Mercurial > repos > big-tiandm > sirna_plant

comparison Length_Distibution.pl @ 19:e0884a4b996b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author big-tiandm
date Wed, 05 Nov 2014 01:17:26 -0500
parents
children
comparison
equal deleted inserted replaced
18:22d79320085c 19:e0884a4b996b
1 #!/usr/bin/perl -w
2 #==========================================================================================
3 # Date:
4 # Title:
5 # Comment: Program to plot gene structure
6 # Input: 1. input file of Gene region annotation which format like GenePred
7 # 2. input file of Transcripts region annotation which format like GenePred
8 # 3. input file of gene snp detail info
9 # Output: output file of gene structure graph by html or svg formt
10 # Test Usage:
11 #========================================================================================
12 #use strict;
13 my $version=1.00;
14 use SVG;
15 use Getopt::Long;
16 my %opt;
17 GetOptions(\%opt,"i=s","o=s",,"h");
18 if (!(defined $opt{i} and defined $opt{o}) || defined $opt{h}) {
19 &usage;
20 }
21 #===============================Define Attribute==========================================
22 my %attribute=(
23 canvas=>{
24 'width'=>1500,
25 'height'=>1800
26 },
27 text=>{
28 'stroke'=>"#000000",
29 'fill'=>"none",
30 'stroke-width'=>0.5
31 #'stroke-width2'=>1
32 },
33 line=>{
34 'stroke'=>"black",
35 'stroke-width'=>1
36 },
37 font=>{
38 'fill'=>"#000000",
39 'font-size'=>12,
40 'font-size2'=>10,
41 'font-weight'=>'bold',
42 'font-family'=>"Arial"
43 #'font-family2'=>"ArialNarrow-bold"
44 },
45 rect=>{
46 'fill'=>"lightgreen",
47 'stroke'=>"black",
48 'stroke-width'=>0.5
49 },
50 readwidth=>0.5
51 );
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
53 #========================================data============================
54 open(IN,"$opt{i}")||die"cannot open the file $opt{i}";
55 my @R_length;
56 my @T_length;
57 my $R_number=0;
58 my $T_number=0;
59 my $R_max=0;
60 my $T_max=0;
61
62 my $title=<IN>;
63 chomp $title;
64 my @title=split/\t/,$title;
65 my @mark=split/\s+/,$title[1];
66 my $sample_number=@mark;
67 while (my $aline=<IN>) {
68 if ($aline=~/^\s/) {
69 my $T_title=<IN>;
70 chomp $T_title;
71 while (my $a_aline=<IN>) {
72 chomp $a_aline;
73 my @temp=split/\t/,$a_aline;
74 my @number=split/\s+/,$temp[1];
75 for (my $i=0;$i<@number ;$i++) {
76 if ($R_max<$number[$i]) {
77 $R_max=$number[$i];
78 }
79 }
80 push @R_length,[$temp[0],@number];
81 $R_number++;
82 }
83 }
84 else {
85 chomp $aline;
86 my @temp=split/\t/,$aline;
87 my @number=split/\s+/,$temp[1];
88 for (my $i=0;$i<@number ;$i++) {
89 if ($T_max<$number[$i]) {
90 $T_max=$number[$i];
91 }
92 }
93 push @T_length,[$temp[0],@number];
94 $T_number++;
95 }
96 }
97 close IN;
98 print "Tag max: $T_max\nRead max: $R_max\n";
99 my $kd_number=5;
100 ##=======================Reads 纵坐标刻度==========================
101 my $r=1;
102 my $rr=1;
103 my $R=$R_max;
104 while ($R>10) {
105 $R=$R/10;
106 $r=$r*10;
107 $rr++;
108 }
109 $R=int($R+0.5);
110 my $R_xg=$R/$kd_number*$r;#纵坐标一小格大小（一共10格）
111 my $R_kedu_scale_x=6*$rr;#纵坐标刻度文字
112 ##=======================Tags 纵坐标刻度==========================
113 my $t=1;
114 my $tt=1;
115 my $T=$T_max;
116 while ($T>10) {
117 $T=$T/10;
118 $t=$t*10;
119 $tt++;
120 }
121 $T=int($T+0.5);
122 my $T_xg=$T/$kd_number*$t;#纵坐标一小格大小（一共10格）
123 my $T_kedu_scale_x=6*$tt;#纵坐标刻度文字
124
125 #############################s#define start coordinate and scale
126 my $XOFFSET=50;
127 my $YOFFSET=60;
128 my $width=800;
129 my $heigth=800;
130 my $X_width=600;
131 #my $height=1600;
132 #### Starting ####
133 #新建画布
134 my $svg=SVG->new(width=>$width,height=>$heigth);
135 ####坐标轴
136 my $axisL=300;#read 纵坐标长度
137 my $x_margin = 50;
138 #=========Reads number setting==========================================
139 my $Y_R_title=30;#标题的纵向宽度
140 my $Y_R_0=$YOFFSET+$axisL+$Y_R_title;
141 my $X_R_0=$XOFFSET+$x_margin;
142 my $R_Yscale=$axisL/$R_xg/$kd_number;
143 my $R_Xscale=$X_width/$R_number/($sample_number+1);
144 #=====================================Reads Y axis======================
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'});
146 for (my $i=1;$i<$kd_number ;$i++) {
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'});
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);
149 }
150 #=====================================Reads X axis======================
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'});
152
153 #print "$R_number\t$sample_number\n";
154 for ($i=0;$i<$R_number ;$i++) {
155 for (my $j=1;$j<$sample_number+1 ;$j++) {
156 my $red=$j/$sample_number*255;
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)");
158 }
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]);
160 }
161 #===Reads number title
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");
163 #===Reads
164 for (my $i=0;$i<$sample_number ;$i++) {
165 my $red=($i+1)/$sample_number*255;
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)");
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]);
168 }
169 ####==================================================================================
170 #=========================================Tag s
171 my $Y_T_title=30;#标题的纵向宽度
172 my $Y_T_0=$Y_R_0+$axisL+$Y_R_title+50;#length size
173 my $X_T_0=$XOFFSET+$x_margin;
174 my $T_Yscale=$axisL/$T_xg/$kd_number;
175 my $T_Xscale=$X_width/$T_number/($sample_number+1);
176 #=====================================Tags Y axis======================
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'});
178 for (my $i=1;$i<$kd_number ;$i++) {
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'});
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);
181 }
182 #=====================================Tags X axis======================
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'});
184
185 #print "$R_number\t$sample_number\n";
186 for ($i=0;$i<$T_number ;$i++) {
187 for (my $j=1;$j<$sample_number+1 ;$j++) {
188 my $red=$j/$sample_number*255;
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)");
190 }
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]);
192 }
193 #===Reads number title
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");
195 #===Reads
196 for (my $i=0;$i<$sample_number ;$i++) {
197 my $red=($i+1)/$sample_number*255;
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)");
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]);
200 }
201
202
203
204
205 open (OUT,">$opt{o}");
206 print OUT $svg->xmlify();
207
208 sub usage{
209 print <<"USAGE";
210 Version $version
211 Usage:
212 $0
213 options:
214 -i
215 -o svg output
216 -h help
217 USAGE
218 exit(1);
219 }