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comparison html.pl @ 0:07745c0958dd draft

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author big-tiandm
date Thu, 18 Sep 2014 21:40:25 -0400
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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,$annotatepath,$degpath);
20 my ($predir,$rfamdir,$genomedir,$clusterdir,$annotatedir,$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 $degpath=<IN>; chomp $degpath;
29 close IN;
30 my @tmp=split/\//,$prepath;
31 $predir=$tmp[-1];
32 @tmp=split/\//,$rfampath;
33 $rfamdir=$tmp[-1];
34 @tmp=split/\//,$genomepath;
35 $genomedir=$tmp[-1];
36 @tmp=split/\//,$clusterpath;
37 $clusterdir=$tmp[-1];
38 @tmp=split/\//,$annotatepath;
39 $annotatedir=$tmp[-1];
40 @tmp=split/\//,$degpath;
41 $degdir=$tmp[-1];
42
43 my $dir=dirname($opts{'o'});
44
45 open OUT ,">$opts{'o'}";
46 print OUT "<HTML>\n <HEAD>\n <TITLE> Analysis Report </TITLE>\n </HEAD>
47 <BODY bgcolor=\"lightgray\">\n <h1 align=\"center\">\n <font face=\"ºÚÌå\">\n <b>Small RNA Analysis Report</b>\n </font>\n </h1>
48 <h2>1. Sequence No. and quality</h2>
49 <h3>1.1 Sequece No.</h3>
50 ";
51
52 ### raw data no
53 open IN,"<$config";
54 my @files;my @marks; my @rawNo;
55 while (my $aline=<IN>) {
56 chomp $aline;
57 my @tmp=split/\t/,$aline;
58 push @files,$tmp[0];
59
60 my $no=`less $tmp[0] |wc -l `;
61 chomp $no;
62 if ($opts{'format'} eq "fq" || $opts{'format'} eq "fastq") {
63 $no=$no/4;
64 }
65 else{
66 $no=$no/2;
67 }
68 push @rawNo,$no;
69
70 push @marks,$tmp[1];
71 }
72 close IN;
73
74 ### preprocess
75 unless ($prepath=~/\/$/) {
76 $prepath .="/";
77 }
78
79 my @trimNo;my @collapse;
80 my $collapsefile=$prepath."collapse_reads.fa";
81 open IN,"<$collapsefile";
82 while (my $aline=<IN>) {
83 chomp $aline;
84 <IN>;
85 $aline=~/:([\d|_]+)_x(\d+)$/;
86 my @lng=split/_/,$1;
87 for (my $i=0;$i<@lng;$i++) {
88 if ($lng[$i]>0) {
89 $trimNo[$i] +=$lng[$i];
90 $collapse[$i] ++;
91 }
92 }
93 }
94 close IN;
95
96 my @cleanR;my @cleanT;
97 my $clean=$prepath."collapse_reads_18-40.fa";
98 open IN,"<$clean";
99 while (my $aline=<IN>) {
100 chomp $aline;
101 <IN>;
102 $aline=~/:([\d|_]+)_x(\d+)$/;
103 my @lng=split/_/,$1;
104 for (my $i=0;$i<@lng;$i++) {
105 if ($lng[$i]>0) {
106 $cleanR[$i] +=$lng[$i];
107 $cleanT[$i] ++;
108 }
109 }
110 }
111 close IN;
112
113 my @filterR;my @filterT;
114 my $filter=$prepath."collapse_reads_out.fa";
115 open IN,"<$filter";
116 while (my $aline=<IN>) {
117 chomp $aline;
118 <IN>;
119 $aline=~/:([\d|_]+)_x(\d+)$/;
120 my @lng=split/_/,$1;
121 for (my $i=0;$i<@lng;$i++) {
122 if ($lng[$i]>0) {
123 $filterR[$i] +=$lng[$i];
124 $filterT[$i] ++;
125 }
126 }
127 }
128 close IN;
129
130
131 print OUT "<table border=\"1\">
132 <tr align=\"center\">
133 <th>&nbsp;</th>
134 ";
135 foreach (@marks) {
136 print OUT "<th> $_ </th>\n";
137 }
138 print OUT "</tr>
139 <tr align=\"center\">
140 <th align=\"left\">Raw Reads No. </th>
141 ";
142 foreach (@rawNo) {
143 print OUT "<td> $_ </td>\n";
144 }
145 print OUT "</tr>
146 <tr align=\"center\">
147 <th align=\"left\">Reads No. After Trimed 3\' adapter </th>
148 ";
149 foreach (@trimNo) {
150 print OUT "<td> $_ </td>\n";
151 }
152 print OUT "</tr>
153 <tr align=\"center\">
154 <th align=\"left\">Unique Tags No. </th>
155 ";
156 foreach (@collapse) {
157 print OUT "<td> $_ </td>\n";
158 }
159 print OUT "</tr>
160 <tr align=\"center\">
161 <th align=\"left\">Clean Reads No. </th>
162 ";
163 foreach (@cleanR) {
164 print OUT "<td> $_ </td>\n";
165 }
166 print OUT "</tr>
167 <tr align=\"center\">
168 <th align=\"left\">Clean Tags No. </th>
169 ";
170 foreach (@cleanT) {
171 print OUT "<td> $_ </td>\n";
172 }
173 print OUT "</tr>
174 <tr align=\"center\">
175 <th align=\"left\">Filter Reads No. \(reads count \>3\) </th>
176 ";
177 foreach (@filterR) {
178 print OUT "<td> $_ </td>\n";
179 }
180 print OUT "</tr>
181 <tr align=\"center\">
182 <th align=\"left\">Filter Tags No. \(reads count \>3\) </th>
183 ";
184 foreach (@filterT) {
185 print OUT "<td> $_ </td>\n";
186 }
187 print OUT "</tr>\n</table>";
188 print OUT "<p>
189 Note:<br />
190 The raw data file path is: <b>$files[0]</b><br />
191 ";
192 for (my $i=1;$i<@files;$i++) {
193 print OUT "&nbsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;<b>$files[$i]</b><br />";
194 }
195 print OUT "The collapsed file path is: <b>$collapsefile</b><br />
196 The clean data file path is: <b>$clean</b><br />
197 The filter (remain total reads>3) data file path is: <b>$filter</b><br />
198 </p>
199 <h2> 1. Sequence length count</h2>
200 <h3> 1.1 Reads length</h3>
201 ";
202
203 print OUT "<img src=\"./$predir/Reads_length_after_count_filter.png\" alt=\"Reads_length_after_count_filter.png\" width=\"400\" height=\"300\"/>
204 <h3> 1.2 Tags length count</h3>
205 <img src=\"./$predir/Tags_length_after_count_filter.png\" alt=\"Tags_length_after_count_filter.png\" width=\"400\" height=\"300\"/>
206 <p> Note:<br />The sequence length data: <a href=\"./$predir/reads_length_distribution_after_count_filter.txt\"> length file</a>
207 </p>
208 ";
209
210 #### rfam
211 unless ($rfampath=~/\/$/) {
212 $rfampath .="/";
213 }
214 unless ($genomepath=~/\/$/) {
215 $genomepath .="/";
216 }
217 print OUT "<h2>2. Rfam non-miRNA annotation</h2>
218 <h3>2.1 Reads count</h3>
219 <table border=\"1\">
220 <tr align=\"center\">
221 ";
222
223 my @rfamR; my @rfamT;
224 my $tag=1;
225 open IN,"<$dir/rfam_match/rfam_non-miRNA_annotation.txt";
226 while (my $aline=<IN>) {
227 chomp $aline;
228 $tag=0 if($aline=~/tags\s+number/);
229 next if($aline=~/^\#/);
230 next if($aline=~/^\s*$/);
231 my @tmp=split/\s+/,$aline;
232 if($tag == 1){push @rfamR,[@tmp];}
233 else{push @rfamT,[@tmp];}
234 }
235 close IN;
236
237
238 print OUT "<th>RNA Name</th>\n";
239 foreach (@marks) {
240 print OUT "<th> $_ </th>\n";
241 }
242 for (my $i=0;$i<@rfamR;$i++) {
243 print OUT "</tr>
244 <tr align=\"center\">
245 <th align=\"left\">$rfamR[$i][0]</th>
246 ";
247 for (my $j=1;$j<@{$rfamR[$i]} ;$j++) {
248 print OUT "<td> $rfamR[$i][$j]</td>\n";
249 }
250 }
251
252 print OUT "</tr>\n</table>
253 <h3>2.2 Tags count</h3>
254 <table border=\"1\">
255 <tr align=\"center\">
256 <th>RNA Name</th>\n";
257 foreach (@marks) {
258 print OUT "<th> $_ </th>\n";
259 }
260 for (my $i=0;$i<@rfamT;$i++) {
261 print OUT "</tr>
262 <tr align=\"center\">
263 <th align=\"left\">$rfamT[$i][0]</th>
264 ";
265 for (my $j=1;$j<@{$rfamT[$i]} ;$j++) {
266 print OUT "<td> $rfamT[$i][$j]</td>\n";
267 }
268 }
269 print OUT "</tr>\n</table>
270 <p>Note:<br />The rfam mapping results is: <b>$rfampath</b>";
271 print OUT "<b>rfam_mapped.bwt</b></p>";
272
273 open IN,"<$dir/genome_match/genome_mapped.bwt";
274 my @genome_r_u;
275 my @genome_r_m;
276 my @genome_t_u;
277 my @genome_t_m;
278 my $tags_map_number=0;
279 while (my $aline=<IN>) {
280 chomp $aline;
281 my @temp=split/\t/,$aline;
282 if ($temp[6]==0) {
283 $aline=~/:([\d|_]+)_x(\d+)/;
284 my @lng=split/_/,$1;
285 for (my $i=0;$i<@lng;$i++) {
286 if ($lng[$i]>0) {
287 $genome_r_u[$i] +=$lng[$i];
288 $genome_t_u[$i] ++;
289 }
290 }
291 $tags_map_number++;
292 }
293 if ($temp[6]>0) {
294 $aline=~/:([\d|_]+)_x(\d+)/;
295 my @lng=split/_/,$1;
296 for (my $i=0;$i<@lng;$i++) {
297 if ($lng[$i]>0) {
298 $genome_r_m[$i] +=$lng[$i];
299 $genome_t_m[$i] ++;
300 }
301 }
302 for (my $i=0;$i<$temp[6] ;$i++) {
303 my $next=<IN>;
304 }
305 $tags_map_number++;
306 }
307 }
308 close IN;
309 #<h3>3.1 Reads count</h3>
310 #<table border=\"1\">
311 #<tr align=\"center\">
312 print OUT "<h2>3. genome mapping result</h2>
313 <table border=\"1\">
314 <tr align=\"center\">
315 <th align=\"left\">Map</th>\n
316 ";
317 foreach (@marks) {
318 print OUT "<th> $_ </th>\n";
319 }
320 print OUT "</tr>
321 <tr align=\"center\">
322 <th align=\"left\">Uniq Map Reads No.</th>
323 ";
324 for (my $i=0;$i<@genome_r_u ;$i++) {
325 print OUT "<td> $genome_r_u[$i]</td>\n";
326 }
327
328 print OUT "</tr>
329 <tr align=\"center\">
330 <th align=\"left\">Uniq Map Tags No.</th>
331 ";
332 for (my $i=0;$i<@genome_t_u ;$i++) {
333 print OUT "<td> $genome_t_u[$i]</td>\n";
334 }
335
336 print OUT "</tr>
337 <tr align=\"center\">
338 <th align=\"left\">Multiple Map Reads No.</th>
339 ";
340 for (my $i=0;$i<@genome_r_m ;$i++) {
341 print OUT "<td> $genome_r_m[$i]</td>\n";
342 }
343
344 print OUT "</tr>
345 <tr align=\"center\">
346 <th align=\"left\">Multiple Map Tags No.</th>
347 ";
348 for (my $i=0;$i<@genome_t_m ;$i++) {
349 print OUT "<td> $genome_t_m[$i]</td>\n";
350 }
351
352 print OUT "</tr>\n</table>
353 <p>Note:<br />The genome mapping results is: <b>$genomepath</b>";
354 print OUT "<b>genome_mapped.bwt</b></p>";
355
356 my $cluster="$clusterpath/sample_reads.cluster";
357 my $cluster_number=`less $cluster |wc -l `;
358 $cluster_number=$cluster_number-1;
359 my (%cluster_length,@exp,@rpkm);
360 my @exp_range=qw(0 1--9 10--99 100--999 1000--9999 10000--99999 100000--**);
361 my @rpkm_range=qw(0 0--0.25 0.25--0.5 0.5--1 1.0--5.0 5.0--10 10--50 50--100 100--500 500--1000 1000--**);
362
363 open IN,"<$cluster";
364 while (my $aline=<IN>) {
365 next if($aline=~/^\"/);
366 chomp $aline;
367 my @temp=split/\t/,$aline;
368 my @id=split/:|-/,$temp[0];
369 $cluster_length{$id[2]-$id[1]+1}++;
370 for (my $i=0;$i<@marks ;$i++) {
371 if ($temp[$i+3] == 0) {$exp[$i][0]++;}
372 elsif ($temp[$i+3]>0 && $temp[$i+3]<= 10 ){$exp[$i][1]++;}
373 elsif ($temp[$i+3]>10 && $temp[$i+3]<=100){$exp[$i][2]++;}
374 elsif ($temp[$i+3]>100 && $temp[$i+3]<=1000){$exp[$i][3]++;}
375 elsif ($temp[$i+3]>1000 && $temp[$i+3]<=10000){$exp[$i][4]++;}
376 elsif ($temp[$i+3]>10000 && $temp[$i+3]<=100000){$exp[$i][5]++;}
377 elsif ($temp[$i+3]>100000){$exp[$i][6]++;}
378 }
379 }
380 close IN;
381
382 my $cluster_rpkm="$clusterpath/sample_rpkm.cluster";
383 open IN,"<$cluster_rpkm";
384 while (my $aline=<IN>) {
385 next if($aline=~/^\#/);
386 chomp $aline;
387 my @temp=split/\t/,$aline;
388 for (my $i=0;$i<@marks ;$i++) {
389 if ($temp[$i+3]==0) {$rpkm[$i][0]++;}
390 elsif($temp[$i+3]>0 && $temp[$i+3]<=0.25){$rpkm[$i][1]++;}
391 elsif($temp[$i+3]>0.25 && $temp[$i+3]<=0.5){$rpkm[$i][2]++;}
392 elsif($temp[$i+3]>0.5 && $temp[$i+3]<=1){$rpkm[$i][3]++;}
393 elsif($temp[$i+3]>1 && $temp[$i+3]<=5){$rpkm[$i][4]++;}
394 elsif($temp[$i+3]>5 && $temp[$i+3]<=10){$rpkm[$i][5]++;}
395 elsif($temp[$i+3]>10 && $temp[$i+3]<=50){$rpkm[$i][6]++;}
396 elsif($temp[$i+3]>50 && $temp[$i+3]<=100){$rpkm[$i][7]++;}
397 elsif($temp[$i+3]>100 && $temp[$i+3]<=500){$rpkm[$i][8]++;}
398 elsif($temp[$i+3]>500 && $temp[$i+3]<=1000){$rpkm[$i][9]++;}
399 else{$rpkm[$i][10]++;}
400 }
401 }
402
403 close IN;
404
405 my $cluster_length_file="$clusterpath/cluster_length.txt";
406 open LEN,">$cluster_length_file";
407 print LEN "\#length\tcluster_number\n";
408 foreach my $key (sort keys %cluster_length) {
409 print LEN "$key\t$cluster_length{$key}\n";
410 }
411 close LEN;
412 print OUT "<h2>4. cluster result</h2>
413 <h3>4.1 Cluster count</h3>
414 <table border=\"1\">
415 <tr align=\"center\">
416 <th align=\"left\"> </th>
417 <td>Merged samples</td></tr>
418 <tr align=\"center\">
419 <th align=\"left\">Tags number</th>
420 <td>$tags_map_number</td></tr>
421 <tr align=\"center\">
422 <th align=\"left\">Cluster number</th>
423 <td>$cluster_number</td></tr>\n</table>
424 ";
425
426 print OUT "<h3>4.2 Cluster length</h3>
427 <p> Note:<br />The clusters length data: <a href=\"./$clusterdir/cluster_length.txt\"> length file</a>
428 </p>
429 ";
430 print OUT "<h3>4.3 Quantify</h3>
431 <table border=\"1\">
432 <tr align=\"center\">
433 <th align=\"left\">Reads Range</th>\n
434 ";
435 foreach (@marks) {
436 print OUT "<th> $_ </th>\n";
437 }
438 for (my $i=0;$i<@exp_range;$i++) {
439 print OUT "</tr>
440 <tr align=\"center\">
441 <th align=\"left\">$exp_range[$i]</th>
442 ";
443 for (my $j=0;$j<@marks ;$j++) {
444 if (!(defined($exp[$i][$j]))) {
445 print OUT "<td> 0</td>\n";
446 }
447 else{print OUT "<td> $exp[$i][$j]</td>\n";}
448 }
449 }
450 print OUT "</tr>\n</table>";
451
452 print OUT "\n<table border=\"1\">
453 <tr align=\"center\">
454 <th align=\"left\">RPKM Range</th>\n
455 ";
456 foreach (@marks) {
457 print OUT "<th> $_ </th>\n";
458 }
459 for (my $i=0;$i<@rpkm_range;$i++) {
460 print OUT "</tr>
461 <tr align=\"center\">
462 <th align=\"left\">$rpkm_range[$i]</th>
463 ";
464 for (my $j=0;$j<@marks ;$j++) {
465 if (!(defined($rpkm[$i][$j]))) {
466 print OUT "<td> 0</td>\n";
467 }
468 else{print OUT "<td> $rpkm[$i][$j]</td>\n";}
469 }
470 }
471 print OUT "</tr>\n</table>";
472
473 my $annotate="$annotatepath/sample_c_p.anno";
474 my (%posit,%repeat,%nat1,%nat2);
475 my (@phase,@long,@repeat,@nat);
476 for (my $j=0;$j<@marks ;$j++) {
477 $phase[$j]=0;
478 $long[$j]=0;
479 $repeat[$j]=0;
480 $nat[$j]=0;
481 }
482 open ANNO,"<$annotate";
483 while (my $aline=<ANNO>) {
484 next if($aline=~/^\#/);
485 chomp $aline;
486 my @temp=split/\t/,$aline;
487 for (my $i=3+@marks+6;$i<@temp;$i++) {
488 my @posit=split/\;/,$temp[$i];
489 for (my $j=0;$j<@marks ;$j++) {
490 if ($temp[3+$j]>0) {
491 $posit{$posit[0]}[$j]++;
492 }
493 else{
494 if (!(defined($posit{$posit[0]}[$j]))) {
495 $posit{$posit[0]}[$j]=0;
496 }
497 }
498 }
499 }
500 for (my $j=0;$j<@marks ;$j++) {
501 if ($temp[3+$j]>0) {
502 if ($temp[6] eq "phase") {
503 $phase[$j]++;
504 }
505 if ($temp[7] eq "long") {
506 $long[$j]++;
507 }
508 if ($temp[8] ne "\/") {
509 $repeat[$j]++;
510 my @rr=split/\;/,$temp[8];
511 foreach (@rr) {
512 $repeat{$_}[$j]++;
513 }
514 }
515 if ($temp[9] ne "\/") {
516 $nat[$j]++;
517 my @nn1=split/\;/,$temp[9];
518 my @nn2=split/\;/,$temp[10];
519 for (my $k=0;$k<@nn1 ;$k++) {
520 $nat1{$nn1[$k]}[$j]++;
521 $nat2{$nn2[$k]}[$j]++;
522 }
523 }
524 }
525 }
526 }
527 close ANNO;
528
529 print OUT "<h2>5. Cluster Annotate</h2>
530 <h3>5.1 Cluster genome position annotate</h3>
531 <table border=\"1\">
532 <tr align=\"center\">
533 <th align=\"left\">clusters number</th>\n
534 ";
535
536 foreach (@marks) {
537 print OUT "<th> $_ </th>\n";
538 }
539 foreach my $key (sort keys %posit) {
540 print OUT "</tr>
541 <tr align=\"center\">
542 <th align=\"left\">$key</th>
543 ";
544 foreach (@{$posit{$key}}) {
545 print OUT "<td> $_</td>\n";
546 }
547 }
548 print OUT "</tr>\n</table>";
549 print OUT "<p>
550 Note:<br />
551 One cluster mybe annotate to multiple genes<br />
552 ";
553
554 print OUT "<h3>5.2 Cluster source mechanism annotate</h3>
555 <table border=\"1\">
556 <tr align=\"center\">
557 <th align=\"left\">clusters number</th>\n
558 ";
559
560 foreach (@marks) {
561 print OUT "<th> $_ </th>\n";
562 }
563 print OUT "</tr>
564 <tr align=\"center\">
565 <th align=\"left\">Phase</th>\n
566 ";
567 foreach (@phase) {
568 print OUT "<td> $_ </td>\n";
569 }
570
571 print OUT "</tr>
572 <tr align=\"center\">
573 <th align=\"left\">Long</th>\n
574 ";
575 foreach (@long) {
576 print OUT "<td> $_ </td>\n";
577 }
578
579 print OUT "</tr>
580 <tr align=\"center\">
581 <th align=\"left\">Repeat</th>\n
582 ";
583 foreach (@repeat) {
584 print OUT "<td> $_ </td>\n";
585 }
586
587 print OUT "</tr>
588 <tr align=\"center\">
589 <th align=\"left\">Nat</th>\n
590 ";
591 foreach (@nat) {
592 print OUT "<td> $_ </td>\n";
593 }
594 print OUT "</tr>\n</table>";
595
596 print OUT "<p>
597 Repeat subclass annotate:
598 ";
599
600 print OUT "<table border=\"1\">
601 <tr align=\"center\">
602 <th align=\"left\">Repeat subclass</th>\n
603 ";
604 foreach (@marks) {
605 print OUT "<th> $_ </th>\n";
606 }
607
608 foreach my $key (sort keys %repeat) {
609 print OUT "</tr>
610 <tr align=\"center\">
611 <th align=\"left\">$key</th>
612 ";
613 for (my $i=0;$i<@marks ;$i++) {
614 if (defined($repeat{$key}[$i])) {
615 print OUT "<td> $repeat{$key}[$i] </td>\n";
616 }
617 else{print OUT "<td> 0 </td>\n";}
618 }
619 }
620 print OUT "</tr>\n</table>";
621
622
623 print OUT "<p>
624 Nat subclass1 annotate:
625 ";
626
627 print OUT "<table border=\"1\">
628 <tr align=\"center\">
629 <th align=\"left\">Nat subclass1</th>\n
630 ";
631 foreach (@marks) {
632 print OUT "<th> $_ </th>\n";
633 }
634 foreach my $key (sort keys %nat1) {
635 print OUT "</tr>
636 <tr align=\"center\">
637 <th align=\"left\">$key</th>
638 ";
639 for (my $i=0;$i<@marks ;$i++) {
640 if (defined($nat1{$key}[$i])) {
641 print OUT "<td> $nat1{$key}[$i] </td>\n";
642 }
643 else{print OUT "<td> 0 </td>\n";}
644 }
645 }
646 print OUT "</tr>\n</table>";
647
648 print OUT "<p>
649 Nat subclass2 annotate:
650 ";
651
652 print OUT "<table border=\"1\">
653 <tr align=\"center\">
654 <th align=\"left\">Nat subclass2</th>\n
655 ";
656 foreach (@marks) {
657 print OUT "<th> $_ </th>\n";
658 }
659 foreach my $key (sort keys %nat2) {
660 print OUT "</tr>
661 <tr align=\"center\">
662 <th align=\"left\">$key</th>
663 ";
664 for (my $i=0;$i<@marks ;$i++) {
665 if (defined($nat2{$key}[$i])) {
666 print OUT "<td> $nat2{$key}[$i] </td>\n";
667 }
668 else{print OUT "<td> 0 </td>\n";}
669 }
670 }
671 print OUT "</tr>\n</table>";
672 print OUT "<p>
673 Note:<br />
674 One cluster mybe annotate to multiple repeats or nats<br />
675 ";
676
677 my $deg_file=`ls $degpath`;
678 chomp $deg_file;
679 my @deg_file=split/\n/,$deg_file;
680 my %deg;
681 foreach (@deg_file) {
682 my $output="$degpath/$_/output_score.txt";
683 open IN,"<$output";
684 $deg{$_}[0]=0;
685 $deg{$_}[1]=0;
686 $deg{$_}[2]=0;
687 while (my $aline=<IN>) {
688 next if ($aline=~/^\"/);
689 chomp $aline;
690 my @temp=split/\t/,$aline;
691 if ($temp[9] eq "TRUE") {
692 $deg{$_}[0]++;
693 if ($temp[4] >0) {
694 $deg{$_}[1]++;
695 }
696 if ($temp[4] <0) {
697 $deg{$_}[2]++;
698 }
699 }
700 }
701 close IN;
702 }
703
704
705 print OUT "<h2>6. DEG</h2>
706 <table border=\"1\">
707 <tr align=\"center\">
708 <th align=\"left\">Genes number</th>\n
709 <th> DEG </th>\n
710 <th> UP </th>\n
711 <th> DOWN </th>\n
712 ";
713
714 foreach my $key (sort keys %deg) {
715 print OUT "</tr>
716 <tr align=\"center\">
717 <th align=\"left\">$key</th>
718 ";
719 for (my $i=0;$i<@{$deg{$key}} ;$i++) {
720 print OUT "<td> $deg{$key}[$i] </td>\n";
721 }
722 }
723 print OUT "</tr>\n</table>";
724
725 print OUT "
726 </BODY>
727 </HTML>
728 ";
729 close OUT;
730
731
732
733
734 sub usage{
735 print <<"USAGE";
736 Version $version
737 Usage:
738 $0 -o
739 options:
740 -i
741 -format
742 -o output file
743 -h help
744 USAGE
745 exit(1);
746 }