_depth){
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354 return 2;
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355 # 2 : insufficient depth
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356 }
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357 elsif ($current_coverage>$max_depth){
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358 return 6;
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359 # 6 : too much depth
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360 }
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361 else {
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362 if ($#IN>=0){
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363 if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){
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364 return 1;
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365 # 1 : variant type overload (multiple variant type detected insertion/deletion/mutation)
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366 }
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367 else {
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368 ########## TEST de coherence des insertions ################
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369 # for (my $i=0;$i<=$#IN;$i++){
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370 # if (uc($IN[0]) ne uc($IN[$i])){
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371 # print uc($IN[0]),"\n";
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372 # print uc($IN[$i]),"\n";
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373 # return "1i";
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374 # }
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375 # }
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376 ###########################################################
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377
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378 if($#IN+1 < $current_coverage*$min_variant_frequency ){
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379 return 3;
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380 # 3 : insufficient variant frequency
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381 }
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382 }
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383 }
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384 elsif ($#DEL>=0){
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385 if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){
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386 return 1;
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387 # 1 : variant type overload (multiple variant type detected insertion/deletion/mutation)
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388 }
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389 else {
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390 ########## TEST de coherence des deletions ################
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391 # for (my $i=0;$i<=$#DEL;$i++){
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392 # if (uc($DEL[0]) ne uc($DEL[$i])){
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393 # print uc($DEL[0]),"\n";
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394 # print uc($DEL[$i]),"\n";
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395 # return "1d";
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396 # }
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397 # }
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398 ###########################################################
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399
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400 if($#DEL+1 < $current_coverage*$min_variant_frequency){
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401 return 3;
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402 # 3 : insufficient variant frequency
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403 }
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404 }
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405 }
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406 else {
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407 my $nbA=0;
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408 $nbA++ while ($current_readbase_string =~ m/A/g);
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409 my $nbC=0;
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410 $nbC++ while ($current_readbase_string =~ m/C/g);
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411 my $nbT=0;
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412 $nbT++ while ($current_readbase_string =~ m/T/g);
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413 my $nbG=0;
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414 $nbG++ while ($current_readbase_string =~ m/G/g);
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415 my $nbN=0;
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416 $nbN++ while ($current_readbase_string =~ m/N/g);
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417 my $nba=0;
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418 $nba++ while ($current_readbase_string =~ m/a/g);
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419 my $nbc=0;
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420 $nbc++ while ($current_readbase_string =~ m/c/g);
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421 my $nbt=0;
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422 $nbt++ while ($current_readbase_string =~ m/t/g);
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423 my $nbg=0;
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424 $nbg++ while ($current_readbase_string =~ m/g/g);
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425 my $nbn=0;
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426 $nbn++ while ($current_readbase_string =~ m/n/g);
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427
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428 if (($nbA+$nba>0)&&($nbT+$nbt+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){
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429 return "1m";
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430 }
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431 if (($nbT+$nbt>0)&&($nbA+$nba+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){
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432 return "1m";
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433 }
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434 if (($nbG+$nbg>0)&&($nbA+$nba+$nbT+$nbt+$nbC+$nbc+$nbN+$nbn>0)){
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435 return "1m";
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436 }
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437 if (($nbC+$nbc>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbN+$nbn>0)){
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438 return "1m";
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439 }
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440 if (($nbN+$nbn>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbC+$nbc>0)){
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441 return "1m";
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|
|
442 }
|
|
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443
|
|
|
444 if ($nbA+$nba >= $current_coverage*$min_variant_frequency){
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|
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445 if (($nbA<$min_forward_reverse)||($nba<$min_forward_reverse)){
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|
|
446 return 4;
|
|
|
447 # 4 : variant position not covered by forward and reverse reads
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|
|
448 }
|
|
|
449 }
|
|
|
450 elsif ($nbT+$nbt >= $current_coverage*$min_variant_frequency){
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|
|
451 if (($nbT<$min_forward_reverse)||($nbt<$min_forward_reverse)){
|
|
|
452 return 4;
|
|
|
453 # 4 : variant position not covered by forward and reverse reads
|
|
|
454 }
|
|
|
455 }
|
|
|
456 elsif ($nbG+$nbg >= $current_coverage*$min_variant_frequency){
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|
|
457 if (($nbG<$min_forward_reverse)||($nbg<$min_forward_reverse)){
|
|
|
458 return 4;
|
|
|
459 # 4 : variant position not covered by forward and reverse reads
|
|
|
460 }
|
|
|
461 }
|
|
|
462 elsif ($nbC+$nbc >= $current_coverage*$min_variant_frequency){
|
|
|
463 if (($nbC<$min_forward_reverse)||($nbc<$min_forward_reverse)){
|
|
|
464 return 4;
|
|
|
465 # 4 : variant position not covered by forward and reverse reads
|
|
|
466 }
|
|
|
467 }
|
|
|
468 elsif ($nbN+$nbn >= $current_coverage*$min_variant_frequency){
|
|
|
469 if (($nbN<$min_forward_reverse)||($nbn<$min_forward_reverse)){
|
|
|
470 return 4;
|
|
|
471 # 4 : variant position not covered by forward and reverse reads
|
|
|
472 }
|
|
|
473 }
|
|
|
474 else {
|
|
|
475 return 3;
|
|
|
476 # 3 : insufficient variant frequency
|
|
|
477 }
|
|
|
478 }
|
|
|
479 }
|
|
|
480
|
|
|
481 return 0;
|
|
|
482 }
|
