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1 #!/usr/bin/perl -w
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2 #Filename:
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3 #Author: Chentt
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4 #Email: chentt@big.ac.cn
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5 #Date: 2014/4/10
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6 #Modified:
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7 #Description: cluster annotate by priority
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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","d=i","g=s","o=s","t=s","h");
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15 if (!(defined $opts{i} and defined $opts{g} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
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16 &usage;
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17 }
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18 #my $genelistout=$opts{'t'};
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19 my $dis=defined $opts{'d'}? $opts{'d'}:1000;
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20 my %gene;
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21
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22 #open OUT,">$genelistout"; #output file
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23 #print OUT "#ID\tchr\tstart\tend\tstrand\ns";
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24 open IN,"<$opts{g}";
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25 while (my $aline=<IN>) {
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26 chomp $aline;
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27 next if($aline=~/^\#/);
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28 my @tmp=split/\t/,$aline;#ID chr start end strand
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29 #push @{$gene1{$tmp[0]}},[$tmp[2],$tmp[3],$tmp[1]];
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30 $gene{$tmp[1]}{$tmp[0]}=[$tmp[2],$tmp[3],$tmp[4]];
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31 }
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32 #while (my $aline=<IN>) {
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33 # chomp $aline;
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34 # next if($aline=~/^\#/);
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35 # my @tmp=split/\t/,$aline;
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36 # my $ID;
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37 # if ($tmp[2] eq "gene") {
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38 # $tmp[0]=~s/Chr\./Chr/;
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39 # $tmp[0]=~s/Chr/chr/;
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40 # my @infor=split/;/,$tmp[8];
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41 # for (my $i=0;$i<@infor ;$i++) {
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42 # if ($infor[$i]=~/Alias\=(\S+)$/) {
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43 # $ID=$1;
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44 # last;
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45 # }
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46 # }
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47 # $gene{$tmp[0]}{$ID}=[$tmp[3],$tmp[4],$tmp[6]];#$gene{chr}{geneID}=[start,end,strand]
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48 # print OUT "$ID\t$tmp[0]\t$tmp[3]\t$tmp[4]\t$tmp[6]\n";
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49 # }
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50 #}
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51 close IN;
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52 #close OUT;
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53
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54
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55 my $filein=$opts{'i'};
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56 my $fileout=$opts{'o'};
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57
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58 open IN,"<$filein"; #input file
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59 open OUT,">$fileout"; #output file
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60 while (my $aline=<IN>) {
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61 chomp $aline;
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62 my @tmp=split/\t/,$aline;
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63 if($aline=~/^\#/){print OUT "$aline\tP_annotate\n";next}
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64 my @result;
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65 #shift @tmp;
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66 my @id=split/:/,$tmp[0];
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67 $id[0]=~s/Chr0/Chr/;
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68 my @posi=split/-/,$id[1];
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69 foreach my $key (keys %{$gene{$id[0]}}) {
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70 if ($posi[0]<$gene{$id[0]}{$key}[1] && $posi[1]>$gene{$id[0]}{$key}[0]) {
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71 push @result,"gene-body;$key;$gene{$id[0]}{$key}[2]";#$te{$key}";
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72 next;
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73 }
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74 #if ($posi[0]<$gene{$id[0]}{$key}[0] && $posi[1]>$gene{$id[0]}{$key}[0]-1000) {
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75 if ($posi[0]<$gene{$id[0]}{$key}[0] && $posi[1]>$gene{$id[0]}{$key}[0]-$dis) {
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76 push @result,"up1-kb;$key;$gene{$id[0]}{$key}[2]" if($gene{$id[0]}{$key}[2] eq "+");
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77 push @result,"down1-kb;$key;$gene{$id[0]}{$key}[2]" if($gene{$id[0]}{$key}[2] eq "-");
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78 next;
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79 }
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80 #if ($posi[0]<$gene{$id[0]}{$key}[1]+1000 && $posi[1]>$gene{$id[0]}{$key}[1]) {
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81 if ($posi[0]<$gene{$id[0]}{$key}[1]+$dis && $posi[1]>$gene{$id[0]}{$key}[1]) {
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82 push @result,"down1-kb;$key;$gene{$id[0]}{$key}[2]" if($gene{$id[0]}{$key}[2] eq "+");
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83 push @result,"up1-kb;$key;$gene{$id[0]}{$key}[2]" if($gene{$id[0]}{$key}[2] eq "-");
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84 next;
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85 }
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86 }
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87 my $result;
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88 if (!(@result)) {
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89 $result="intergenic";
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90 }
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91 elsif($#result==0){
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92 $result=$result[0];
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93
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94 }
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95 else{
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96 $result=join "\t",@result;
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97 }
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98 # else{
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99 # my $te_num=0;
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100 # my @te_overlap;
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101 # my @te_up_down;
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102 # my @non_overlap;
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103 # my @non_up_down;
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104 # for (my $k=0;$k<@result ;$k++) {
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105 # my @rr=split/\;/,$result[$k];
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106 # if ($rr[3] eq "Y") {
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107 # $te_num++;
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108 # if ($rr[0] eq "overlap") {
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109 # push @te_overlap,$result[$k];
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110 # }
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111 # else{
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112 # push @te_up_down,$result[$k];
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113 # }
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114 # }
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115 # else{
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116 # if ($rr[0] eq "overlap") {
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117 # push @non_overlap,$result[$k];
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118 # }
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119 # else{
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120 # push @non_up_down,$result[$k];
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121 # }
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122 # }
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123 # }
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124 # if ($te_num==0) {#non TE
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125 # if (!(@te_overlap)) {#down up
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126 # if ($#non_up_down==0) {
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127 # $result=$non_up_down[0];
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128 # }
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129 # else{#overlap
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130 # my $all_2=join "\t",@non_up_down;
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131 # $result="up&down1-kb\t".$all_2;
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132 # }
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133 # }
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134 # else{
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135 # $result=join "\t",@non_overlap;
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136 # if ($#non_overlap>=1) {
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137 # print "$aline\t$result\n";
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138 # }
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139 # }
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140 # }
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141 # else{#TE
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142 # if (!(@te_overlap)) {#down up
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143 # if ($#te_up_down==0) {
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144 # $result=$te_up_down[0];
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145 # }
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146 # else{#overlap
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147 # my $all_2=join "\t",@te_up_down;
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148 # $result="up&down1-kb\t".$all_2;
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149 # }
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150 # }
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151 # else{
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152 # $result=join "\t",@te_overlap;
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153 # if ($#te_overlap>=1) {
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154 # print "$aline\t$result\n";
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155 # }
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156 # }
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157 # }
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158 # }
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159 print OUT "$aline\t$result\n";
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160 }
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161
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162 close IN;
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163 close OUT;
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164 sub usage{
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165 print <<"USAGE";
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166 Version $version
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167 Usage:
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168 $0 -i -o -g -d
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169 options:
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170 -i input file
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171 -g genelist file
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172 -d int the length of the upstream and downstream,default 1000
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173 -o output file
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174 -h help
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175 USAGE
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176 exit(1);
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177 }
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178
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