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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. input file of Gene region annotation which format like GenePred
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7 # 2. input file of Transcripts region annotation which format like GenePred
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8 # 3. input file of gene snp detail info
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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,"i=s","o=s",,"h");
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18 if (!(defined $opt{i} and defined $opt{o}) || defined $opt{h}) {
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19 &usage;
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20 }
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21 #===============================Define Attribute==========================================
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22 my %attribute=(
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23 canvas=>{
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24 'width'=>1500,
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25 'height'=>1800
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26 },
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27 text=>{
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28 'stroke'=>"#000000",
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29 'fill'=>"none",
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30 'stroke-width'=>0.5
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31 #'stroke-width2'=>1
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32 },
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33 line=>{
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34 'stroke'=>"black",
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35 'stroke-width'=>1
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36 },
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37 font=>{
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38 'fill'=>"#000000",
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39 'font-size'=>12,
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40 'font-size2'=>10,
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41 'font-weight'=>'bold',
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42 'font-family'=>"Arial"
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43 #'font-family2'=>"ArialNarrow-bold"
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44 },
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45 rect=>{
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46 'fill'=>"lightgreen",
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47 'stroke'=>"black",
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48 'stroke-width'=>0.5
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49 },
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50 readwidth=>0.5
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51 );
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52 #my $Xscale=600/$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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53 #========================================data============================
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54 open(IN,"$opt{i}")||die"cannot open the file $opt{i}";
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55 my @R_length;
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56 my @T_length;
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57 my $R_number=0;
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58 my $T_number=0;
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59 my $R_max=0;
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60 my $T_max=0;
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61
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62 my $title=<IN>;
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63 chomp $title;
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64 my @title=split/\t/,$title;
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65 my @mark=split/\s+/,$title[1];
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66 my $sample_number=@mark;
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67 while (my $aline=<IN>) {
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68 if ($aline=~/^\s/) {
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69 my $T_title=<IN>;
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70 chomp $T_title;
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71 while (my $a_aline=<IN>) {
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72 chomp $a_aline;
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73 my @temp=split/\t/,$a_aline;
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74 my @number=split/\s+/,$temp[1];
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75 for (my $i=0;$i<@number ;$i++) {
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76 if ($R_max<$number[$i]) {
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77 $R_max=$number[$i];
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78 }
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79 }
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80 push @R_length,[$temp[0],@number];
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81 $R_number++;
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82 }
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83 }
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84 else {
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85 chomp $aline;
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86 my @temp=split/\t/,$aline;
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87 my @number=split/\s+/,$temp[1];
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88 for (my $i=0;$i<@number ;$i++) {
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89 if ($T_max<$number[$i]) {
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90 $T_max=$number[$i];
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91 }
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92 }
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93 push @T_length,[$temp[0],@number];
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94 $T_number++;
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95 }
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96 }
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97 close IN;
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98 print "Tag max: $T_max\nRead max: $R_max\n";
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99 my $kd_number=5;
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100 ##=======================Reads 纵坐标刻度==========================
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101 my $r=1;
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102 my $rr=1;
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103 my $R=$R_max;
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104 while ($R>10) {
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105 $R=$R/10;
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106 $r=$r*10;
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107 $rr++;
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108 }
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109 $R=int($R+0.5);
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110 my $R_xg=$R/$kd_number*$r;#纵坐标一小格大小（一共10格）
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111 my $R_kedu_scale_x=6*$rr;#纵坐标刻度文字
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112 ##=======================Tags 纵坐标刻度==========================
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113 my $t=1;
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114 my $tt=1;
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115 my $T=$T_max;
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116 while ($T>10) {
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117 $T=$T/10;
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118 $t=$t*10;
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119 $tt++;
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120 }
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121 $T=int($T+0.5);
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122 my $T_xg=$T/$kd_number*$t;#纵坐标一小格大小（一共10格）
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123 my $T_kedu_scale_x=6*$tt;#纵坐标刻度文字
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124
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125 #############################s#define start coordinate and scale
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126 my $XOFFSET=50;
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127 my $YOFFSET=60;
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128 my $width=800;
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129 my $heigth=800;
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130 my $X_width=600;
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131 #my $height=1600;
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132 #### Starting ####
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133 #新建画布
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134 my $svg=SVG->new(width=>$width,height=>$heigth);
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135 ####坐标轴
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136 my $axisL=300;#read 纵坐标长度
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137 my $x_margin = 50;
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138 #=========Reads number setting==========================================
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139 my $Y_R_title=30;#标题的纵向宽度
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140 my $Y_R_0=$YOFFSET+$axisL+$Y_R_title;
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141 my $X_R_0=$XOFFSET+$x_margin;
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142 my $R_Yscale=$axisL/$R_xg/$kd_number;
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143 my $R_Xscale=$X_width/$R_number/($sample_number+1);
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144 #=====================================Reads Y axis======================
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145 $svg->line('x1',$X_R_0,'y1',$Y_R_0,'x2',$X_R_0,'y2',$Y_R_0-$axisL,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
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146 for (my $i=1;$i<$kd_number ;$i++) {
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147 $svg->line('x1',$X_R_0-5,'y1',$Y_R_0-$i*$R_xg*$R_Yscale,'x2',$X_R_0,'y2',$Y_R_0-$i*$R_xg*$R_Yscale,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
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148 $svg->text('x',$X_R_0-$R_kedu_scale_x,'y',$Y_R_0-$i*$R_xg*$R_Yscale+4,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',6,'font-family',$attribute{font}{'font-family'},'-cdata',$i*$R_xg);
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149 }
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150 #=====================================Reads X axis======================
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151 $svg->line('x1',$X_R_0,'y1',$Y_R_0,'x2',$X_R_0+$X_width,'y2',$Y_R_0,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
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152
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153 #print "$R_number\t$sample_number\n";
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154 for ($i=0;$i<$R_number ;$i++) {
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155 for (my $j=1;$j<$sample_number+1 ;$j++) {
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156 my $red=$j/$sample_number*255;
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157 $svg->rect('x',$X_R_0+($j+$i*($sample_number+1))*$R_Xscale,'y',$Y_R_0-$R_length[$i][$j]*$R_Yscale,'width',$R_Xscale,'height',$R_length[$i][$j]*$R_Yscale,'stroke',"black",'stroke-width',"0.5",'fill',"rgb($red,125,0)");
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158 }
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159 $svg->text('x',$X_R_0+(1+$sample_number/2+$i*($sample_number+1))*$R_Xscale,'y',$Y_R_0+15,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',6,'font-family',$attribute{font}{'font-family'},'-cdata',$R_length[$i][0]);
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160 }
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161 #===Reads number title
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162 $svg->text('x',$XOFFSET+400,'y',$YOFFSET,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',"1",'font-size',15,'font-family',$attribute{font}{'font-family'},'-cdata',"Reads Length Distribution");
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163 #===Reads
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164 for (my $i=0;$i<$sample_number ;$i++) {
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165 my $red=($i+1)/$sample_number*255;
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166 $svg->rect('x',$X_R_0+550,'y',$YOFFSET+$Y_R_title+20*$i,'width',15,'height',10,'stroke',"black",'stroke-width',"0.5",'fill',"rgb($red,125,0)");
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167 $svg->text('x',$X_R_0+550+30,'y',$YOFFSET+$Y_R_title+20*$i+10,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',10,'font-family',$attribute{font}{'font-family'},'-cdata',$mark[$i]);
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168 }
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169 ####==================================================================================
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170 #=========================================Tag s
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171 my $Y_T_title=30;#标题的纵向宽度
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172 my $Y_T_0=$Y_R_0+$axisL+$Y_R_title+50;#length size
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173 my $X_T_0=$XOFFSET+$x_margin;
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174 my $T_Yscale=$axisL/$T_xg/$kd_number;
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175 my $T_Xscale=$X_width/$T_number/($sample_number+1);
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176 #=====================================Tags Y axis======================
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177 $svg->line('x1',$X_T_0,'y1',$Y_T_0,'x2',$X_T_0,'y2',$Y_T_0-$axisL,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
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178 for (my $i=1;$i<$kd_number ;$i++) {
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179 $svg->line('x1',$X_T_0-5,'y1',$Y_T_0-$i*$T_xg*$T_Yscale,'x2',$X_T_0,'y2',$Y_T_0-$i*$T_xg*$T_Yscale,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
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180 $svg->text('x',$X_T_0-$T_kedu_scale_x,'y',$Y_T_0-$i*$T_xg*$T_Yscale+4,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',6,'font-family',$attribute{font}{'font-family'},'-cdata',$i*$T_xg);
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181 }
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182 #=====================================Tags X axis======================
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183 $svg->line('x1',$X_T_0,'y1',$Y_T_0,'x2',$X_T_0+$X_width,'y2',$Y_T_0,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
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184
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185 #print "$R_number\t$sample_number\n";
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186 for ($i=0;$i<$T_number ;$i++) {
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187 for (my $j=1;$j<$sample_number+1 ;$j++) {
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188 my $red=$j/$sample_number*255;
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189 $svg->rect('x',$X_T_0+($j+$i*($sample_number+1))*$T_Xscale,'y',$Y_T_0-$T_length[$i][$j]*$T_Yscale,'width',$T_Xscale,'height',$T_length[$i][$j]*$T_Yscale,'stroke',"black",'stroke-width',"0.5",'fill',"rgb($red,125,0)");
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190 }
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191 $svg->text('x',$X_T_0+(1+$sample_number/2+$i*($sample_number+1))*$T_Xscale,'y',$Y_T_0+15,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',6,'font-family',$attribute{font}{'font-family'},'-cdata',$T_length[$i][0]);
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192 }
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193 #===Reads number title
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194 $svg->text('x',$XOFFSET+400,'y',$Y_R_0+30+$Y_T_title,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',"1",'font-size',15,'font-family',$attribute{font}{'font-family'},'-cdata',"Tags Length Distribution");
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195 #===Reads
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196 for (my $i=0;$i<$sample_number ;$i++) {
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197 my $red=($i+1)/$sample_number*255;
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198 $svg->rect('x',$X_T_0+550,'y',$Y_R_0+30+$Y_T_title+20*$i,'width',15,'height',10,'stroke',"black",'stroke-width',"0.5",'fill',"rgb($red,125,0)");
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199 $svg->text('x',$X_T_0+550+30,'y',$Y_R_0+30+$Y_T_title+20*$i+10,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',10,'font-family',$attribute{font}{'font-family'},'-cdata',$mark[$i]);
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200 }
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201
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202
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203
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204
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205 open (OUT,">$opt{o}");
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206 print OUT $svg->xmlify();
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207
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208 sub usage{
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209 print <<"USAGE";
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210 Version $version
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211 Usage:
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212 $0
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213 options:
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214 -i
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215 -o svg output
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216 -h help
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217 USAGE
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218 exit(1);
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219 } |
