|
21
|
1 #!/usr/bin/perl -w
|
|
|
2 #Filename:
|
|
|
3 #Author: Tian Dongmei
|
|
|
4 #Email: tiandm@big.ac.cn
|
|
|
5 #Date: 2014-5-29
|
|
|
6 #Modified:
|
|
|
7 #Description:
|
|
|
8 my $version=1.00;
|
|
|
9
|
|
|
10 use strict;
|
|
|
11 use Getopt::Long;
|
|
|
12 use File::Basename;
|
|
|
13
|
|
|
14 my %opts;
|
|
|
15 GetOptions(\%opts,"i=s","format=s","o=s","h");
|
|
|
16 if (!(defined $opts{o} and defined $opts{format} and defined $opts{i} ) || defined $opts{h}) { #necessary arguments
|
|
|
17 &usage;
|
|
|
18 }
|
|
|
19 my ($config,$prepath,$rfampath,$genomepath,$clusterpath,$annotatepath,$plotpath,$degpath);
|
|
|
20 my ($predir,$rfamdir,$genomedir,$clusterdir,$annotatedir,$plotdir,$degdir);
|
|
|
21 open IN,"<$opts{i}";
|
|
|
22 $config=<IN>; chomp $config;
|
|
|
23 $prepath=<IN>; chomp $prepath;
|
|
|
24 $rfampath=<IN>;chomp $rfampath;
|
|
|
25 $genomepath=<IN>; chomp $genomepath;
|
|
|
26 $clusterpath=<IN>; chomp $clusterpath;
|
|
|
27 $annotatepath=<IN>; chomp $annotatepath;
|
|
|
28 $plotpath=<IN>; chomp $plotpath;
|
|
|
29 my $deg_tag=1;
|
|
|
30 if(eof){$deg_tag=0;}
|
|
|
31 else{
|
|
|
32 $degpath=<IN>; chomp $degpath;
|
|
|
33 }
|
|
|
34 close IN;
|
|
|
35 my @tmp=split/\//,$prepath;
|
|
|
36 $predir=$tmp[-1];
|
|
|
37 @tmp=split/\//,$rfampath;
|
|
|
38 $rfamdir=$tmp[-1];
|
|
|
39 @tmp=split/\//,$genomepath;
|
|
|
40 $genomedir=$tmp[-1];
|
|
|
41 @tmp=split/\//,$clusterpath;
|
|
|
42 $clusterdir=$tmp[-1];
|
|
|
43 @tmp=split/\//,$annotatepath;
|
|
|
44 $annotatedir=$tmp[-1];
|
|
|
45 @tmp=split/\//,$plotpath;
|
|
|
46 $plotdir=$tmp[-1];
|
|
|
47
|
|
|
48 my $dir=dirname($opts{'o'});
|
|
|
49
|
|
|
50 open OUT ,">$opts{'o'}";
|
|
|
51 print OUT "<HTML>\n <HEAD>\n <TITLE> Analysis Report </TITLE>\n </HEAD>
|
|
|
52 <BODY bgcolor=\"lightgray\">\n <h1 align=\"center\">\n <font face=\"ºÚÌå\">\n <b>Small RNA Analysis Report</b>\n </font>\n </h1>
|
|
|
53 <h2>1. Sequence No. and quality</h2>
|
|
|
54 <h3>1.1 Sequece No.</h3>
|
|
|
55 ";
|
|
|
56
|
|
|
57 ### raw data no
|
|
|
58 open IN,"<$config";
|
|
|
59 my @files;my @marks; my @rawNo;
|
|
|
60 while (my $aline=<IN>) {
|
|
|
61 chomp $aline;
|
|
|
62 my @tmp=split/\t/,$aline;
|
|
|
63 push @files,$tmp[0];
|
|
|
64
|
|
|
65 my $no=`less $tmp[0] |wc -l `;
|
|
|
66 chomp $no;
|
|
|
67 if ($opts{'format'} eq "fq" || $opts{'format'} eq "fastq") {
|
|
|
68 $no=$no/4;
|
|
|
69 }
|
|
|
70 else{
|
|
|
71 $no=$no/2;
|
|
|
72 }
|
|
|
73 push @rawNo,$no;
|
|
|
74
|
|
|
75 push @marks,$tmp[1];
|
|
|
76 }
|
|
|
77 close IN;
|
|
|
78
|
|
|
79 ### preprocess
|
|
|
80 unless ($prepath=~/\/$/) {
|
|
|
81 $prepath .="/";
|
|
|
82 }
|
|
|
83
|
|
|
84 my @trimNo;my @collapse;
|
|
|
85 my $collapsefile=$prepath."collapse_reads.fa";
|
|
|
86 open IN,"<$collapsefile";
|
|
|
87 while (my $aline=<IN>) {
|
|
|
88 chomp $aline;
|
|
|
89 <IN>;
|
|
|
90 $aline=~/:([\d|_]+)_x(\d+)$/;
|
|
|
91 my @lng=split/_/,$1;
|
|
|
92 for (my $i=0;$i<@lng;$i++) {
|
|
|
93 if ($lng[$i]>0) {
|
|
|
94 $trimNo[$i] +=$lng[$i];
|
|
|
95 $collapse[$i] ++;
|
|
|
96 }
|
|
|
97 }
|
|
|
98 }
|
|
|
99 close IN;
|
|
|
100
|
|
|
101 my @cleanR;my @cleanT;
|
|
|
102 my $clean=$prepath."collapse_reads_18-40.fa";
|
|
|
103 open IN,"<$clean";
|
|
|
104 while (my $aline=<IN>) {
|
|
|
105 chomp $aline;
|
|
|
106 <IN>;
|
|
|
107 $aline=~/:([\d|_]+)_x(\d+)$/;
|
|
|
108 my @lng=split/_/,$1;
|
|
|
109 for (my $i=0;$i<@lng;$i++) {
|
|
|
110 if ($lng[$i]>0) {
|
|
|
111 $cleanR[$i] +=$lng[$i];
|
|
|
112 $cleanT[$i] ++;
|
|
|
113 }
|
|
|
114 }
|
|
|
115 }
|
|
|
116 close IN;
|
|
|
117
|
|
|
118 my @filterR;my @filterT;
|
|
|
119 my $filter=$prepath."collapse_reads_out.fa";
|
|
|
120 open IN,"<$filter";
|
|
|
121 while (my $aline=<IN>) {
|
|
|
122 chomp $aline;
|
|
|
123 <IN>;
|
|
|
124 $aline=~/:([\d|_]+)_x(\d+)$/;
|
|
|
125 my @lng=split/_/,$1;
|
|
|
126 for (my $i=0;$i<@lng;$i++) {
|
|
|
127 if ($lng[$i]>0) {
|
|
|
128 $filterR[$i] +=$lng[$i];
|
|
|
129 $filterT[$i] ++;
|
|
|
130 }
|
|
|
131 }
|
|
|
132 }
|
|
|
133 close IN;
|
|
|
134
|
|
|
135
|
|
|
136 print OUT "<table border=\"1\">
|
|
|
137 <tr align=\"center\">
|
|
|
138 <th> </th>
|
|
|
139 ";
|
|
|
140 foreach (@marks) {
|
|
|
141 print OUT "<th> $_ </th>\n";
|
|
|
142 }
|
|
|
143 print OUT "</tr>
|
|
|
144 <tr align=\"center\">
|
|
|
145 <th align=\"left\">Raw Reads No. </th>
|
|
|
146 ";
|
|
|
147 foreach (@rawNo) {
|
|
|
148 print OUT "<td> $_ </td>\n";
|
|
|
149 }
|
|
|
150 print OUT "</tr>
|
|
|
151 <tr align=\"center\">
|
|
|
152 <th align=\"left\">Reads No. After Trimed 3\' adapter </th>
|
|
|
153 ";
|
|
|
154 foreach (@trimNo) {
|
|
|
155 print OUT "<td> $_ </td>\n";
|
|
|
156 }
|
|
|
157 print OUT "</tr>
|
|
|
158 <tr align=\"center\">
|
|
|
159 <th align=\"left\">Unique Tags No. </th>
|
|
|
160 ";
|
|
|
161 foreach (@collapse) {
|
|
|
162 print OUT "<td> $_ </td>\n";
|
|
|
163 }
|
|
|
164 print OUT "</tr>
|
|
|
165 <tr align=\"center\">
|
|
|
166 <th align=\"left\">Clean Reads No. </th>
|
|
|
167 ";
|
|
|
168 foreach (@cleanR) {
|
|
|
169 print OUT "<td> $_ </td>\n";
|
|
|
170 }
|
|
|
171 print OUT "</tr>
|
|
|
172 <tr align=\"center\">
|
|
|
173 <th align=\"left\">Clean Tags No. </th>
|
|
|
174 ";
|
|
|
175 foreach (@cleanT) {
|
|
|
176 print OUT "<td> $_ </td>\n";
|
|
|
177 }
|
|
|
178 print OUT "</tr>
|
|
|
179 <tr align=\"center\">
|
|
|
180 <th align=\"left\">Filter Reads No. \(reads count \>3\) </th>
|
|
|
181 ";
|
|
|
182 foreach (@filterR) {
|
|
|
183 print OUT "<td> $_ </td>\n";
|
|
|
184 }
|
|
|
185 print OUT "</tr>
|
|
|
186 <tr align=\"center\">
|
|
|
187 <th align=\"left\">Filter Tags No. \(reads count \>3\) </th>
|
|
|
188 ";
|
|
|
189 foreach (@filterT) {
|
|
|
190 print OUT "<td> $_ </td>\n";
|
|
|
191 }
|
|
|
192 print OUT "</tr>\n</table>";
|
|
|
193 print OUT "<p>
|
|
|
194 Note:<br />
|
|
|
195 The raw data file path is: <b>$files[0]</b><br />
|
|
|
196 ";
|
|
|
197 for (my $i=1;$i<@files;$i++) {
|
|
|
198 print OUT "          <b>$files[$i]</b><br />";
|
|
|
199 }
|
|
|
200 print OUT "The collapsed file path is: <b>$collapsefile</b><br />
|
|
|
201 The clean data file path is: <b>$clean</b><br />
|
|
|
202 The filter (remain total reads>3) data file path is: <b>$filter</b><br />
|
|
|
203 </p>
|
|
|
204 <h2> 1. Sequence length count</h2>
|
|
|
205 ";
|
|
|
206 print OUT "\n";
|
|
|
207
|
|
|
208 my $length=$prepath."length.html";
|
|
|
209 open IN,"<$length";
|
|
|
210 while (my $aline=<IN>) {
|
|
|
211 chomp $aline;
|
|
|
212 print OUT "$aline\n";
|
|
|
213 }
|
|
|
214 close IN;
|
|
|
215
|
|
|
216 print OUT "<p> Note:<br />The sequence length data: <a href=\"./$predir/reads_length_distribution_after_count_filter.txt\"> length file</a>
|
|
|
217 </p>
|
|
|
218 ";
|
|
|
219
|
|
|
220 #### rfam
|
|
|
221 unless ($rfampath=~/\/$/) {
|
|
|
222 $rfampath .="/";
|
|
|
223 }
|
|
|
224 unless ($genomepath=~/\/$/) {
|
|
|
225 $genomepath .="/";
|
|
|
226 }
|
|
|
227 print OUT "<h2>2. Rfam non-miRNA annotation</h2>
|
|
|
228 <h3>2.1 Reads count</h3>
|
|
|
229 <table border=\"1\">
|
|
|
230 <tr align=\"center\">
|
|
|
231 ";
|
|
|
232
|
|
|
233 my @rfamR; my @rfamT;
|
|
|
234 my $tag=1;
|
|
|
235 open IN,"<$dir/rfam_match/rfam_non-miRNA_annotation.txt";
|
|
|
236 while (my $aline=<IN>) {
|
|
|
237 chomp $aline;
|
|
|
238 $tag=0 if($aline=~/tags\s+number/);
|
|
|
239 next if($aline=~/^\#/);
|
|
|
240 next if($aline=~/^\s*$/);
|
|
|
241 my @tmp=split/\s+/,$aline;
|
|
|
242 if($tag == 1){push @rfamR,[@tmp];}
|
|
|
243 else{push @rfamT,[@tmp];}
|
|
|
244 }
|
|
|
245 close IN;
|
|
|
246
|
|
|
247
|
|
|
248 print OUT "<th>RNA Name</th>\n";
|
|
|
249 foreach (@marks) {
|
|
|
250 print OUT "<th> $_ </th>\n";
|
|
|
251 }
|
|
|
252 for (my $i=0;$i<@rfamR;$i++) {
|
|
|
253 print OUT "</tr>
|
|
|
254 <tr align=\"center\">
|
|
|
255 <th align=\"left\">$rfamR[$i][0]</th>
|
|
|
256 ";
|
|
|
257 for (my $j=1;$j<@{$rfamR[$i]} ;$j++) {
|
|
|
258 print OUT "<td> $rfamR[$i][$j]</td>\n";
|
|
|
259 }
|
|
|
260 }
|
|
|
261
|
|
|
262 print OUT "</tr>\n</table>
|
|
|
263 <h3>2.2 Tags count</h3>
|
|
|
264 <table border=\"1\">
|
|
|
265 <tr align=\"center\">
|
|
|
266 <th>RNA Name</th>\n";
|
|
|
267 foreach (@marks) {
|
|
|
268 print OUT "<th> $_ </th>\n";
|
|
|
269 }
|
|
|
270 for (my $i=0;$i<@rfamT;$i++) {
|
|
|
271 print OUT "</tr>
|
|
|
272 <tr align=\"center\">
|
|
|
273 <th align=\"left\">$rfamT[$i][0]</th>
|
|
|
274 ";
|
|
|
275 for (my $j=1;$j<@{$rfamT[$i]} ;$j++) {
|
|
|
276 print OUT "<td> $rfamT[$i][$j]</td>\n";
|
|
|
277 }
|
|
|
278 }
|
|
|
279 print OUT "</tr>\n</table>
|
|
|
280 <p>Note:<br />The rfam mapping results is: <b>$rfampath</b>";
|
|
|
281 print OUT "<b>rfam_mapped.bwt</b></p>";
|
|
|
282
|
|
|
283 open IN,"<$dir/genome_match/genome_mapped.bwt";
|
|
|
284 my @genome_r_u;
|
|
|
285 my @genome_r_m;
|
|
|
286 my @genome_t_u;
|
|
|
287 my @genome_t_m;
|
|
|
288 my $tags_map_number=0;
|
|
|
289 while (my $aline=<IN>) {
|
|
|
290 chomp $aline;
|
|
|
291 my @temp=split/\t/,$aline;
|
|
|
292 if ($temp[6]==0) {
|
|
|
293 $aline=~/:([\d|_]+)_x(\d+)/;
|
|
|
294 my @lng=split/_/,$1;
|
|
|
295 for (my $i=0;$i<@lng;$i++) {
|
|
|
296 if ($lng[$i]>0) {
|
|
|
297 $genome_r_u[$i] +=$lng[$i];
|
|
|
298 $genome_t_u[$i] ++;
|
|
|
299 }
|
|
|
300 }
|
|
|
301 $tags_map_number++;
|
|
|
302 }
|
|
|
303 if ($temp[6]>0) {
|
|
|
304 $aline=~/:([\d|_]+)_x(\d+)/;
|
|
|
305 my @lng=split/_/,$1;
|
|
|
306 for (my $i=0;$i<@lng;$i++) {
|
|
|
307 if ($lng[$i]>0) {
|
|
|
308 $genome_r_m[$i] +=$lng[$i];
|
|
|
309 $genome_t_m[$i] ++;
|
|
|
310 }
|
|
|
311 }
|
|
|
312 for (my $i=0;$i<$temp[6] ;$i++) {
|
|
|
313 my $next=<IN>;
|
|
|
314 }
|
|
|
315 $tags_map_number++;
|
|
|
316 }
|
|
|
317 }
|
|
|
318 close IN;
|
|
|
319 #<h3>3.1 Reads count</h3>
|
|
|
320 #<table border=\"1\">
|
|
|
321 #<tr align=\"center\">
|
|
|
322 print OUT "<h2>3. genome mapping result</h2>
|
|
|
323 <table border=\"1\">
|
|
|
324 <tr align=\"center\">
|
|
|
325 <th align=\"left\">Map</th>\n
|
|
|
326 ";
|
|
|
327 foreach (@marks) {
|
|
|
328 print OUT "<th> $_ </th>\n";
|
|
|
329 }
|
|
|
330 print OUT "</tr>
|
|
|
331 <tr align=\"center\">
|
|
|
332 <th align=\"left\">Uniq Map Reads No.</th>
|
|
|
333 ";
|
|
|
334 for (my $i=0;$i<@genome_r_u ;$i++) {
|
|
|
335 print OUT "<td> $genome_r_u[$i]</td>\n";
|
|
|
336 }
|
|
|
337
|
|
|
338 print OUT "</tr>
|
|
|
339 <tr align=\"center\">
|
|
|
340 <th align=\"left\">Uniq Map Tags No.</th>
|
|
|
341 ";
|
|
|
342 for (my $i=0;$i<@genome_t_u ;$i++) {
|
|
|
343 print OUT "<td> $genome_t_u[$i]</td>\n";
|
|
|
344 }
|
|
|
345
|
|
|
346 print OUT "</tr>
|
|
|
347 <tr align=\"center\">
|
|
|
348 <th align=\"left\">Multiple Map Reads No.</th>
|
|
|
349 ";
|
|
|
350 for (my $i=0;$i<@genome_r_m ;$i++) {
|
|
|
351 print OUT "<td> $genome_r_m[$i]</td>\n";
|
|
|
352 }
|
|
|
353
|
|
|
354 print OUT "</tr>
|
|
|
355 <tr align=\"center\">
|
|
|
356 <th align=\"left\">Multiple Map Tags No.</th>
|
|
|
357 ";
|
|
|
358 for (my $i=0;$i<@genome_t_m ;$i++) {
|
|
|
359 print OUT "<td> $genome_t_m[$i]</td>\n";
|
|
|
360 }
|
|
|
361
|
|
|
362 print OUT "</tr>\n</table>
|
|
|
363 <p>Note:<br />The genome mapping results is: <b>$genomepath</b>";
|
|
|
364 print OUT "<b>genome_mapped.bwt</b></p>";
|
|
|
365
|
|
|
366 my $cluster="$clusterpath/sample_reads.cluster";
|
|
|
367 my $cluster_number=`less $cluster |wc -l `;
|
|
|
368 $cluster_number=$cluster_number-1;
|
|
|
369 my (%cluster_length,@exp,@rpkm);
|
|
|
370 my @exp_range=qw(0 \(0--10] \(10--100] \(100--1000] \(1000--10000] \(10000--100000] \(100000--**\));
|
|
|
371 my @rpkm_range=qw(0 \(0--0.25] \(0.25--0.5] \(0.5--1] \(1.0-5.0] \(5--10] \(10--50] \(50--100] \(100--500] \(500--1000] \(1000--**]);
|
|
|
372
|
|
|
373 open IN,"<$cluster";
|
|
|
374 while (my $aline=<IN>) {
|
|
|
375 next if($aline=~/^\"/);
|
|
|
376 chomp $aline;
|
|
|
377 my @temp=split/\t/,$aline;
|
|
|
378 my @id=split/:|-/,$temp[0];
|
|
|
379 $cluster_length{$id[2]-$id[1]+1}++;
|
|
|
380 for (my $i=0;$i<@marks ;$i++) {
|
|
|
381 if ($temp[$i+3] == 0) {$exp[0][$i]++;}
|
|
|
382 elsif ($temp[$i+3]>0 && $temp[$i+3]<= 10 ){$exp[1][$i]++;}
|
|
|
383 elsif ($temp[$i+3]>10 && $temp[$i+3]<=100){$exp[2][$i]++;}
|
|
|
384 elsif ($temp[$i+3]>100 && $temp[$i+3]<=1000){$exp[3][$i]++;}
|
|
|
385 elsif ($temp[$i+3]>1000 && $temp[$i+3]<=10000){$exp[4][$i]++;}
|
|
|
386 elsif ($temp[$i+3]>10000 && $temp[$i+3]<=100000){$exp[5][$i]++;}
|
|
|
387 elsif ($temp[$i+3]>100000){$exp[6][$i]++;}
|
|
|
388 }
|
|
|
389 }
|
|
|
390 close IN;
|
|
|
391
|
|
|
392 my $cluster_rpkm="$clusterpath/sample_rpkm.cluster";
|
|
|
393 open IN,"<$cluster_rpkm";
|
|
|
394 while (my $aline=<IN>) {
|
|
|
395 next if($aline=~/^\#/);
|
|
|
396 chomp $aline;
|
|
|
397 my @temp=split/\t/,$aline;
|
|
|
398 for (my $i=0;$i<@marks ;$i++) {
|
|
|
399 if ($temp[$i+3]==0) {$rpkm[0][$i]++;}
|
|
|
400 elsif($temp[$i+3]>0 && $temp[$i+3]<=0.25){$rpkm[1][$i]++;}
|
|
|
401 elsif($temp[$i+3]>0.25 && $temp[$i+3]<=0.5){$rpkm[2][$i]++;}
|
|
|
402 elsif($temp[$i+3]>0.5 && $temp[$i+3]<=1){$rpkm[3][$i]++;}
|
|
|
403 elsif($temp[$i+3]>1 && $temp[$i+3]<=5){$rpkm[4][$i]++;}
|
|
|
404 elsif($temp[$i+3]>5 && $temp[$i+3]<=10){$rpkm[5][$i]++;}
|
|
|
405 elsif($temp[$i+3]>10 && $temp[$i+3]<=50){$rpkm[6][$i]++;}
|
|
|
406 elsif($temp[$i+3]>50 && $temp[$i+3]<=100){$rpkm[7][$i]++;}
|
|
|
407 elsif($temp[$i+3]>100 && $temp[$i+3]<=500){$rpkm[8][$i]++;}
|
|
|
408 elsif($temp[$i+3]>500 && $temp[$i+3]<=1000){$rpkm[9][$i]++;}
|
|
|
409 else{$rpkm[10][$i]++;}
|
|
|
410 }
|
|
|
411 }
|
|
|
412
|
|
|
413 close IN;
|
|
|
414
|
|
|
415 my $cluster_length_file="$clusterpath/cluster_length.txt";
|
|
|
416 open LEN,">$cluster_length_file";
|
|
|
417 print LEN "\#length\tcluster_number\n";
|
|
|
418 foreach my $key (sort keys %cluster_length) {
|
|
|
419 print LEN "$key\t$cluster_length{$key}\n";
|
|
|
420 }
|
|
|
421 close LEN;
|
|
|
422 print OUT "<h2>4. cluster result</h2>
|
|
|
423 <h3>4.1 Cluster count</h3>
|
|
|
424 <table border=\"1\">
|
|
|
425 <tr align=\"center\">
|
|
|
426 <th align=\"left\"> </th>
|
|
|
427 <td>Merged samples</td></tr>
|
|
|
428 <tr align=\"center\">
|
|
|
429 <th align=\"left\">Tags number</th>
|
|
|
430 <td>$tags_map_number</td></tr>
|
|
|
431 <tr align=\"center\">
|
|
|
432 <th align=\"left\">Cluster number</th>
|
|
|
433 <td>$cluster_number</td></tr>\n</table>
|
|
|
434 ";
|
|
|
435
|
|
|
436 print OUT "<h3>4.2 Cluster length</h3>
|
|
|
437 <p> Note:<br />The clusters length data: <a href=\"./$clusterdir/cluster_length.txt\"> length file</a>
|
|
|
438 </p>
|
|
|
439 ";
|
|
|
440 print OUT "<h3>4.3 Quantify</h3>
|
|
|
441 <table border=\"1\">
|
|
|
442 <tr align=\"center\">
|
|
|
443 <th align=\"left\">Reads Range</th>\n
|
|
|
444 ";
|
|
|
445 foreach (@marks) {
|
|
|
446 print OUT "<th> $_ </th>\n";
|
|
|
447 }
|
|
|
448 for (my $i=0;$i<@exp_range;$i++) {
|
|
|
449 print OUT "</tr>
|
|
|
450 <tr align=\"center\">
|
|
|
451 <th align=\"left\">$exp_range[$i]</th>
|
|
|
452 ";
|
|
|
453 for (my $j=0;$j<@marks ;$j++) {
|
|
|
454 if (!(defined($exp[$i][$j]))) {
|
|
|
455 print OUT "<td> 0</td>\n";
|
|
|
456 }
|
|
|
457 else{print OUT "<td> $exp[$i][$j]</td>\n";}
|
|
|
458 }
|
|
|
459 }
|
|
|
460 print OUT "</tr>\n</table>";
|
|
|
461
|
|
|
462 print OUT "\n<table border=\"1\">
|
|
|
463 <tr align=\"center\">
|
|
|
464 <th align=\"left\">RPKM Range</th>\n
|
|
|
465 ";
|
|
|
466 foreach (@marks) {
|
|
|
467 print OUT "<th> $_ </th>\n";
|
|
|
468 }
|
|
|
469 for (my $i=0;$i<@rpkm_range;$i++) {
|
|
|
470 print OUT "</tr>
|
|
|
471 <tr align=\"center\">
|
|
|
472 <th align=\"left\">$rpkm_range[$i]</th>
|
|
|
473 ";
|
|
|
474 for (my $j=0;$j<@marks ;$j++) {
|
|
|
475 if (!(defined($rpkm[$i][$j]))) {
|
|
|
476 print OUT "<td> 0</td>\n";
|
|
|
477 }
|
|
|
478 else{print OUT "<td> $rpkm[$i][$j]</td>\n";}
|
|
|
479 }
|
|
|
480 }
|
|
|
481 print OUT "</tr>\n</table>";
|
|
|
482
|
|
|
483 my $annotate="$annotatepath/sample_c_p.anno";
|
|
|
484 my (%posit,%repeat,%nat1,%nat2);
|
|
|
485 my (@phase,@long,@repeat,@nat);
|
|
|
486 for (my $j=0;$j<@marks ;$j++) {
|
|
|
487 $phase[$j]=0;
|
|
|
488 $long[$j]=0;
|
|
|
489 $repeat[$j]=0;
|
|
|
490 $nat[$j]=0;
|
|
|
491 }
|
|
|
492
|
|
|
493 my $class_anno=1;
|
|
|
494 open ANNO,"<$annotate";
|
|
|
495 while (my $aline=<ANNO>) {
|
|
|
496 chomp $aline;
|
|
|
497 my @temp=split/\t/,$aline;
|
|
|
498 if($aline=~/^\#/){
|
|
|
499 if (@temp != 10+@marks) {
|
|
|
500 $class_anno=0;
|
|
|
501 }
|
|
|
502 next;
|
|
|
503 }
|
|
|
504 for (my $i=3+@marks+$class_anno;$i<@temp;$i++) {
|
|
|
505 my @posit=split/\;/,$temp[$i];
|
|
|
506 for (my $j=0;$j<@marks ;$j++) {
|
|
|
507 if ($temp[3+$j]>0) {
|
|
|
508 $posit{$posit[0]}[$j]++;
|
|
|
509 }
|
|
|
510 else{
|
|
|
511 if (!(defined($posit{$posit[0]}[$j]))) {
|
|
|
512 $posit{$posit[0]}[$j]=0;
|
|
|
513 }
|
|
|
514 }
|
|
|
515 }
|
|
|
516 }
|
|
|
517 if ($class_anno) {
|
|
|
518 for (my $j=0;$j<@marks ;$j++) {
|
|
|
519 if ($temp[3+$j]>0) {
|
|
|
520 if ($temp[6] eq "phase") {
|
|
|
521 $phase[$j]++;
|
|
|
522 }
|
|
|
523 if ($temp[7] eq "long") {
|
|
|
524 $long[$j]++;
|
|
|
525 }
|
|
|
526 if ($temp[8] ne "\/") {
|
|
|
527 $repeat[$j]++;
|
|
|
528 my @rr=split/\;/,$temp[8];
|
|
|
529 foreach (@rr) {
|
|
|
530 $repeat{$_}[$j]++;
|
|
|
531 }
|
|
|
532 }
|
|
|
533 if ($temp[9] ne "\/") {
|
|
|
534 $nat[$j]++;
|
|
|
535 my @nn1=split/\;/,$temp[9];
|
|
|
536 my @nn2=split/\;/,$temp[10];
|
|
|
537 for (my $k=0;$k<@nn1 ;$k++) {
|
|
|
538 $nat1{$nn1[$k]}[$j]++;
|
|
|
539 $nat2{$nn2[$k]}[$j]++;
|
|
|
540 }
|
|
|
541 }
|
|
|
542 }
|
|
|
543 }
|
|
|
544 }
|
|
|
545 }
|
|
|
546 close ANNO;
|
|
|
547
|
|
|
548 print OUT "<h2>5. Cluster Annotate</h2>
|
|
|
549 <h3>5.1 Cluster genome position annotate</h3>
|
|
|
550 <table border=\"1\">
|
|
|
551 <tr align=\"center\">
|
|
|
552 <th align=\"left\">clusters number</th>\n
|
|
|
553 ";
|
|
|
554
|
|
|
555 foreach (@marks) {
|
|
|
556 print OUT "<th> $_ </th>\n";
|
|
|
557 }
|
|
|
558 foreach my $key (sort keys %posit) {
|
|
|
559 print OUT "</tr>
|
|
|
560 <tr align=\"center\">
|
|
|
561 <th align=\"left\">$key</th>
|
|
|
562 ";
|
|
|
563 foreach (@{$posit{$key}}) {
|
|
|
564 print OUT "<td> $_</td>\n";
|
|
|
565 }
|
|
|
566 }
|
|
|
567 print OUT "</tr>\n</table>";
|
|
|
568 print OUT "<p>
|
|
|
569 Note:<br />
|
|
|
570 One cluster mybe annotate to multiple genes<br />
|
|
|
571 ";
|
|
|
572
|
|
|
573 if ($class_anno) {
|
|
|
574 print OUT "<h3>5.2 Cluster source mechanism annotate</h3>
|
|
|
575 <table border=\"1\">
|
|
|
576 <tr align=\"center\">
|
|
|
577 <th align=\"left\">clusters number</th>\n
|
|
|
578 ";
|
|
|
579
|
|
|
580 foreach (@marks) {
|
|
|
581 print OUT "<th> $_ </th>\n";
|
|
|
582 }
|
|
|
583 print OUT "</tr>
|
|
|
584 <tr align=\"center\">
|
|
|
585 <th align=\"left\">Phase</th>\n
|
|
|
586 ";
|
|
|
587 foreach (@phase) {
|
|
|
588 print OUT "<td> $_ </td>\n";
|
|
|
589 }
|
|
|
590
|
|
|
591 print OUT "</tr>
|
|
|
592 <tr align=\"center\">
|
|
|
593 <th align=\"left\">Long</th>\n
|
|
|
594 ";
|
|
|
595 foreach (@long) {
|
|
|
596 print OUT "<td> $_ </td>\n";
|
|
|
597 }
|
|
|
598
|
|
|
599 print OUT "</tr>
|
|
|
600 <tr align=\"center\">
|
|
|
601 <th align=\"left\">Repeat</th>\n
|
|
|
602 ";
|
|
|
603 foreach (@repeat) {
|
|
|
604 print OUT "<td> $_ </td>\n";
|
|
|
605 }
|
|
|
606
|
|
|
607 print OUT "</tr>
|
|
|
608 <tr align=\"center\">
|
|
|
609 <th align=\"left\">Nat</th>\n
|
|
|
610 ";
|
|
|
611 foreach (@nat) {
|
|
|
612 print OUT "<td> $_ </td>\n";
|
|
|
613 }
|
|
|
614 print OUT "</tr>\n</table>";
|
|
|
615
|
|
|
616 print OUT "<p>
|
|
|
617 Repeat subclass annotate:
|
|
|
618 ";
|
|
|
619
|
|
|
620 print OUT "<table border=\"1\">
|
|
|
621 <tr align=\"center\">
|
|
|
622 <th align=\"left\">Repeat subclass</th>\n
|
|
|
623 ";
|
|
|
624 foreach (@marks) {
|
|
|
625 print OUT "<th> $_ </th>\n";
|
|
|
626 }
|
|
|
627
|
|
|
628 foreach my $key (sort keys %repeat) {
|
|
|
629 print OUT "</tr>
|
|
|
630 <tr align=\"center\">
|
|
|
631 <th align=\"left\">$key</th>
|
|
|
632 ";
|
|
|
633 for (my $i=0;$i<@marks ;$i++) {
|
|
|
634 if (defined($repeat{$key}[$i])) {
|
|
|
635 print OUT "<td> $repeat{$key}[$i] </td>\n";
|
|
|
636 }
|
|
|
637 else{print OUT "<td> 0 </td>\n";}
|
|
|
638 }
|
|
|
639 }
|
|
|
640 print OUT "</tr>\n</table>";
|
|
|
641
|
|
|
642
|
|
|
643 print OUT "<p>
|
|
|
644 Nat subclass1 annotate:
|
|
|
645 ";
|
|
|
646
|
|
|
647 print OUT "<table border=\"1\">
|
|
|
648 <tr align=\"center\">
|
|
|
649 <th align=\"left\">Nat subclass1</th>\n
|
|
|
650 ";
|
|
|
651 foreach (@marks) {
|
|
|
652 print OUT "<th> $_ </th>\n";
|
|
|
653 }
|
|
|
654 foreach my $key (sort keys %nat1) {
|
|
|
655 print OUT "</tr>
|
|
|
656 <tr align=\"center\">
|
|
|
657 <th align=\"left\">$key</th>
|
|
|
658 ";
|
|
|
659 for (my $i=0;$i<@marks ;$i++) {
|
|
|
660 if (defined($nat1{$key}[$i])) {
|
|
|
661 print OUT "<td> $nat1{$key}[$i] </td>\n";
|
|
|
662 }
|
|
|
663 else{print OUT "<td> 0 </td>\n";}
|
|
|
664 }
|
|
|
665 }
|
|
|
666 print OUT "</tr>\n</table>";
|
|
|
667
|
|
|
668 print OUT "<p>
|
|
|
669 Nat subclass2 annotate:
|
|
|
670 ";
|
|
|
671
|
|
|
672 print OUT "<table border=\"1\">
|
|
|
673 <tr align=\"center\">
|
|
|
674 <th align=\"left\">Nat subclass2</th>\n
|
|
|
675 ";
|
|
|
676 foreach (@marks) {
|
|
|
677 print OUT "<th> $_ </th>\n";
|
|
|
678 }
|
|
|
679 foreach my $key (sort keys %nat2) {
|
|
|
680 print OUT "</tr>
|
|
|
681 <tr align=\"center\">
|
|
|
682 <th align=\"left\">$key</th>
|
|
|
683 ";
|
|
|
684 for (my $i=0;$i<@marks ;$i++) {
|
|
|
685 if (defined($nat2{$key}[$i])) {
|
|
|
686 print OUT "<td> $nat2{$key}[$i] </td>\n";
|
|
|
687 }
|
|
|
688 else{print OUT "<td> 0 </td>\n";}
|
|
|
689 }
|
|
|
690 }
|
|
|
691 print OUT "</tr>\n</table>";
|
|
|
692 print OUT "<p>
|
|
|
693 Note:<br />
|
|
|
694 One cluster mybe annotate to multiple repeats or nats<br />
|
|
|
695 ";
|
|
|
696 }
|
|
|
697 else {
|
|
|
698 print OUT "<h3>5.2 Cluster source mechanism annotate</h3>
|
|
|
699 <br />Do not do source mechanism annotate <br />";
|
|
|
700
|
|
|
701 }
|
|
|
702
|
|
|
703 print OUT "<h2>6. Graph of Clusters of all samples</h2> \n";
|
|
|
704
|
|
|
705 my $plot=$plotpath."cluster.html";
|
|
|
706 open IN,"<$plot";
|
|
|
707 while (my $aline=<IN>) {
|
|
|
708 chomp $aline;
|
|
|
709 print OUT "$aline\n";
|
|
|
710 }
|
|
|
711 close IN;
|
|
|
712
|
|
|
713
|
|
|
714 if ($deg_tag) {
|
|
|
715 my $deg_file=`ls $degpath`;
|
|
|
716 chomp $deg_file;
|
|
|
717 my @deg_file=split/\n/,$deg_file;
|
|
|
718 my %deg;
|
|
|
719 foreach (@deg_file) {
|
|
|
720 my $output="$degpath/$_/output_score.txt";
|
|
|
721 open IN,"<$output";
|
|
|
722 $deg{$_}[0]=0;
|
|
|
723 $deg{$_}[1]=0;
|
|
|
724 $deg{$_}[2]=0;
|
|
|
725 while (my $aline=<IN>) {
|
|
|
726 next if ($aline=~/^\"/);
|
|
|
727 chomp $aline;
|
|
|
728 my @temp=split/\t/,$aline;
|
|
|
729 if ($temp[9] eq "TRUE") {
|
|
|
730 $deg{$_}[0]++;
|
|
|
731 if ($temp[4] >0) {
|
|
|
732 $deg{$_}[1]++;
|
|
|
733 }
|
|
|
734 if ($temp[4] <0) {
|
|
|
735 $deg{$_}[2]++;
|
|
|
736 }
|
|
|
737 }
|
|
|
738 }
|
|
|
739 close IN;
|
|
|
740 }
|
|
|
741
|
|
|
742 print OUT "<h2>7. DEG</h2>
|
|
|
743 <table border=\"1\">
|
|
|
744 <tr align=\"center\">
|
|
|
745 <th align=\"left\">Genes number</th>\n
|
|
|
746 <th> DEG </th>\n
|
|
|
747 <th> UP </th>\n
|
|
|
748 <th> DOWN </th>\n
|
|
|
749 ";
|
|
|
750
|
|
|
751 foreach my $key (sort keys %deg) {
|
|
|
752 print OUT "</tr>
|
|
|
753 <tr align=\"center\">
|
|
|
754 <th align=\"left\">$key</th>
|
|
|
755 ";
|
|
|
756 for (my $i=0;$i<@{$deg{$key}} ;$i++) {
|
|
|
757 print OUT "<td> $deg{$key}[$i] </td>\n";
|
|
|
758 }
|
|
|
759 }
|
|
|
760 print OUT "</tr>\n</table>";
|
|
|
761 }
|
|
|
762 else{
|
|
|
763 print OUT "<h2>7. DEG</h2>
|
|
|
764 <br />Do not do DE clusters <br />";
|
|
|
765 }
|
|
|
766
|
|
|
767 print OUT "
|
|
|
768 </BODY>
|
|
|
769 </HTML>
|
|
|
770 ";
|
|
|
771 close OUT;
|
|
|
772
|
|
|
773
|
|
|
774
|
|
|
775
|
|
|
776 sub usage{
|
|
|
777 print <<"USAGE";
|
|
|
778 Version $version
|
|
|
779 Usage:
|
|
|
780 $0 -o
|
|
|
781 options:
|
|
|
782 -i
|
|
|
783 -format
|
|
|
784 -o output file
|
|
|
785 -h help
|
|
|
786 USAGE
|
|
|
787 exit(1);
|
|
|
788 }
|
