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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,"g=s","l=s","span=s","c=s","o=s","out=s","cen: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 my @mark=split/\#/,$mark;
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25 my $genelist=$opt{g};
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26 #===============================Define Attribute==========================================
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27 my %attribute=(
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28 canvas=>{
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29 'width'=>1500,
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30 'height'=>1800
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31 },
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32 text=>{
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33 'stroke'=>"#000000",
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34 'fill'=>"none",
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35 'stroke-width'=>0.5
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36 },
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37 line=>{
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38 'stroke'=>"black",
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39 'stroke-width'=>1
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40 },
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41 csv=>{
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42 'stroke'=>"red",
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43 'stroke-width'=>0.5
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44 },
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45 exon=>{
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46 'stroke'=>"black",
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47 'stroke-width'=>1
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48 },
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49 intron=>{
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50 'stroke'=>"black",
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51 'stroke-width'=>1.5
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52 },
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53 font=>{
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54 'fill'=>"#000000",
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55 'font-size'=>12,
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56 'font-size2'=>10,
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57 #'font-weight'=>'bold',
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58 'font-family'=>"Arial"
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59 #'font-family'=>"ArialNarrow-bold"
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60 },
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61 rect=>{
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62 'fill'=>"lightgreen",
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63 'stroke'=>"black",
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64 'stroke-width'=>0.5
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65 },
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66 readwidth=>0.5
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67 );
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68 #############################s#define start coordinate and scale
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69 open(TXT,">$opt{out}");
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70 open(LENGTH,"$opt{l}")||die"cannot open the file $opt{l}";
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71 my %length;
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72 while (my $aline=<LENGTH>) {
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73 chomp $aline;
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74 next if($aline=~/^\#/);
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75 my @temp=split/\t/,$aline;
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76 $temp[0]=~s/^c/C/;
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77 $length{$temp[0]}=$temp[1];
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78 }
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79 close LENGTH;
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80 #---------------------------------------------------------------
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81 open(GENE,"$opt{g}")||die"cannot open the file $opt{g}";
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82 my %genelist;
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83 while (my $aline=<GENE>) {
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84 chomp $aline;#LOC_Os01g01280 Chr1 133291 134685 +
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85 next if($aline=~/^\#/);
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86 my @temp=split/\t/,$aline;
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87 if ($temp[1]=~/^Chr(\d)$/) {
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88 $temp[1]="Chr0$1";
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89 }
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90 push @{$genelist{$temp[1]}},[$temp[0],$temp[2],$temp[3]];
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91
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92 }
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93 close GENE;
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94 #my %have_gene;
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95 #foreach my $chr (sort keys %genelist) {
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96 # my @genelist=sort{$a->[1] <=> $b->[1]}@{$genelist{$chr}};
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97 # my $start=$genelist[0][1];
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98 # my $end=$genelist[0][2];
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99 # for (my $i=0;$i<@genelist ;$i++) {
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100 # if ($gene) {
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101 # }
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102 # }
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103 #}
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104
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105 my %gene_desity;
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106 foreach my $chr (sort keys %genelist) {
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107 my @genelist=sort{$a->[1] <=> $b->[1]}@{$genelist{$chr}};
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108 for (my $i=0;$i<@genelist ;$i++) {
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109 my $start=int($genelist[$i][1]/$span);
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110 my $end=int($genelist[$i][2]/$span);
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111 #my @t_rpkm=split/\t/,$target_rpkm{$genelist[$i][0]};
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112 if ($start==$end) {
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113 $gene_desity{$chr}[$start]++;
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114 }
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115 else{
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116 for (my $k=$start;$k<=$end ;$k++) {
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117 $gene_desity{$chr}[$k]++;
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118 }
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119 }
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120 }
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121 }
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122 #------------------------------------------region_gene_number-------------------------
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123 my $max_gene_number=0;
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124 my $total=0;
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125 foreach my $chr (sort keys %genelist) {
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126 for (my $i=0;$i<@{$gene_desity{$chr}} ;$i++) {
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127 if (!(defined($gene_desity{$chr}[$i]))) {
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128 $gene_desity{$chr}[$i]=0;
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129 }
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130 if ($gene_desity{$chr}[$i]>$max_gene_number) {
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131 $max_gene_number=$gene_desity{$chr}[$i];
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132 #print "$gene_desity{$chr}[$i]\n";
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133 }
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134 #print TXT "$i\t$gene_desity[$i]\n";
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135 $total+=$gene_desity{$chr}[$i];
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136 #print "$chr\t$i\t$gene_desity{$chr}[$i]\n";
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137 }
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138 }
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139 #print "Gene max:$max_gene_number\ntotal:$total\n";
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140
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141 #---------------------------------------------------------------
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142 my %centromere;
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143 if (defined($opt{cen})) {
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144 open CEN,"$opt{cen}";
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145 while (my $aline=<CEN>) {
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146 chomp $aline;
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147 next if($aline=~/^\#/);
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148 my @temp=split/\t/,$aline;
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149 $temp[0]=~s/^c/C/;
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150 $centromere{$temp[0]}[0]=$temp[1];
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151 $centromere{$temp[0]}[1]=$temp[2];
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152 }
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153 close CEN;
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154 }
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155
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156 #---------------------------------------------------------------
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157 my $max_length=0;
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158 foreach my $chr (keys %length) {
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159 if ($max_length<$length{$chr}) {
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160 $max_length=$length{$chr};
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161 }
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162 print "$chr\n";
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163 }
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164 #====================================cluster data=======================================
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165 open(CLUSTER,"$opt{c}")||die"cannot open the file $opt{c}";
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166 my %cluster;
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167 my %cluster_density;
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168 #my @sample=qw(39B3 3PA3 3LC3);
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169 my @cluster_non_add;
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170 while (my $aline=<CLUSTER>) {
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171 next if($aline=~/^\#/);
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172 chomp $aline;##Chr MajorLength Percent end 19B1
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173 my @temp=split/\t/,$aline;
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174 my @ID=split/\:/,$temp[0];
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175 my @posi=split/\-/,$ID[1];
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176 my @all_rpkm=@temp;
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177 shift @all_rpkm;
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178 shift @all_rpkm;
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179 shift @all_rpkm;
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180 # for (my $s=0;$s<@all_rpkm ;$s++) {#log transfer
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181 # $all_rpkm[$s]=log2($all_rpkm[$s]);
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182 # }
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183 push @{$cluster{$ID[0]}},[$temp[0],$posi[0],$posi[1],@all_rpkm];#ID start end rpkm(19B1,1PA1,1LC1);
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184 }
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185 close CLUSTER;
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186 my %max_cluster;
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187 my $chr_number=0;
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188 print "@mark\n$mark\n";
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189 foreach my $chr (sort keys %cluster) {
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190 for (my $i=0;$i<@mark ;$i++) {
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191 $max_cluster{$chr}[$i]=0;
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192 }
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193 $chr_number++;
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194 }
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195 foreach my $chr (sort keys %cluster) {
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196 @{$cluster{$chr}}=sort{$a->[1] <=> $b->[1]}@{$cluster{$chr}};
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197 for (my $i=0;$i<$#{$cluster{$chr}} ;$i++) {
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198 for (my $s=0;$s<@mark;$s++) {
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199 if ($cluster{$chr}[$i][3+$s]>$max_cluster{$chr}) {
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200 $max_cluster{$chr}[$s]=$cluster{$chr}[$i][3+$s];
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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 }
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206 foreach my $chr (sort keys %max_cluster) {
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207 for (my $s=0; $s<@mark;$s++) {
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208 # print "$max_cluster{$chr}[$s]\n";
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209 }
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210 }
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211 #---------------------------------------------------------------------------------------
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212 foreach my $chr(keys %cluster) {
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213 for(my $i=0;$i<$#{$cluster{$chr}};$i++) {
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214 my $start=int($cluster{$chr}[$i][1]/$span);
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215 my $end=int($cluster{$chr}[$i][2]/$span);
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216 if ($start==$end) {
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217 for (my $s=0;$s<@mark ;$s++) {
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218 $cluster_density{$chr}[$start][$s]+=$cluster{$chr}[$i][3+$s];
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219 }
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220
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221 }
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222 else{
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223 for (my $m=$start;$m<=$end ;$m++) {
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224 for (my $s=0;$s<@mark ;$s++) {
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225 $cluster_density{$chr}[$m][$s]+=$cluster{$chr}[$i][3+$s];
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226 }
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227 }
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228 }
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229 }
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230 }
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231 my %max_cluster_density;
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232 my $max_all_density=0;
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233 foreach my $chr (sort keys %cluster) {#
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234 for (my $s=0;$s<@mark ;$s++) {
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235 for (my $i=0;$i<$#{$cluster{$chr}} ;$i++) {
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236 $max_cluster_density{$chr}[$s]=0;
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237 }
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238 }
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239
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240 }
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241 foreach my $chr (sort keys %cluster_density) {
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242 print "$#{$cluster_density{$chr}}\n";
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243 for (my $k=0;$k<$#{$cluster_density{$chr}} ;$k++) {
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244 print TXT "$chr\t$k";
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245 for (my $s=0;$s<@mark;$s++) {
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246 if (!(defined($cluster_density{$chr}[$k][$s]))) {
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247 $cluster_density{$chr}[$k][$s]=0;
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248 }
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249 if ($cluster_density{$chr}[$k][$s]>$max_cluster_density{$chr}[$s]) {
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250 $max_cluster_density{$chr}[$s]=$cluster_density{$chr}[$k][$s];
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251 }
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252 if ($cluster_density{$chr}[$k][$s]>$max_all_density) {
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253 $max_all_density=$cluster_density{$chr}[$k][$s];
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254 }
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255 print TXT "\t$cluster_density{$chr}[$k][$s]";
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256 }
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257 print TXT "\n";
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258 }
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259 }
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260 print "max density: $max_all_density\n";
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261 #--------------------------------------------------------------------
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262 my $top_margin=30;
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263 my $tail_margin=30;
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264 my $XOFFSET=50;
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265 my $YOFFSET=60;
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266 my $chr_length=600;
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267 my $Xscale=$chr_length/$max_length;#¶¨ÒåXÖá±ÈÀý³ß 1:1000 xÖáµÄ×ø±ê³¤¶È¶¼Òª°´Õմ˱ÈÀý³ß»»Ëã
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268 #my $high_cov=$high_cov9B1=0.5;#¶¨Òå·åͼ×î¸ß·å
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269 #my $Yscale=1/$high_cov;#¶¨ÒåYÖá±ÈÀý³ß 1:60 yÖáµÄ×ø±ê³¤¶È¶¼Òª°´Õմ˱ÈÀý³ß»»Ëã
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270 #========================================New canvas============================
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271 #### Starting ####
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272 #н¨»²¼
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273 my $width=1000;
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274 my $heigth=100+130*$chr_number;
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275 my $svg=SVG->new(width=>$width, height=>$heigth);
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276 #»Í¼Æðʼµã
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277 my $canvas_start_x=$XOFFSET;
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278 my $canvas_end_x=$XOFFSET+$max_length*$Xscale;#°´ÕÕ±ÈÀý³ß »Ïß
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279 my $canvas_start_y=$YOFFSET;
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280 my $canvas_end_y=$YOFFSET;
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281 my $chr_heigth=$heigth-$YOFFSET-$tail_margin;
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282 print "chr number:$chr_number\n";
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283 my $one_chr_heigth=$chr_heigth/$chr_number;
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284 my $Yscale=($one_chr_heigth-15)/$max_all_density;
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285 #my $chr_width=$YOFFSET;
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286 #my $chr_start_y;
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287 #my $chr_end_y;
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288 #my $Yscale=0.01;
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289 #=======================================title of the graph===============================
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290 #my $span_k=$span/1000;
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291 #$svg->text('x',$width/2,'y',$YOFFSET-20,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',15,'font-family',$attribute{font}{'font-family'},'-cdata',"Clusters rpkm/"."$span_k"."kb Distribution");
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292 #=======================================the top max chr line=============================
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293 $svg->line(id=>'l1',x1=>$canvas_start_x,y1=>$canvas_start_y,x2=>$canvas_end_x,y2=>$canvas_end_y,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
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294 $long_scale=int ($max_length/10);#Ê®µÈ·Ö ´ó¿Ì¶È
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295 #´ó×ø±ê¿Ì¶È
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296 for ($i=0;$i<=10;$i++) {
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297 my $long_x_start=$XOFFSET+$long_scale*$i*$Xscale;
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298 my $long_x_end=$long_x_start;
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299 my $long_y_start=$YOFFSET;
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300 my $long_y_end=$YOFFSET-5;
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301 $svg->line('x1',$long_x_start,'y1',$long_y_start,'x2',$long_x_end,'y2',$long_y_end,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
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302 my $Bscale=$long_scale*$i;
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303 my $cdata=int ($Bscale/1000000);
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304 $svg->text('x',$long_x_start,'y',$long_y_start-10,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',$cdata."M");
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305 }
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306 #=========================================================================================
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307 my $cc=1;
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308 foreach my $chr (sort keys %length) {
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309 my $chr_end_x=$XOFFSET+$length{$chr}*$Xscale;
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310 my $chr_start_x=$XOFFSET;
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311 my $chr_start_y=$YOFFSET+$cc*$one_chr_heigth;
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312 my $chr_end_y=$chr_start_y;
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313 #$chr_start_y+=$chr_width;
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314 #$chr_end_y+=$chr_width;
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315 # for (my $i=0;$i<@{$gene_desity{$chr}};$i++) {
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316 # print "$chr\t$i\t$gene_desity{$chr}[$i]\n";
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317 # my $red=$gene_desity{$chr}[$i]/$max_gene_number*255;
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318 # my $green=$gene_desity{$chr}[$i]/$max_gene_number*255;
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319 # print "$red\t$green\t0\n";
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320 # $svg->rect('x',$chr_start_x+$i*$span*$Xscale,'y',$chr_start_y,'width',$span*$Xscale,'height',8,'stroke',"rgb($red,$green,0)",'stroke-width',0.1,'fill',"rgb($red,$green,0)");
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321 # }
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322
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323 $svg->line(x1=>$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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324 $svg->text('x',$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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325 my $m_length=$length{$chr}%1000000;
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326 $svg->text('x',$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',$m_length."M");
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327
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328
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329 if (defined($centromere{$chr}[0])) {
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330 $svg->rect('x',$XOFFSET+$centromere{$chr}[0]*$Xscale,'y',$chr_start_y-2,'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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331 }
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332 for (my $s=0;$s<@mark ;$s++) {
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333 for (my $i=0;$i<$#{$cluster_density{$chr}}-1 ;$i++) {
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334 #if ($cluster_density{$chr}[$i]*$Yscale>40) {
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335 #$cluster_density{$chr}[$i]=40/$Yscale;
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336 #$svg->rect('x',$XOFFSET+$i*$span*$Xscale,'y',$chr_start_y-45,'width',$span*$Xscale,'height',5,'stroke',"green",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"green");
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337 #}
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338 #print "$i\t$cluster_density{$chr}[$i][$s]\t$cluster_density{$chr}[$i+1][$s]\n";
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339 my $cluster_density_start_x=$XOFFSET+$i*$span*$Xscale;
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340 my $cluster_density_end_x=$XOFFSET+($i+1)*$span*$Xscale;
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341 my $cluster_density_start_y=$chr_start_y-$cluster_density{$chr}[$i][$s]*$Yscale;
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342 my $cluster_density_end_y=$chr_start_y-$cluster_density{$chr}[$i+1][$s]*$Yscale;
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343 my $c_red=($s+1)/@mark*255;
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344 $svg->line('x1',$cluster_density_start_x,'y1',$cluster_density_start_y,'x2',$cluster_density_end_x,'y2',$cluster_density_end_y,'stroke',"rgb($c_red,125,0)",'stroke-width',0.3);
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345 }
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346
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347 }
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348 #=======Y axis
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349 $svg->line(x1=>$chr_start_x,y1=>$chr_start_y,x2=>$chr_start_x,y2=>$chr_start_y-$one_chr_heigth+15,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
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350 #=======Y axis ===>3 xiaoge
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351 my $s10=1;
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352 my $e10=0;
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353 my $chr_max=$max_all_density;
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354 while ($chr_max>10) {
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355 $chr_max=int($chr_max/10);
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356 $s10=$s10*10;
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357 $e10++;
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358 }
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359 $chr_max=$chr_max/2;
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360 #print "*****$max_all_density\t$chr_max\t$s10\n";
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361 for (my $i=1;$i<3 ;$i++) {
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362 my $y1=$chr_start_y-$chr_max*$s10*$Yscale*$i;
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363 my $xiaoge_Y=$chr_max*$i;
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364 $svg->line('x1',$chr_start_x,'y1',$y1,'x2',$chr_start_x+3,'y2',$y1,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
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365 $svg->text('x',$chr_start_x-26,'y',$y1+4,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',8,'font-family',$attribute{font}{'font-family'},'-cdata',$xiaoge_Y."e".$e10);
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366 }
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367 $cc++;
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368 }
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369
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370 for (my $s=0;$s<@mark ;$s++) {
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371 my $c_red=($s+1)/@mark*255;
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372 print "**$c_red\n";
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373 $svg->line('x1',$canvas_end_x+100,'y1',$YOFFSET+$s*20+30,'x2',$canvas_end_x+130,'y2',$YOFFSET+$s*20+30,'stroke',"rgb($c_red,125,0)",'stroke-width',1);
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374 $svg->text('x',$canvas_end_x+150,'y',$YOFFSET+$s*20+5+30,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',10,'font-family',$attribute{font}{'font-family'},'-cdata',$mark[$s]);
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375 }
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376 #
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377 #
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378 if (defined($opt{cen})) {
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379 $svg->rect('x',$canvas_end_x+100,'y',$YOFFSET+@mark*20+30,'width',30,'height',5,'stroke',"blue",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"blue");
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380 $svg->text('x',$canvas_end_x+150,'y',$YOFFSET+@mark*20+30+5,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',10,'font-family',$attribute{font}{'font-family'},'-cdata',"centromere");
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381 }
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382
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383 close TXT;
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384
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385 open (OUT,">$opt{o}");
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386 print OUT $svg->xmlify();
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387
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388 sub log2 {
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389 my $n = shift;
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390 return log($n)/log(2);
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391 }
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392
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393 sub usage{
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394 print <<"USAGE";
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395 Version $version
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396 Usage:
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397 $0
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398 options:
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399 -g genelist
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400 -span
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401 -n sample cloumn
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402 -mark sample name
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403 -o output graph file name with html or svg extension
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404 -c cluster file input
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405 -out txt output
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406 -l length of chr
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407 -cen centromere
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408 -h help
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409 USAGE
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410 exit(1);
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411 } |
