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10
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1 #!/usr/bin/perl
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2 #V1.0.0
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3 use strict;
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4 use warnings;
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5 use Getopt::Long;
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6
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7
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8 my $input_log_files;
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9 GetOptions (
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10 "input_log_files=s" => \$input_log_files
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11 ) or die("Error in command line arguments\n");
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12
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13 my @files = split(/,/,$input_log_files);
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13
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14
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15
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16
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17 my $FastqPrep_detected=0;
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18 my $FastqPrep_type="NA";
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19 my $FastqPrep_before_read1_nbreads=0;
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20 my $FastqPrep_before_read1_nbbases=0;
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21 my $FastqPrep_before_read2_nbreads=0;
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22 my $FastqPrep_before_read2_nbbases=0;
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23 my $FastqPrep_after_read1_nbreads=0;
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24 my $FastqPrep_after_read1_nbbases=0;
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25 my $FastqPrep_after_read2_nbreads=0;
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26 my $FastqPrep_after_read2_nbbases=0;
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27
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28 my $Samfilter_detected = 0;
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29 my %Samfilter_before_hash;
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30 my %Samfilter_after_hash;
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31 my $Samfilter_before_nbreads=0;
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32 my $Samfilter_after_nbreads=0;
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33
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34 my $Pileupvariant_detected = 0;
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35 my $Pileupvariant="";
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36
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37 my $Listfiltering_detected = 0;
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38 my $Listfiltering="";
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39
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40 my $Pileupfiltering_detected = 0;
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41 my $Pileupfiltering="";
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42
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43 my $Blastfiltering_detected = 0;
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44 my $Blastfiltering_checked = 0;
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45 my $Blastfiltering_selected = 0;
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46
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47
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48
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49 for (my $f=0;$f<=$#files;$f++){
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50 my $current_file = $files[$f];
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51 open(IN, $current_file) or die ("Can't open $current_file\n");
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52 if ( -z IN){
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53 next;
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54 }
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55
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56 while (my $line =<IN>){
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57 if ($line =~ /Fastq preparation/){
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58 $FastqPrep_detected=1;
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59 my $line1 = <IN>;
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60 my $line2 = <IN>;
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61 my $line3 = <IN>;
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62 my $line4 = <IN>;
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63 my $line5 = <IN>;
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64 my $line6 = <IN>;
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65 my $line7 = <IN>;
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66 if ($line1=~/Fastq format \:\s*(\w+)\s*/){
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67 $FastqPrep_type=$1;
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68 }
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69 if ($line3=~/.*?\:\s*(\d+).*?\:\s*(\d+)/){
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70 $FastqPrep_before_read1_nbreads += $1;
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71 $FastqPrep_before_read1_nbbases += $2;
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72 }
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73 if ($line4=~/.*?\:\s*(\d+).*?\:\s*(\d+)/){
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74 $FastqPrep_before_read2_nbreads += $1;
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75 $FastqPrep_before_read2_nbbases += $2;
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76 }
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77 if ($line6=~/.*?\:\s*(\d+).*?\:\s*(\d+)/){
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78 $FastqPrep_after_read1_nbreads += $1;
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79 $FastqPrep_after_read1_nbbases += $2;
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80 }
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81 if ($line7=~/.*?\:\s*(\d+).*?\:\s*(\d+)/){
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82 $FastqPrep_after_read2_nbreads += $1;
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83 $FastqPrep_after_read2_nbbases += $2;
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84 }
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85
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86 }
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87 elsif ($line =~ /Blast filtering/){
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88 $Blastfiltering_detected=1;
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89 my $line1 = <IN>;
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90 my $line2 = <IN>;
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91 my $current_checked = 0;
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92 my $current_selected = 0;
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93 if ($line1=~/(\d+)/){
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94 $current_checked = $1;
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95 $Blastfiltering_checked += $current_checked;
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96 }
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97 if ($line2=~/(\d+)/){
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98 $current_selected = $1;
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99 $Blastfiltering_selected += $current_selected;
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100 }
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101
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102 }
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103 elsif ($line=~/Sam filtering/){
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104 $Samfilter_detected=1;
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105 my $line1 = <IN>;
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106 my $line2 = <IN>;
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107 my $line3 = <IN>;
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108 my $line4 = <IN>;
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109 my $line5 = <IN>;
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110 my $line6 = <IN>;
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111 my @tbl_score_before = split(/[\*\:]/,$line2);
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112 my @tbl_number_before = split(/[\*\:]/,$line3);
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113
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114 my @tbl_score_after = split(/[\*\:]/,$line5);
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115 my @tbl_number_after = split(/[\*\:]/,$line6);
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116
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117 if ($#tbl_score_before != $#tbl_number_before){
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118 print STDERR "Error Formating in Sam Filtering\n";
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119 exit(0);
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120 }
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121 else {
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122 for (my $i=0;$i<=$#tbl_score_before;$i++){
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123 if ($tbl_score_before[$i] =~ /(\d+)/){
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124 my $current_score_before = $1;
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125 if ($tbl_number_before[$i] =~ /(\d+)/){
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126 my $current_number_before = $1;
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127 $Samfilter_before_nbreads += $current_number_before;
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128 if ($Samfilter_before_hash{$current_score_before}){
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129 $Samfilter_before_hash{$current_score_before} += $current_number_before;
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130 }
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131 else {
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132 $Samfilter_before_hash{$current_score_before} = $current_number_before;
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133 }
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134 }
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135 else {
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136 print STDERR "Error Formating in Sam Filtering\n";
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137 exit(0);
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138 }
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139 }
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140 else {
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141 next;
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142 }
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143 }
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144 }
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145
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146 if ($#tbl_score_after != $#tbl_number_after){
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147 print STDERR "Error Formating in Sam Filtering\n";
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148 exit(0);
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149 }
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150 else {
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151 for (my $i=0;$i<=$#tbl_score_after;$i++){
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152 if ($tbl_score_after[$i] =~ /(\d+)/){
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153 my $current_score_after = $1;
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154 if ($tbl_number_after[$i] =~ /(\d+)/){
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155 my $current_number_after = $1;
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156 $Samfilter_after_nbreads += $current_number_after;
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157 if ($Samfilter_after_hash{$current_score_after}){
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158 $Samfilter_after_hash{$current_score_after} += $current_number_after;
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159 }
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160 else {
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161 $Samfilter_after_hash{$current_score_after} = $current_number_after;
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162 }
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163 }
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164 else {
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165 print STDERR "Error Formating in Sam Filtering\n";
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166 exit(0);
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167 }
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168 }
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169 else {
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170 next;
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171 }
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172 }
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173 }
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174 }
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175 elsif ($line=~/Variant extraction/){
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176 $Pileupvariant_detected=1;
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177 $Pileupvariant .= $line;
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178 while ($line = <IN>){
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179 $Pileupvariant .= $line;
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180 if ($line=~/^\s*$/){
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181 last;
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182 }
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183 }
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184 }
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185 elsif ($line=~/List Filtering/){
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186 $Listfiltering_detected =1;
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187 $Listfiltering .= $line;
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188 while ($line = <IN>){
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189 $Listfiltering .= $line;
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190 if ($line=~/^\s*$/){
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191 last;
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192 }
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193 }
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194 }
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195 elsif ($line=~/MPileup filtering/){
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196 $Pileupfiltering_detected =1;
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197 $Pileupfiltering.= $line;
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198 while ($line = <IN>){
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199 $Pileupfiltering .= $line;
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200 if ($line=~/^\s*$/){
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201 last;
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202 }
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203 }
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204 }
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205
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206 }
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207 close (IN);
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208 }
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209
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210 if ($FastqPrep_detected == 1){
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211 print "####\tFastq preparation\n";
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212 print "Fastq format : ",$FastqPrep_type,"\n";
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213 print "## Before preparation\n";
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214 print "#Read1 : ",$FastqPrep_before_read1_nbreads,"\t#Base : ",$FastqPrep_before_read1_nbbases,"\n";
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215 print "#Read2 : ",$FastqPrep_before_read2_nbreads,"\t#Base : ",$FastqPrep_before_read2_nbbases,"\n";
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216 print "## After preparation\n";
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217 print "#Read1 : ",$FastqPrep_after_read1_nbreads,"\t#Base : ",$FastqPrep_after_read1_nbbases,"\n";
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218 print "#Read2 : ",$FastqPrep_after_read2_nbreads,"\t#Base : ",$FastqPrep_after_read2_nbbases,"\n";
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219 print "\n";
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220 }
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221
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222
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223 if ($Samfilter_detected == 1){
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224 print "#### Sam filtering \n";
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225 print "## Before filtering ($Samfilter_before_nbreads)\n";
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226 print "bitscore :";
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227 foreach my $key (sort{$Samfilter_before_hash{$b}<=>$Samfilter_before_hash{$a}} keys %Samfilter_before_hash){
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228 print "\t$key\t*";
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229 }
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230 print "\n";
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231 print " number :";
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232 foreach my $key (sort{$Samfilter_before_hash{$b}<=>$Samfilter_before_hash{$a}} keys %Samfilter_before_hash){
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233 print "\t",$Samfilter_before_hash{$key},"\t*";
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234 }
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235 print "\n";
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236 print "## After filtering ($Samfilter_after_nbreads)\n";
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237 print "bitscore :";
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238 foreach my $key (sort{$Samfilter_after_hash{$b}<=>$Samfilter_after_hash{$a}} keys %Samfilter_after_hash){
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239 print "\t$key\t";
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240 }
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241 print "\n";
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242 print " number :";
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243 foreach my $key (sort{$Samfilter_after_hash{$b}<=>$Samfilter_after_hash{$a}} keys %Samfilter_after_hash){
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244 print "\t",$Samfilter_after_hash{$key},"\t*";
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245 }
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246 print "\n";
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247 print "\n";
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248 }
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249
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250 if ($Pileupvariant_detected == 1){
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251 print $Pileupvariant,"\n";
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252 }
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253
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254 if ($Listfiltering_detected == 1){
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255 print $Listfiltering,"\n";
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256 }
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257
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258 if ($Blastfiltering_detected == 1){
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259 print "#### Blast filtering\n";
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260 print "Variant checked :\t$Blastfiltering_checked\n";
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261 print "Variant selected :\t$Blastfiltering_selected\n";
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262 print "\n";
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263 }
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264
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265 if ($Pileupfiltering_detected == 1){
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266 print $Pileupfiltering,"\n";
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10
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267 } |
