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1 #!/usr/bin/perl -w
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2
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3 #for a complete list of genes and a list of sites, sorts genes close to sites
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4 #printDistance
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5
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6 #read only gene files with refSeqGenes
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7 #counts only once overlapping transcripts or genes
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8
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9 #calculates some stats about locations of peaks
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10
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11 use strict;
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12
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13 my $SitesFilename ;
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14 my $SitesFilename2 ="";
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15 my $GenesFilename ;
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16 my $MirFilename = "";
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17 my $BIGNUMBER = 10000000;
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18 my $verbose = 0;
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19 my $header = 0;
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20 my $noXY = 0;
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21 my $minscore = 0;
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22
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23 my $usage = qq{
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24 $0
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25
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26 -----------------------------
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27 mandatory parameters:
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28
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29 -g filename file with all genes
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30 -f filename file with sites in BED format
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31
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32 -----------------------------
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33 optional parameters:
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34 -v for verbose
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35 -minScore minimal score
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36 -mir filename file with positions of miRNA
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37 -head if there is a header
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38 -reg filename file with FoldChanges or expression values and annotation (should in colomn 4)
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39 -noXY
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40 -o filename output file
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41 };
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42
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43 if(scalar(@ARGV) == 0){
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44 print $usage;
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45 exit(0);
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46 }
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47
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48 my $ResFilename = "";
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49
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50 my $regFilename = "";
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51
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52 while(scalar(@ARGV) > 0){
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53 my $this_arg = shift @ARGV;
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54 if ( $this_arg eq '-h') {print "$usage\n"; exit; }
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55
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56 elsif ( $this_arg eq '-g') {$GenesFilename = shift @ARGV;}
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57 elsif ( $this_arg eq '-f') {$SitesFilename = shift @ARGV;}
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58 elsif ( $this_arg eq '-mir') {$MirFilename = shift @ARGV;}
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59 elsif ( $this_arg eq '-v') {$verbose = 1;}
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60 elsif ( $this_arg eq '-head') {$header = 1;}
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61 elsif ( $this_arg eq '-noXY') {$noXY = 1;}
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62 elsif ( $this_arg eq '-o') {$ResFilename = shift @ARGV;}
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63 elsif ( $this_arg eq '-reg') {$regFilename = shift @ARGV;}
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64 elsif ( $this_arg eq '-minScore') {$minscore = shift @ARGV;}
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65 elsif ( $this_arg =~ m/^-/ ) { print "unknown flag: $this_arg\n";}
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66 }
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67
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68 if ($ResFilename eq "") {
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69 $ResFilename = $SitesFilename.".withGenes.txt";
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70 }
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71
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72
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73
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74 #------------read expression/foldChange annotation of genes---------
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75
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76 my %geneReg;
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77 if ( $regFilename eq ""){
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78 print "you did not specify file with expression of fold change values\n";
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79 }
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80 else {
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81 open (REG, "<$regFilename ") or die "Cannot open file $regFilename !!!!: $!";
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82 #Gene median mad flag
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83 #RPL41 13.60755187 0.074233841 EXPRESSED
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84 #A 1110013L07Rik 0.26 up-regulated
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85
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86 while (<REG>) {
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87 chomp;
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88 my ($name, $value) = (split)[1,3];
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89 $geneReg{$name} = $value;
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90 }
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91 close REG;
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92 }
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93 #-----------read genes----------------
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94
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95 my %genes;
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96
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97 my $count = 0;
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98
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99 open (GENES, "<$GenesFilename") or die "Cannot open file $GenesFilename!!!!: $!";
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100 <GENES>;
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101
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102 my ($name,$chr,$strand,$leftPos,$rightPos);
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103
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104 while (<GENES>) {
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105 chomp;
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106 if (/(chr\S*)\s(\d+)\s(\d+)\s([-]?1)\s\S+\s\S+\s(\S+)/){
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107 $name = $5;
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108 $chr = $1;
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109
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110 $strand = $4;
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111 if ($strand eq '1') {
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112 $strand = 1;
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113 }
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114 else {
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115 $strand = -1;
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116 }
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117 $leftPos = $2;
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118 $rightPos = $3;
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119 next if (($chr =~ m/[XY]/)&&($noXY));
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120 next if ($name =~ m/MIR/);
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121 } elsif (/(chr\S*)\s([+-])\s(\d+)\s(\d+)\s(\d+)\s(\d+)\s(\d+)\s(\S+)\s(\S+)\s\S+\s(\S+)/) {
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122 $name = $10;
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123 $chr = $1;
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124 $strand = $2;
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125 $leftPos = $3;
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126 $rightPos = $4;
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127 next if (($chr =~ m/[XY]/)&&($noXY));
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128 next if ($name =~ m/MIR/);
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129
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130 if ($strand eq '+') {
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131 $strand = 1;
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132 }
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133 else {
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134 $strand = -1;
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135 }
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136 } else {
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137 print "Wrong type: ",$_,"\n";
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138 }
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139 my $ID = "$name\t$chr:$leftPos-$rightPos";
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140 my $reg = "NA";
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141 if (exists($geneReg{$name})) {
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142 $reg = $geneReg{$name};
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143 }
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144 unless (exists($genes{$chr})) {
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145 my %h;
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146 $genes{$chr} = \%h;
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147 }
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148 unless (exists($genes{$chr}->{$ID})) {
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149 my %h1;
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150 $genes{$chr}->{$ID} = \%h1;
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151 $count++;
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152 }
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153 $genes{$chr}->{$ID}{'name'} = $name ;
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154 $genes{$chr}->{$ID}{'left'} = $leftPos ;
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155 $genes{$chr}->{$ID}{'right'} = $rightPos ;
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156
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157 $genes{$chr}->{$ID}{'strand'} = $strand;
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158
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159 $genes{$chr}->{$ID}{'TSS'} = ($strand == 1) ? $leftPos :$rightPos ;
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160 $genes{$chr}->{$ID}{'TE'} = ($strand == -1) ? $leftPos :$rightPos ;
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161 $genes{$chr}->{$ID}{'reg'} = $reg;
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162 $genes{$chr}->{$ID}{'length'} = abs ($leftPos-$rightPos);
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163 $genes{$chr}->{$ID}{'closestPicDist'} = $BIGNUMBER;
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164 $genes{$chr}->{$ID}{'closestPositivePicDist'} = $BIGNUMBER;
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165 $genes{$chr}->{$ID}{'closestNegativePicDist'} = -$BIGNUMBER;
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166
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167 $genes{$chr}->{$ID}{'closestPicDistTE'} = $BIGNUMBER;
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168
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169 }
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170 print "Total genes : $count\n";
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171
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172
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173
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174 close GENES;
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175 print "\t\t$GenesFilename is read!\n";
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176 #for my $gName (sort keys %{$genes{'chr18'}}) {
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177
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178 # print "$gName\t$genes{'chr18'}->{$gName}{'TSS'}\n";
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179 #}
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180
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181 #-----------read file with sites miRNA, store as genes-----
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182
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183 if ( $MirFilename eq ""){
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184 print "you did not specify file with miRNA\n";
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185 }
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186 else {
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187
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188
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189 open (MIR, "<$MirFilename ") or die "Cannot open file $MirFilename !!!!: $!";
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190 #chr1 20669090 20669163 mmu-mir-206 960 +
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191 while (<MIR>) {
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192 chomp;
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193 my ($name, $chr, $leftPos, $rightPos, $strand );
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194 #1 . miRNA 20669091 20669163 . + . ACC="MI0000249"; ID="mmu-mir-206";
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195 if (/([0-9XYM]+)\s.\smiRNA\s(\d+)\s(\d+)\s.\s([+-])\s.\sACC=.*ID=\"(.*)\"/) {
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196 $name = $5;
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197 $chr = $1;
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198 $leftPos = $2;
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199 $rightPos = $3;
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200 $strand = $4;
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201 }
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202 elsif (/(.*)\s(\d+)\s(\d+)\s(.*)\s(.*)\s(.*)/){
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203 $name = $4;
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204 $chr = $1;
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205 $leftPos = $2;
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206 $rightPos = $3;
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207 $strand = $6;
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208 } else {
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209 next;
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210 }
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211
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212 unless ($chr =~ m/chr/) {
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213 $chr = "chr".$chr;
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214 }
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215 my $ID = "$name\t$chr:$leftPos-$rightPos";
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216
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217 if ($strand eq '+') {
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218 $strand = 1;
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219 }
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220 else {
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221 $strand = -1;
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222 }
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223
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224 unless (exists($genes{$chr})) {
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225 my %h;
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226 $genes{$chr} = \%h;
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227 }
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228 unless (exists($genes{$chr}->{$ID})) {
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229 my %h1;
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230 $genes{$chr}->{$ID} = \%h1;
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231 $count++;
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232 }
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233 $genes{$chr}->{$ID}{'name'} = $name ;
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234 $genes{$chr}->{$ID}{'left'} = $leftPos ;
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235 $genes{$chr}->{$ID}{'right'} = $rightPos ;
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236 $genes{$chr}->{$ID}{'cdsStart'} = $leftPos ;
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237 $genes{$chr}->{$ID}{'cdsEnd'} = $rightPos ;
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238 $genes{$chr}->{$ID}{'strand'} = $strand;
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239 $genes{$chr}->{$ID}{'length'} = abs ($leftPos-$rightPos);
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240 $genes{$chr}->{$ID}{'exonCount'} = 1;
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241 $genes{$chr}->{$ID}{'exonStarts'} = $leftPos ;
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242 $genes{$chr}->{$ID}{'exonEnds'} = $rightPos ;
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243 $genes{$chr}->{$ID}{'TSS'} = ($strand == 1) ? $leftPos :$rightPos ;
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244 $genes{$chr}->{$ID}{'TE'} = ($strand == -1) ? $leftPos :$rightPos ;
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245 $genes{$chr}->{$ID}{'reg'} = "miRNA";
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246 ($genes{$chr}->{$ID}{'firstIntronStart'},$genes{$chr}->{$ID}{'firstIntronEnd'}) = (0,0);
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247 $genes{$chr}->{$ID}{'closestPicDist'} = $BIGNUMBER;
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248 $genes{$chr}->{$ID}{'closestPicDistTE'} = $BIGNUMBER;
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249 $genes{$chr}->{$ID}{'closestPositivePicDist'} = $BIGNUMBER;
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250 $genes{$chr}->{$ID}{'closestNegativePicDist'} = -$BIGNUMBER;
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251
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252
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253 }
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254
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255
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256 close MIR;
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257 print "\t\t$MirFilename is read!\n" if ($verbose) ;
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258 }
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259
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260
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261
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262 #-----------read file with sites and find overlapping genes-----
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263 my $numberOfAllSites = 0;
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264
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265 my $lengthLosses = 0;
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266 my $lengthGains = 0;
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267
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268 open (FILE, "<$SitesFilename") or die "Cannot open file $SitesFilename!!!!: $!";
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269 open (OUT , ">$ResFilename") or die "Cannot open file $ResFilename!!!!: $!";
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270 print OUT "chrom start end max_coord score Dist DistTE geneName geneCoord Reg\n";
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271 open (GENESOUT , ">$ResFilename.genes") or die "Cannot open file $ResFilename.genes!!!!: $!";
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272
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273 print GENESOUT "Name\tGeneCoord\tDistS\tDistE\tDistTE\tReg\n";
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274
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275 my $correction = 0;
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276
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277 if ($header) {
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278 my $headerString = <FILE>; #read header
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279 my @a = split (/\t/,$header );
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280
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281 if ($a[1] =~m/chr/) {
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282 $correction=1;
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283 }
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284 }
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285
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286 $count = 0;
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287 print $SitesFilename, "\n";
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288 while (<FILE>) {
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289 chomp;
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290 next if (/track/);
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291 my $string = $_;
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292 chomp $string;
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293 $numberOfAllSites++;
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294 my @a = split /\t/;
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295 if (($a[1] =~m/chr/)&&($correction==0)) {
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296 $correction=1;
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297 }
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298 my $chro = $a[0+$correction];
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299 next if (($chro =~ m/[XY]/)&&($noXY));
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300 unless ($chro =~ m/chr/) {
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301 $chro = "chr".$chro;
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302 }
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303
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304 my $fpos = $a[1+$correction];
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305 my $lpos = $a[2+$correction];
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306 my $score = $a[4+$correction];
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307 if ($minscore>0) {
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308 next if ($score<$minscore);
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309 }
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310 next if ($chro=~m/M/);
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311
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312 print OUT $string, "\t";
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313
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314 findClosestTSS ($fpos,$lpos,$chro,\%genes);
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315
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316 $count ++;
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317 }
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318 close FILE;
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319 close OUT ;
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320 close GENESOUT;
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321 print "Total Sites: $count\n";
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322
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323 open (GENESOUT , ">$ResFilename.genes.ClosestPeakDist") or die "Cannot open file $ResFilename.genes.ClosestPeakDist!!!!: $!";
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324 print GENESOUT "Name Coord Dist DistTE Reg posDist negDist\n";
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325 for my $chro (keys %genes) {
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326 for my $gName (keys %{$genes{$chro}}) {
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327 print GENESOUT "$gName\t",$genes{$chro}->{$gName}{'closestPicDist'},"\t",$genes{$chro}->{$gName}{'closestPicDistTE'},"\t",$genes{$chro}->{$gName}{'reg'},"\t",$genes{$chro}->{$gName}{'closestPositivePicDist'},"\t",$genes{$chro}->{$gName}{'closestNegativePicDist'},"\n";
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328 }
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329 }
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330 close GENESOUT;
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331
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332 #my @arr = @{$genes{'chr'}};
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333
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334 sub overlapGenes {
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335 my ($otherGene,$bestGene,$chro,$genes)= @_;
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336 my $a1 = $genes->{$chro}{$otherGene}{'left'};
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337 my $a2 = $genes->{$chro}{$bestGene}{'left'};
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338 my $e1 = $genes->{$chro}{$otherGene}{'right'};
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339 my $e2 = $genes->{$chro}{$bestGene}{'right'};
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340 if (($a1 >= $a2)&&($a1 <= $e2)) {
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341 return 1;
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342 }
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343 if (($a2 >= $a1)&&($a2 <= $e1)) {
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344 return 1;
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345 }
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346 return 0;
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347 }
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348
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349 sub overlap {
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350 my ($a1,$a2,$e1,$e2)= @_; #e for genes
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351
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352 if ($a1 > $a2) {
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353 ($a1,$a2) = ($a2,$a1);
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354 }
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355
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356 if ($e1 > $e2) {
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357 ($e1,$e2) = ($e2,$e1);
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358 }
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359
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360
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361 if (($a1 >= $e1)&&($a1 <= $e2)) {
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362 return 2;
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363 }
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364 if (($a2 >= $e1)&&($a2 <= $e2)) {
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365 return 2;
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366 }
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367 if (($e1 >= $a1)&&($e2 <= $a2)) {
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368 return 1;
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369 }
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370
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371 return 0;
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372 }
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373
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374
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375 sub findClosestTSS {
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376 my ($fpos,$lpos,$chro,$genes) = @_;
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377 my $pos = ($fpos+$lpos)/2;
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378 my $gene = "";
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379 my $tssDist=$BIGNUMBER;
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380 my $teDist=$BIGNUMBER;
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381
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382 for my $gName (keys %{$genes->{$chro}}) {
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383 my $TSS = $genes->{$chro}{$gName}{'TSS'};
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384 #print $gName,":",$TSS," " if ($chro eq "chr15");
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385 my $geneDist = ($pos-$TSS)*$genes->{$chro}{$gName}{'strand'};
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386 $geneDist = ($fpos-$TSS)*$genes->{$chro}{$gName}{'strand'} if (abs($fpos-$TSS)<abs($geneDist)) ;
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387 $geneDist = ($lpos-$TSS)*$genes->{$chro}{$gName}{'strand'} if (abs($lpos-$TSS)<abs($geneDist)) ;
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388 $geneDist = 0 if ($TSS>=$fpos && $TSS<=$lpos);
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389
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390 if (abs($geneDist)<abs($tssDist)) {
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391 $gene=$gName;
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392 $tssDist = $geneDist;
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393 $teDist = ($pos-$genes->{$chro}{$gName}{'TE'})*$genes->{$chro}{$gName}{'strand'};
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394 }
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395 if (abs($geneDist)<$BIGNUMBER) {
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396 ###HERE!!!
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397 print GENESOUT "$gName\t",($fpos-$TSS)*$genes->{$chro}{$gName}{'strand'},"\t",($lpos-$TSS)*$genes->{$chro}{$gName}{'strand'},"\t",($pos-$genes->{$chro}{$gName}{'TE'})*$genes->{$chro}{$gName}{'strand'},"\t",$genes->{$chro}{$gName}{'reg'},"\n";
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398
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399 if (abs($geneDist)<abs($genes->{$chro}{$gName}{'closestPicDist'})) {
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400 $genes->{$chro}{$gName}{'closestPicDist'} = $geneDist;
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401 $genes->{$chro}{$gName}{'closestPicDistTE'} = ($pos-$genes->{$chro}{$gName}{'TE'})*$genes->{$chro}{$gName}{'strand'};
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402 }
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403 if ($geneDist>=0 && abs($geneDist)<$genes{$chro}->{$gName}{'closestPositivePicDist'} ) {
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404 $genes->{$chro}{$gName}{'closestPositivePicDist'} = $geneDist;
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405 }
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406 if (($geneDist)*$genes->{$chro}{$gName}{'strand'}<=0 && -1*abs($pos-$TSS)>$genes{$chro}->{$gName}{'closestNegativePicDist'} ) {
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407 $genes->{$chro}{$gName}{'closestNegativePicDist'} = ($pos-$TSS)*$genes->{$chro}{$gName}{'strand'};
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408 }
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409
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410 }
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411 }
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412 print OUT "$tssDist\t$teDist\t$gene\t$genes{$chro}->{$gene}{'reg'}\n" if ($gene ne "");
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413 if ($gene eq "") {
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414 print OUT "$tssDist $teDist NA NA NA\n";
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415 }
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416
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417 }
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418
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419 sub printOvelapingGenes {
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420 my ($fpos,$lpos,$chro,$genes,$globalH,$type) = @_;
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421 #print $fpos,$lpos,$chro,$genes,$globalH,$type,"\n";
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422 my %hash1;
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423 my %hash2;
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424 my @array2return;
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425 for my $gName (keys %{$genes->{$chro}}) {
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426 my $TSS = $genes->{$chro}{$gName}{'TSS'};
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427 my $TE = $genes->{$chro}{$gName}{'TE'};
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428
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429 if (overlap($fpos,$lpos,$TSS,$TE)==1) {
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430 $hash1{$gName} = overlap($fpos,$lpos,$TSS,$TE);
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431 }
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432 if (overlap($fpos,$lpos,$TSS,$TE)==2) {
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433 $hash2{$gName} = overlap($fpos,$lpos,$TSS,$TE);
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434 }
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435 }
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436 print OUT join(",", sort keys %hash1),"\t",join(",", sort keys %hash2),"\n";
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437 if ($type eq "loss") {
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438 for my $key (sort keys %hash1) {
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439 $globalH->{$key} = 1;
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440 }
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441 for my $key (sort keys %hash2) {
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442 $globalH->{$key} = 1;
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443 }
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444 }else {
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445 for my $key (sort keys %hash1) {
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446 $globalH->{$key} = 1;
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447 }
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448 }
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449
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450 }
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451
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452 sub min {
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453 return $_[0] if ($_[0]<$_[1]);
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454 $_[1];
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455 }
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