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1 #!/usr/bin/perl -w
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2 #Filename:
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3 #Author: Tian Dongmei
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4 #Email: tiandm@big.ac.cn
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5 #Date: 2013/7/19
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6 #Modified:
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7 #Description:
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8 my $version=1.00;
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9
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10 use strict;
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11 use Getopt::Long;
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12 #use Math::Cephes qw(:hypergeometrics);
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13
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14 my %opts;
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15 GetOptions(\%opts,"i=s","o=s","h");
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16 if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
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17 &usage;
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18 }
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19
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20 my $filein=$opts{'i'};
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21 my $fileout=$opts{'o'};
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22
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23 open IN,"<$filein"; #input file
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24 open OUT,">$fileout"; #output file
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25
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26 while (my $aline=<IN>) {
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27 chomp $aline;
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28 if ($aline=~/^\#/) {
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29 print OUT $aline,"\tp-value\n";
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30 next;
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31 }
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32 my @tmp=split/\t/,$aline;
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33 my @pos=split/:|-/,$tmp[0];
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34 $tmp[1]=~s/nt//;
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35 my $pv=&phase($tmp[1],$pos[1],$pos[2],$tmp[4]);
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36
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37 print OUT $aline,"\t",$pv,"\n";
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38 }
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39 close IN;
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40 close OUT;
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41
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42 sub phase{
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43 my ($tagL,$start,$end,$tags)=@_;
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44 my @tmp=split/\;/,$tags;
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45 my %tag;
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46 for (my $i=0;$i<@tmp;$i++) {
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47 my @aa=split/\,/,$tmp[$i];
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48 next if($aa[1]-$aa[0]+1 != $tagL);
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49 # $tag{$aa[0].",".$aa[2]}+=$aa[3] if($aa[2] eq "+");
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50 # $tag{($aa[1]).",".$aa[2]}+=$aa[3] if($aa[2] eq "-");
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51 $tag{$aa[0]}+=$aa[3] if($aa[2] eq "+");
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52 $tag{($aa[1]+3)}+=$aa[3] if($aa[2] eq "-");
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53 }
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54
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55 my $pv=&pvalue2(\%tag,$tagL,$start,$end);
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56
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57 return $pv;
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58 }
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59
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60 sub pvalue2{
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61 my ($tag,$tagL,$start,$end)=@_;
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62
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63 my $p=1; my $pp=1;
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64 foreach my $ccs(keys %{$tag}){
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65 my $n=0;
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66 my $k=0;
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67 my $K=0;
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68 my $N=0;
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69
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70 my $cor= $ccs;
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71 my $ss=$cor;
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72 my $ee=($cor+$tagL*10-1)<$end ? $cor+$tagL*10-1 : $end;
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73
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74 my $max=0;
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75 for (my $i=$ss; $i<=$ee; $i++) # calculate n on the sense strand
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76 {
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77 my $x=$i;
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78 if (defined $$tag{$x})
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79 {
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80 if ($max<$$tag{$x}) {$max=$$tag{$x};}
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81 $n +=$$tag{$x};
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82 $N++;
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83 }
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84 }
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85 for (my $i=$ss; $i<=$ee; $i=$i+$tagL) # calculate k on the sense strand
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86 {
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87 my $x=$i;
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88 if (defined $$tag{$x})
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89 {
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90 $k +=$$tag{$x};
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91 $K++;
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92 }
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93 }
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94
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95
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96 return $p if($K<3);
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97 return $p if($max/$n>0.8);
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98
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99 my $pn=0;
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100 next if($n==$k);
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101 $pn=10*$k/($n-$k)+1;
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102 $pn = $pn ** ($K-2);
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103 $pn = log($pn);
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104 if ($p<$pn) {
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105 $p=$pn;
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106 }
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107
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108 }
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109
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110 return $p;
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111
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112 }
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113
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114 sub pvalue{
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115 my ($tag,$tagL,$start,$end)=@_;
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116
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117 my $p=1;
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118 foreach my $ccs(keys %{$tag}){
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119 my $n=-1;
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120 my $k=-1;
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121
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122 my ($cor, $str)=split(/,/, $ccs);
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123 if ($str eq "+") # small RNAs on the Watson strand
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124 {
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125 my $ss=$cor;
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126 my $ee=($cor+$tagL*11-1)<$end ? $cor+$tagL*11-1 : $end;
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127 for (my $i=$ss; $i<=$ee; $i++) # calculate n on the sense strand
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128 {
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129 my $x=$i.","."+";
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130 if (defined $$tag{$x})
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131 {
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132 $n=$n+1;
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133 }
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134 }
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135 for (my $i=$ss; $i<=$ee; $i=$i+$tagL) # calculate k on the sense strand
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136 {
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137 my $x=$i.","."+";
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138 if (defined $$tag{$x})
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139 {
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140 $k=$k+1;
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141 }
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142 }
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143
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144 for (my $j=$ss-2; $j<=$ee-2; $j++) # calculate n on the antisense strand
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145 {
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146 my $x=$j.","."-";
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147 if (defined $$tag{$x})
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148 {
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149 $n=$n+1;
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150 }
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151 }
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152
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153 for (my $j=$ss+$tagL-2; $j<=$ee-2; $j=$j+$tagL) # calculate k on the antisense strand
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154 {
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155 my $x=$j.","."-";
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156 if (defined $$tag{$x})
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157 {
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158 $k=$k+1;
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159 }
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160 }
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161 }
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162
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163 elsif ($str eq "-") # small RNAs on the Crick strand
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164 {
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165 my $ee=$cor;
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166 my $ss=$cor-$tagL*11+1> $start ? $cor-$tagL*11+1 : $start;
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167 for (my $i=$ss; $i<=$ee; $i++) # calculate n on the sense strand
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168 {
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169 my $x=$i.","."-";
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170 if (defined $$tag{$x})
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171 {
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172 $n=$n+1;
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173 }
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174 }
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175 for (my $i=$ss+$tagL-1; $i<=$ee; $i=$i+$tagL) # calculate k on the sense strand
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176 {
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177 my $x=$i.","."-";
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178 if (defined $$tag{$x})
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179 {
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180 $k=$k+1;
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181 }
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182 }
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183
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184 for (my $j=$ss+2; $j<=$ee+2; $j++) # calculate n on the antisense strand
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185 {
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186 my $x=$j.","."+";
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187 if (defined $$tag{$x})
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188 {
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189 $n=$n+1;
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190 }
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191 }
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192 for (my $j=$ss+2; $j<=$ee+2; $j=$j+$tagL) # calculate k on the antisense strand
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193 {
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194 my $x=$j.","."+";
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195 if (defined $$tag{$x})
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196 {
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197 $k=$k+1;
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198 }
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199 }
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200 }
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201
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202 next if($k<3);
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203
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204 my $pn=0; my $N=$tagL*11*2-1; my $M=21;
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205 for (my $w=$k; $w<=$M; $w++) # calculate p-value from n and k
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206 {
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207 my $c=1;
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208 my $rr=1;
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209 my $rw=1;
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210
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211 for (my $j=0; $j<=$w-1; $j++)
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212 {
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213 $c=$c*($M-$j)/($j+1);
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214 }
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215 for (my $x=0; $x<=$n-$w-1; $x++)
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216 {
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217 $rr=$rr*($N-$M-$x)/($x+1);
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218 }
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219 for (my $y=0; $y<=$n-1; $y++)
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220 {
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221 $rw=$rw*($y+1)/($N-$y);
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222 }
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223 my $pr=$c*$rr*$rw;
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224
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225 $pn=$pn+$pr;
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226 }
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227
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228 $p=$pn<$p ? $pn :$p;
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229
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230 if ($p<0.001) #select and output small RNA clusters with p<0.001
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231
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232 {
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233
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234 return $p;
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235
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236 }
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237
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238 }
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239 return $p;
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240 }
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241
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242 sub usage{
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243 print <<"USAGE";
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244 Version $version
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245 Usage:
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246 $0 -i -o
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247 options:
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248 -i input file
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249 -o output file
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250 -h help
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251 USAGE
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252 exit(1);
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253 }
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254
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