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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: 2014-6-4
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6 #Modified:
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7 #Description: solexa miRNA express and sequence
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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
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13 my %opts;
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14 GetOptions(\%opts,"i=s","list=s","fa=s","pre=s","tag=s","h");
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15 if (!(defined $opts{i} and defined $opts{list} and defined $opts{fa} and defined $opts{pre} and defined $opts{tag}) || defined $opts{h}) { #necessary arguments
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16 &usage;
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17 }
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18
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19 my $filein=$opts{'i'};
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20 my $fileout=$opts{'list'};
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21 my $out=$opts{'fa'};
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22 my $preout=$opts{'pre'};
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23
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24 =cut
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25 my %hash_pri;
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26 open PRI,"<$opts{p}";
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27 while (my $aline=<PRI>) {
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28 chomp $aline;
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29 if($aline=~/^>(\S+)/){$hash_pri{$1}=$aline;}
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30 }
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31 close PRI;
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32 =cut
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33
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34 open IN,"<$filein"; #input file
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35 open OUT,">$fileout"; #output file
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36 open FA ,">$out";
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37 open PRE,">$preout";
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38
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39 print OUT "#ID\tcoordinate\tpos1\tpos2";
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40 my @marks=split/\,/,$opts{'tag'};
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41 foreach (@marks) {
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42 print OUT "\t",$_,"_matureExp";
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43 }
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44 foreach (@marks) {
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45 print OUT "\t",$_,"_starExp";
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46 }
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47 foreach (@marks) {
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48 print OUT "\t",$_,"_totalExp";
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49 }
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50
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51 print OUT "\n";
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52
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53 my (%uniq_id,$novel);
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54 while (my $aline=<IN>) {
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55 chomp $aline;
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56 until ($aline =~ /^score\s+[-\d\.]+/){
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57 $aline = <IN>;
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58 if (eof) {last;}
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59 }
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60 if (eof) {last;}
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61 ########## miRNA ID ################
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62 $novel++;
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63 ########### annotate####################
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64 do {$aline=<IN>;} until($aline=~/flank_first_end/) ;
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65 chomp $aline;
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66 my @flank1=split/\t/,$aline;
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67 do {$aline=<IN>;} until($aline=~/flank_second_beg/) ;
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68 chomp $aline;
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69 my @flank2=split/\t/,$aline;
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70 #
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71 ########## mature start loop pre ####
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72 do {$aline=<IN>;} until($aline=~/mature_beg/) ;
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73 chomp $aline;
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74 my @start=split/\t/,$aline;
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75 # $start[1] -=$flank1[1];
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76 do {$aline=<IN>;} until($aline=~/mature_end/) ;
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77 chomp $aline;
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78 my @end=split/\t/,$aline;
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79 # $end[1] -=$flank1[1];
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80 do {$aline=<IN>;} until($aline=~/mature_seq/) ;
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81 chomp $aline;
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82 my @arr1=split/\t/,$aline;
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83 do {$aline=<IN>;} until($aline=~/pre_seq/) ;
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84 chomp $aline;
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85 my @arr2=split/\t/,$aline;
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86 do {$aline=<IN>;} until($aline=~/pri_id/) ;
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87 chomp $aline;
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88 my @pri_id=split/\t/,$aline;
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89 do {$aline=<IN>;} until($aline=~/pri_seq/) ;
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90 chomp $aline;
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91 my @pri_seq=split/\t/,$aline;
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92 do {$aline=<IN>;} until($aline=~/star_beg/) ;
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93 chomp $aline;
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94 my @star_start=split/\t/,$aline;
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95 # $star_start[1] -=$flank1[1];
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96 do {$aline=<IN>;} until($aline=~/star_end/) ;
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97 chomp $aline;
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98 my @star_end=split/\t/,$aline;
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99 # $star_end[1] -=$flank1[1];
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100 do {$aline=<IN>;} until($aline=~/star_seq/) ;
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101 chomp $aline;
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102 my @arr3=split/\t/,$aline;
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103 print OUT "miR-c-$novel\t$pri_id[1]\tmature:$start[1]:$end[1]\tstar:$star_start[1]:$star_end[1]\t";
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104 #print OUT "$arr1[1]\t$arr3[1]\t$arr2[1]\t\/\t";
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105 print FA ">miR-c-$novel\n$arr1[1]\n";
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106 print PRE ">miR-c-$novel\n$pri_seq[1]\n";
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107 ########## reads count #############
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108 <IN>;
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109 my @count1;my @count2;my @count3;my @count4;
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110 $aline=<IN>;
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111 do {
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112 chomp $aline;
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113 my @reads=split/\t/,$aline;
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114 my @pos=();
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115 $reads[5]=~/(\d+)\.\.(\d+)/;
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116 # $pos[0] =$1-$flank1[1];
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117 # $pos[1] =$2-$flank1[1];
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118 $pos[0]=$1;
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119 $pos[1]=$2;
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120 $reads[0]=~/:([\d|_]+)_x(\d+)$/;
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121 my @ss=split/_/,$1;
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122 for (my $i=0;$i<@ss ;$i++) {
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123 if (!(defined $count3[$i])) {
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124 $count3[$i]=0;
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125 }
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126 if (!(defined $count4[$i])) {
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127 $count4[$i]=0;
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128 }
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129 $count2[$i]+=$ss[$i];
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130
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131 }
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132 # $count3 +=$1 if($end[1]-$pos[0]>=10 && $pos[1]-$start[1]>=10 );
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133 # $count4 +=$1 if($star_end[1]-$pos[0]>=10 && $pos[1]-$star_start[1]>=10 );
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134 # $count1 =$1 if($end[1]-$pos[0]>=10 && $pos[1]-$start[1]>=10 && $count1<$1);
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135 # $count2 =$1 if($star_end[1]-$pos[0]>=10 && $pos[1]-$star_start[1]>=10 && $count2<$1);
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136 if($end[1]-$pos[1]>=-5 && $end[1]-$pos[1]<=5 && $pos[0]-$start[1]>=-3 && $pos[0]-$start[1]<=3 )
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137 {
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138 for (my $i=0;$i<@ss;$i++) {
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139 $count3[$i]+=$ss[$i];
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140 }
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141 }
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142 if($star_end[1]-$pos[1]<=5 && $star_end[1]-$pos[1]>=-5 && $pos[0]-$star_start[1]>=-3 && $pos[0]-$star_start[1]<=3){
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143 for (my $i=0;$i<@ss;$i++) {
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144 $count4[$i]+=$ss[$i];
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145 }
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146 }
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147 $aline=<IN>;
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148 chomp $aline;
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149 } until(length $aline < 1) ;
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150 $"="\t";
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151 print OUT "@count3\t@count4\t@count2\n";
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152 $"=" ";
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153 }
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154
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155 close IN;
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156 close OUT;
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157
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158 sub usage{
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159 print <<"USAGE";
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160 Version $version
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161 Usage:
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162 $0 -i -list -fa -pre -tag
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163 options:
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164 -i input file,predictions file
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165 -list output file miRNA list file
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166 -fa output file ,miRNA sequence fasta file.
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167 -pre output file, miRNA precursor fasta file.
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168 -tag string, sample names# eg: samA,samB,samC
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169 -h help
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170 USAGE
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171 exit(1);
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172 }
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173
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