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1 #!/usr/bin/perl -w
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2 #==========================================================================================
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3 # Date:
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4 # Title:
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5 # Comment: Program to plot gene structure
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6 # Input: 1.
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7 # 2.
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8 # 3.
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9 # Output: output file of gene structure graph by html or svg formt
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10 # Test Usage:
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11 #========================================================================================
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12 #use strict;
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13 my $version=1.00;
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14 use SVG;
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15 use Getopt::Long;
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16 my %opt;
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17 GetOptions(\%opt,"span=s","c=s","o=s","out=s","l=s","cen:s","n=s","mark=s","h");
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18 if (!( defined $opt{o}) || defined $opt{h}) {
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19 &usage;
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20 }
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21 my $span=$opt{span};
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22 my $sample_cloumn=$opt{n};
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23 my $mark=$opt{mark};
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24 #===============================Define Attribute==========================================
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25 my %attribute=(
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26 canvas=>{
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27 'width'=>1500,
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28 'height'=>1800
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29 },
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30 text=>{
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31 'stroke'=>"#000000",
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32 'fill'=>"none",
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33 'stroke-width'=>0.5
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34 },
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35 line=>{
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36 'stroke'=>"black",
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37 'stroke-width'=>1
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38 },
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39 csv=>{
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40 'stroke'=>"red",
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41 'stroke-width'=>0.5
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42 },
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43 exon=>{
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44 'stroke'=>"black",
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45 'stroke-width'=>1
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46 },
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47 intron=>{
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48 'stroke'=>"black",
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49 'stroke-width'=>1.5
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50 },
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51 font=>{
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52 'fill'=>"#000000",
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53 'font-size'=>12,
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54 'font-size2'=>10,
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55 #'font-weight'=>'bold',
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56 'font-family'=>"Arial"
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57 #'font-family'=>"ArialNarrow-bold"
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58 },
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59 rect=>{
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60 'fill'=>"lightgreen",
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61 'stroke'=>"black",
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62 'stroke-width'=>0.5
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63 },
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64 readwidth=>0.5
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65 );
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66 #############################s#define start coordinate and scale
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67 open(TXT,">$opt{out}");
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68 open(LENGTH,"$opt{l}")||die"cannot open the file $opt{l}";
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69 my %length;
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70 while (my $aline=<LENGTH>) {
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71 chomp $aline;
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72 next if($aline=~/^\#/);
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73 my @temp=split/\t/,$aline;
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74 $temp[0]=~s/^c/C/;
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75 $length{$temp[0]}=$temp[1];
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76 }
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77 close LENGTH;
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78 #---------------------------------------------------------------
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79 my %centromere;
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80 if (defined($opt{cen})) {
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81 open(CEN,"$opt{cen}")||die"cannot open the file $opt{cen}";
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82 while (my $aline=<CEN>) {
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83 chomp $aline;
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84 next if($aline=~/^\#/);
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85 my @temp=split/\t/,$aline;
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86 $temp[0]=~s/^c/C/;
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87 $centromere{$temp[0]}[0]=$temp[1];
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88 $centromere{$temp[0]}[1]=$temp[2];
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89 }
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90 close CEN;
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91 }
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92
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93 #---------------------------------------------------------------
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94 my $max_length=0;
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95 foreach my $chr (keys %length) {
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96 if ($max_length<$length{$chr}) {
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97 $max_length=$length{$chr};
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98 }
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99 print "$chr\n";
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100 }
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101 #====================================cluster data=======================================
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102 open(CLUSTER,"$opt{c}")||die"cannot open the file $opt{c}";
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103 my %cluster;
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104 my %cluster_density;
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105 #my @sample=qw(39B3 3PA3 3LC3);
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106 my @cluster_non_add;
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107 while (my $aline=<CLUSTER>) {
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108 next if($aline=~/^\#/);
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109 chomp $aline;##ID chr strand start end 19B1
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110 my @temp=split/\t/,$aline;
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111 my @ID=split/\:/,$temp[0];
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112 my @posi=split/\-/,$ID[1];
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113 push @{$cluster{$ID[0]}},[$temp[0],$posi[0],$posi[1],$temp[2+$sample_cloumn]];#ID start end rpkm(19B1,1PA1,1LC1);
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114 }
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115 close CLUSTER;
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116 my %max_cluster;
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117 foreach my $chr (sort keys %cluster) {
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118 # for (my $i=0;$i<3 ;$i++) {
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119 # $max_cluster{$chr}[$i]=0;
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120 # }
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121 $max_cluster{$chr}=0
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122 }
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123 foreach my $chr (sort keys %cluster) {
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124 @{$cluster{$chr}}=sort{$a->[1] <=> $b->[1]}@{$cluster{$chr}};
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125 #for (my $s=0;$s<3;$s++) {
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126 for (my $i=0;$i<$#{$cluster{$chr}} ;$i++) {
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127 if ($cluster{$chr}[$i][3]>$max_cluster{$chr}) {
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128 $max_cluster{$chr}=$cluster{$chr}[$i][3];
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129 }
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130 }
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131 #}
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132
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133 }
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134 #---------------------------------------------------------------------------------------
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135 foreach my $chr(keys %cluster) {
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136 for(my $i=0;$i<$#{$cluster{$chr}};$i++) {
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137 my $start=int($cluster{$chr}[$i][1]/$span);
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138 my $end=int($cluster{$chr}[$i][2]/$span);
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139 if ($start==$end) {
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140 #for (my $j=0;$j<3 ;$j++) {
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141 $cluster_density{$chr}[$start]+=$cluster{$chr}[$i][3];
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142 #}
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143
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144 }
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145 else{
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146 for (my $m=$start;$m<=$end ;$m++) {
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147 #for (my $j=0;$j<3 ;$j++) {
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148 $cluster_density{$chr}[$m]+=$cluster{$chr}[$i][3];
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149 #}
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150 }
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151 }
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152 }
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153 }
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154 my %max_cluster_density;
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155 foreach my $chr (sort keys %cluster) {#
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156 #for (my $i=0;$i<3 ;$i++) {
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157 for (my $i=0;$i<$#{$cluster{$chr}} ;$i++) {
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158 $max_cluster_density{$chr}=0;
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159 }
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160 #}
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161 }
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162 foreach my $chr (sort keys %cluster) {
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163 #for (my $i=0;$i<3;$i++) {
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164 for (my $k=0;$k<$#{$cluster_density{$chr}} ;$k++) {
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165 if (!(defined($cluster_density{$chr}[$k]))) {
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166 $cluster_density{$chr}[$k]=0;
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167 }
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168 if ($cluster_density{$chr}[$k]>$max_cluster_density{$chr}) {
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169 $max_cluster_density{$chr}=$cluster_density{$chr}[$k];
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170 }
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171 print TXT "$chr\t$k\t$cluster_density{$chr}[$k]\n";
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172 }
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173 #}
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174 }
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175 #--------------------------------------------------------------------
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176 my $XOFFSET=50;
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177 my $YOFFSET=60;
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178 #my $length=$end-$start+1;
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179 my $Xscale=600/$max_length;#定义X轴比例尺 1:1000 x轴的坐标长度都要按照此比例尺换算
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180 #my $high_cov=$high_cov9B1=0.5;#定义峰图最高峰
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181 #my $Yscale=1/$high_cov;#定义Y轴比例尺 1:60 y轴的坐标长度都要按照此比例尺换算
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182 #========================================New canvas============================
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183 #### Starting ####
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184 #新建画布
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185 my $svg=SVG->new();
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186 #画图起始点
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187 my $canvas_start_x=$XOFFSET;
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188 my $canvas_end_x=$XOFFSET+$max_length*$Xscale;#按照比例尺 画线
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189 my $canvas_start_y=$YOFFSET;
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190 my $canvas_end_y=$YOFFSET;
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191
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192 my $chr_width=$YOFFSET;
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193 my $chr_start_y;
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194 my $chr_end_y;
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195 my $Yscale=0.01;
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196 foreach my $chr (sort keys %length) {
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197 my $chr_start_x=$XOFFSET;
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198 my $chr_end_x=$XOFFSET+$length{$chr}*$Xscale;
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199 $chr_start_y+=$chr_width;
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200 $chr_end_y+=$chr_width;
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201 $svg->line(x1=>$chr_start_x,y1=>$chr_start_y,x2=>$chr_end_x,y2=>$chr_end_y,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
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202 $svg->text('x',$XOFFSET-40,'y',$chr_start_y,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',$chr);
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203 $svg->text('x',$chr_end_x+20,'y',$chr_start_y,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',$length{$chr});
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204
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205
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206 if (defined($centromere{$chr}[0])) {
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207 $svg->rect('x',$XOFFSET+$centromere{$chr}[0]*$Xscale,'y',$chr_start_y,'width',($centromere{$chr}[1]-$centromere{$chr}[0]+1)*$Xscale,'height',5,'stroke',"blue",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"blue");
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208 }
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209 for (my $i=0;$i<$#{$cluster_density{$chr}} ;$i++) {
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210 if ($cluster_density{$chr}[$i]*$Yscale>40) {
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211 $cluster_density{$chr}[$i]=40/$Yscale;
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212 $svg->rect('x',$XOFFSET+$i*$span*$Xscale,'y',$chr_start_y-45,'width',$span*$Xscale,'height',5,'stroke',"green",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"green");
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213 }
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214 my $cluster_density_start_x=$XOFFSET+$i*$span*$Xscale;
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215 my $cluster_density_end_x=$XOFFSET+($i+1)*$span*$Xscale;
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216 my $cluster_density_start_y=$chr_start_y-$cluster_density{$chr}[$i]*$Yscale;
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217 #my $cluster_density_end_y=$chr_start_y-$cluster_density{$chr}[$i+1][0]*$Yscale;
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218 #$svg->line('x1',$cluster_density_start_x,'y1',$cluster_density_start_y,'x2',$cluster_density_end_x,'y2',$cluster_density_end_y,'stroke',"red",'stroke-width',$attribute{csv}{'stroke-width'});
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219 $svg->rect('x',$cluster_density_start_x,'y',$chr_start_y-$cluster_density{$chr}[$i]*$Yscale,'width',$span*$Xscale,'height',$cluster_density{$chr}[$i]*$Yscale,'stroke',"red",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"red");
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220 }
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221
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222 $chr_width=50;
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223
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224 #$svg->rect('x',$c_non_add_start_x,'y',$c_non_add_start_y,'width',$cluster_non_add_width,'height',$cluster_non_add_heigth,'stroke',"blue",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"blue");
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225 }
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226
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227 my $span_k=$span/1000;
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228 $svg->text('x',200,'y',$chr_start_y+20,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',"$mark sRNA rpmk \/ $span_k kb");
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229
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230 $svg->rect('x',600,'y',500,'width',10,'height',10,'stroke',"red",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"red");
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231 $svg->text('x',620,'y',510,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',"sRNA rpkm");
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232
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233 if (defined($opt{cen})) {
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234 $svg->rect('x',600,'y',520,'width',10,'height',10,'stroke',"blue",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"blue");
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235 $svg->text('x',620,'y',530,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',"centromere");
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236 }
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237
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238 close TXT;
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239 open (OUT,">$opt{o}");
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240 print OUT $svg->xmlify();
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241
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242 sub log2 {
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243 my $n = shift;
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244 return log($n)/log(2);
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245 }
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246
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247 sub usage{
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248 print <<"USAGE";
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249 Version $version
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250 Usage:
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251 $0
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252 options:
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253 -span
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254 -n sample cloumn
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255 -mark sample name
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256 -o output graph file name with html or svg extension
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257 -c cluster file input
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258 -out txt output
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259 -l length of chr
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260 -cen centromere
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261 -h help
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262 USAGE
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263 exit(1);
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264 } |
