Mercurial > repos > big-tiandm > sirna_plant

comparison sRNA_rpkm_distribution_along_genome.pl @ 0:07745c0958dd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author big-tiandm
date Thu, 18 Sep 2014 21:40:25 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:07745c0958dd
1 #!/usr/bin/perl -w
2 #==========================================================================================
3 # Date:
4 # Title:
5 # Comment: Program to plot gene structure
6 # Input: 1.
7 # 2.
8 # 3.
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,"span=s","c=s","o=s","out=s","l=s","cen:s","n=s","mark=s","h");
18 if (!( defined $opt{o}) || defined $opt{h}) {
19 &usage;
20 }
21 my $span=$opt{span};
22 my $sample_cloumn=$opt{n};
23 my $mark=$opt{mark};
24 #===============================Define Attribute==========================================
25 my %attribute=(
26 canvas=>{
27 'width'=>1500,
28 'height'=>1800
29 },
30 text=>{
31 'stroke'=>"#000000",
32 'fill'=>"none",
33 'stroke-width'=>0.5
34 },
35 line=>{
36 'stroke'=>"black",
37 'stroke-width'=>1
38 },
39 csv=>{
40 'stroke'=>"red",
41 'stroke-width'=>0.5
42 },
43 exon=>{
44 'stroke'=>"black",
45 'stroke-width'=>1
46 },
47 intron=>{
48 'stroke'=>"black",
49 'stroke-width'=>1.5
50 },
51 font=>{
52 'fill'=>"#000000",
53 'font-size'=>12,
54 'font-size2'=>10,
55 #'font-weight'=>'bold',
56 'font-family'=>"Arial"
57 #'font-family'=>"ArialNarrow-bold"
58 },
59 rect=>{
60 'fill'=>"lightgreen",
61 'stroke'=>"black",
62 'stroke-width'=>0.5
63 },
64 readwidth=>0.5
65 );
66 #############################s#define start coordinate and scale
67 open(TXT,">$opt{out}");
68 open(LENGTH,"$opt{l}")||die"cannot open the file $opt{l}";
69 my %length;
70 while (my $aline=<LENGTH>) {
71 chomp $aline;
72 next if($aline=~/^\#/);
73 my @temp=split/\t/,$aline;
74 $temp[0]=~s/^c/C/;
75 $length{$temp[0]}=$temp[1];
76 }
77 close LENGTH;
78 #---------------------------------------------------------------
79 my %centromere;
80 if (defined($opt{cen})) {
81 open(CEN,"$opt{cen}")||die"cannot open the file $opt{cen}";
82 while (my $aline=<CEN>) {
83 chomp $aline;
84 next if($aline=~/^\#/);
85 my @temp=split/\t/,$aline;
86 $temp[0]=~s/^c/C/;
87 $centromere{$temp[0]}[0]=$temp[1];
88 $centromere{$temp[0]}[1]=$temp[2];
89 }
90 close CEN;
91 }
92
93 #---------------------------------------------------------------
94 my $max_length=0;
95 foreach my $chr (keys %length) {
96 if ($max_length<$length{$chr}) {
97 $max_length=$length{$chr};
98 }
99 print "$chr\n";
100 }
101 #====================================cluster data=======================================
102 open(CLUSTER,"$opt{c}")||die"cannot open the file $opt{c}";
103 my %cluster;
104 my %cluster_density;
105 #my @sample=qw(39B3 3PA3 3LC3);
106 my @cluster_non_add;
107 while (my $aline=<CLUSTER>) {
108 next if($aline=~/^\#/);
109 chomp $aline;##ID chr strand start end 19B1
110 my @temp=split/\t/,$aline;
111 my @ID=split/\:/,$temp[0];
112 my @posi=split/\-/,$ID[1];
113 push @{$cluster{$ID[0]}},[$temp[0],$posi[0],$posi[1],$temp[2+$sample_cloumn]];#ID start end rpkm(19B1,1PA1,1LC1);
114 }
115 close CLUSTER;
116 my %max_cluster;
117 foreach my $chr (sort keys %cluster) {
118 # for (my $i=0;$i<3 ;$i++) {
119 # $max_cluster{$chr}[$i]=0;
120 # }
121 $max_cluster{$chr}=0
122 }
123 foreach my $chr (sort keys %cluster) {
124 @{$cluster{$chr}}=sort{$a->[1] <=> $b->[1]}@{$cluster{$chr}};
125 #for (my $s=0;$s<3;$s++) {
126 for (my $i=0;$i<$#{$cluster{$chr}} ;$i++) {
127 if ($cluster{$chr}[$i][3]>$max_cluster{$chr}) {
128 $max_cluster{$chr}=$cluster{$chr}[$i][3];
129 }
130 }
131 #}
132
133 }
134 #---------------------------------------------------------------------------------------
135 foreach my $chr(keys %cluster) {
136 for(my $i=0;$i<$#{$cluster{$chr}};$i++) {
137 my $start=int($cluster{$chr}[$i][1]/$span);
138 my $end=int($cluster{$chr}[$i][2]/$span);
139 if ($start==$end) {
140 #for (my $j=0;$j<3 ;$j++) {
141 $cluster_density{$chr}[$start]+=$cluster{$chr}[$i][3];
142 #}
143
144 }
145 else{
146 for (my $m=$start;$m<=$end ;$m++) {
147 #for (my $j=0;$j<3 ;$j++) {
148 $cluster_density{$chr}[$m]+=$cluster{$chr}[$i][3];
149 #}
150 }
151 }
152 }
153 }
154 my %max_cluster_density;
155 foreach my $chr (sort keys %cluster) {#
156 #for (my $i=0;$i<3 ;$i++) {
157 for (my $i=0;$i<$#{$cluster{$chr}} ;$i++) {
158 $max_cluster_density{$chr}=0;
159 }
160 #}
161 }
162 foreach my $chr (sort keys %cluster) {
163 #for (my $i=0;$i<3;$i++) {
164 for (my $k=0;$k<$#{$cluster_density{$chr}} ;$k++) {
165 if (!(defined($cluster_density{$chr}[$k]))) {
166 $cluster_density{$chr}[$k]=0;
167 }
168 if ($cluster_density{$chr}[$k]>$max_cluster_density{$chr}) {
169 $max_cluster_density{$chr}=$cluster_density{$chr}[$k];
170 }
171 print TXT "$chr\t$k\t$cluster_density{$chr}[$k]\n";
172 }
173 #}
174 }
175 #--------------------------------------------------------------------
176 my $XOFFSET=50;
177 my $YOFFSET=60;
178 #my $length=$end-$start+1;
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
180 #my $high_cov=$high_cov9B1=0.5;#定义峰图最高峰
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
182 #========================================New canvas============================
183 #### Starting ####
184 #新建画布
185 my $svg=SVG->new();
186 #画图起始点
187 my $canvas_start_x=$XOFFSET;
188 my $canvas_end_x=$XOFFSET+$max_length*$Xscale;#按照比例尺 画线
189 my $canvas_start_y=$YOFFSET;
190 my $canvas_end_y=$YOFFSET;
191
192 my $chr_width=$YOFFSET;
193 my $chr_start_y;
194 my $chr_end_y;
195 my $Yscale=0.01;
196 foreach my $chr (sort keys %length) {
197 my $chr_start_x=$XOFFSET;
198 my $chr_end_x=$XOFFSET+$length{$chr}*$Xscale;
199 $chr_start_y+=$chr_width;
200 $chr_end_y+=$chr_width;
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'});
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);
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});
204
205
206 if (defined($centromere{$chr}[0])) {
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");
208 }
209 for (my $i=0;$i<$#{$cluster_density{$chr}} ;$i++) {
210 if ($cluster_density{$chr}[$i]*$Yscale>40) {
211 $cluster_density{$chr}[$i]=40/$Yscale;
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");
213 }
214 my $cluster_density_start_x=$XOFFSET+$i*$span*$Xscale;
215 my $cluster_density_end_x=$XOFFSET+($i+1)*$span*$Xscale;
216 my $cluster_density_start_y=$chr_start_y-$cluster_density{$chr}[$i]*$Yscale;
217 #my $cluster_density_end_y=$chr_start_y-$cluster_density{$chr}[$i+1][0]*$Yscale;
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'});
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");
220 }
221
222 $chr_width=50;
223
224 #$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");
225 }
226
227 my $span_k=$span/1000;
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");
229
230 $svg->rect('x',600,'y',500,'width',10,'height',10,'stroke',"red",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"red");
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");
232
233 if (defined($opt{cen})) {
234 $svg->rect('x',600,'y',520,'width',10,'height',10,'stroke',"blue",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"blue");
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");
236 }
237
238 close TXT;
239 open (OUT,">$opt{o}");
240 print OUT $svg->xmlify();
241
242 sub log2 {
243 my $n = shift;
244 return log($n)/log(2);
245 }
246
247 sub usage{
248 print <<"USAGE";
249 Version $version
250 Usage:
251 $0
252 options:
253 -span
254 -n sample cloumn
255 -mark sample name
256 -o output graph file name with html or svg extension
257 -c cluster file input
258 -out txt output
259 -l length of chr
260 -cen centromere
261 -h help
262 USAGE
263 exit(1);
264 }