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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: 2014/04/09
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6 #Modified:
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7 #Description: islands merged of merged samples
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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","o=s","N=i","t=s","mark=s","h");
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15 if (!(defined $opts{i} and defined $opts{d} and defined $opts{N} and defined $opts{mark} and defined $opts{t} 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
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19 my $filein=$opts{'i'};
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20 my $fileout=$opts{'o'};
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21 my $distance=$opts{'d'};
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22 my $tempout=$opts{'t'};
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23 my $mark=$opts{'mark'};
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24 my @sample=split/\#/,$mark;
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25 $mark=join"\"\t\"",@sample;
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26
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27 open IN,"<$filein"; #input file
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28 open OUT,">$fileout"; #output file
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29 print OUT "\"Chr\"\t\"MajorLength\"\t\"Percent\"\t\"$mark\"\n";
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30 open TMP,">$tempout";
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31 print TMP "\#Chr\tMajorLength\tPercent\tTagsNumber\tTagsInfor\n";
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32 my %hash;
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33 while (my $aline=<IN>) {
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34 chomp $aline;
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35 if($aline=~/^\#/){
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36 #print OUT "$aline\n";
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37 next;
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38 }
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39 my @tmp=split/\t/,$aline;
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40 my $chr=shift @tmp;
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41 #shift @tmp;
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42 push @{$hash{$chr}},[@tmp];
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43 }
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44
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45 close IN;
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46
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47 foreach my $key (keys %hash) {
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48 my @tag=sort{$a->[1] <=> $b->[1]} @{$hash{$key}};
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49 my @sample;
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50 my $start=$tag[0][1];
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51 my $end=$tag[0][2];
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52 push @sample,[@{$tag[0]}];
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53 for (my $i=1;$i<@tag-1;$i++) {
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54 if ($tag[$i][1]-$end<=$distance) {
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55 if ($tag[$i][2]>$end) {
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56 $end=$tag[$i][2];
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57 }
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58 push @sample,[@{$tag[$i]}];
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59 }
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60 else{
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61 my ($max_length,$max_p,$tag,@cluster_exp)=Max_length(\@sample);
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62 my $cluster_exp=join"\t",@cluster_exp;
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63 if ($max_length>30) {
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64 print TMP "$key\:$start\-$end\t$max_length"."nt\t$max_p\t$tag\n";
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65 $max_length="\>30";
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66 }
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67 else{print TMP "$key\:$start\-$end\t$max_length"."nt\t$max_p\t$tag\n";}
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68 print OUT "$key\:$start\-$end\t$max_length"."nt\t$max_p\t$cluster_exp\n";
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69 $start=$tag[$i][1];
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70 $end=$tag[$i][2];
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71
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72 @sample=();
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73 push @sample,[@{$tag[$i]}];
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74 }
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75 }
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76 if ($tag[$#tag][1]-$end<=$distance) {
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77 if ($tag[$#tag][2]>$end) {
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78 $end=$tag[$#tag][2];
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79 }
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80 push @sample,[@{$tag[$#tag]}];
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81 my ($max_length,$max_p,$tag,@cluster_exp)=Max_length(\@sample);
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82 my $cluster_exp=join"\t",@cluster_exp;
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83 if ($max_length>30) {
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84 $max_length="\>30";
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85 print TMP "$key\:$start\-$end\t$max_length"."nt\t$max_p\t$tag\n";
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86 }
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87 else{print TMP "$key\:$start\-$end\t$max_length"."nt\t$max_p\t$tag\n";}
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88 print OUT "$key\:$start\-$end\t$max_length"."nt\t$max_p\t$cluster_exp\n";
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89 }
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90 else{
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91 my ($max_length,$max_p,$tag,@cluster_exp)=Max_length(\@sample);
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92 my $cluster_exp=join"\t",@cluster_exp;
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93 if ($max_length>30) {
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94 $max_length="\>30";
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95 print TMP "$key\:$start\-$end\t$max_length"."nt\t$max_p\t$tag\n";
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96 }
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97 else{print TMP "$key\:$start\-$end\t$max_length"."nt\t$max_p\t$tag\n";}
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98 print OUT "$key\:$start\-$end\t$max_length"."nt\t$max_p\t$cluster_exp\n";
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99
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100 }
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101 }
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102 close OUT;
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103 close TMP;
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104 sub Max_length{
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105 my @exp=@{$_[0]};
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106 my %sample_length;
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107 my $total_exp;
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108 my @each;
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109 my @tag;
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110 for (my $i=0;$i<=$#exp ;$i++) {
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111 my $length=$exp[$i][2]-$exp[$i][1]+1;
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112 #if ($length>30) {
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113 # $length=40;
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114 #}
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115 my $exp=0;
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116 foreach (1..$opts{'N'}) {
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117 $exp+=$exp[$i][$_+2];
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118 $each[$_-1]+=$exp[$i][$_+2];
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119 }
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120 $sample_length{$length}+=$exp;
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121 $total_exp+=$exp;
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122 push @tag,($exp[$i][1].",".$exp[$i][2].",".$exp[$i][0].",".$exp);
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123 }
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124 my $max=0;
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125 my $max_key;
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126 foreach my $key (sort keys %sample_length) {
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127 my $p=$sample_length{$key}/$total_exp;
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128 if ($p>$max) {
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129 $max=$p;
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130 $max_key=$key;
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131 }
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132 $sample_length{$key}=sprintf("%.2f",$p);
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133 }
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134 my $tag_n=@tag;
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135 my $tag=join";",@tag;
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136 $tag=$tag_n."\t".$tag;
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137 return($max_key,$sample_length{$max_key},$tag,@each);
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138 }
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139
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140 sub usage{
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141 print <<"USAGE";
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142 Version $version
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143 Usage:
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144 $0 -i -o -d -N -t -mark
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145 options:
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146 -i input file
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147 -d distance of two islands
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148 -mark sample name;
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149 -o output file
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150 -N sample number
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151 -t temp output file
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152 -h help
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153 USAGE
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154 exit(1);
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155 }
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156
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