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comparison carpet-src-1/tools/CARPET/calcolo_p_v4_norm_intron.pl @ 0:cdd489d98766

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:50:41 -0400
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-1:000000000000 0:cdd489d98766
1 #! /usr/bin/perl
2
3 # Copyright 2009 Matteo Cesaroni, Lucilla Luzi
4 #
5 # This program is free software; ; you can redistribute it and/or modify
6 # it under the terms of the GNU Lesser General Public License as published by
7 # the Free Software Foundation; either version 3 of the License, or (at your
8 # option) any later version.
9 #
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
14
15
16
17 #prende tutte le probes che mecciano almeno in parte dentro gli esoni
18
19 use Statistics::PointEstimation;
20 use Statistics::TTest;
21 #use Statistics::Test::WilcoxonRankSum;
22 use Getopt::Long;
23
24 GetOptions (
25 "help" => \$OPT{help},
26 "ann=s" => \$OPT{ann},
27 "wt=s" => \$OPT{wt},
28 "treat=s" => \$OPT{treat},
29 "out=s" => \$OPT{out},
30 "pv=s" => \$OPT{prob},
31 "rc=s" => \$OPT{raw_cut},
32 "fc=s" => \$OPT{fc_cut},
33 "exon=s" => \$OPT{exon},
34 "opt=s" => \$OPT{option},
35 "norm=s" =>\$OPT{norm_q},
36 "sum_met=s" =>\$OPT{sum_met},
37 "fdr=s" =>\$OPT{fdr},
38 "log=s" =>\$OPT{log_t},
39 )|| printusage();
40
41 # opzioni da linea di comando
42 my $file_ann=$OPT{ann};
43 my $file_wt=$OPT{wt};
44 my $file_treat=$OPT{treat};
45 my $file_output=$OPT{out};
46 my $pv_cut=$OPT{prob};
47 my $media_cut=$OPT{raw_cut};
48 my $FC_cut=$OPT{fc_cut};
49 my $tipo=$OPT{exon};
50 my $option=$OPT{option};
51 my $normalization_q=$OPT{norm_q};
52 my $sum_meth=$OPT{sum_met};
53 my $corretction=$OPT{fdr};
54 my $data_log=$OPT{log_t};
55
56 $help and printusage();
57
58
59 if($option eq "comp"){
60 if ($sum_meth eq "both"){
61 $header=<<e0c6654;
62 \# annotation_file: $file_ann
63 \# wt_file: $file_wt
64 \# treat_file: $file_treat
65 \# p-value cutoff: $pv_cut
66 \# raw data cutoff cutoff: $media_cut
67 \# summary method: $sum_meth
68 \# fold change cutoff: $FC_cut
69 \# type of analysis: $tipo
70 \# headers: name RefSeq Chr txStart txEnd strand mean_chip1 mean_chip2 FC_mean median_chip1 median_chip2 FC_median num_probes_in_gene p-value FDR(q-value)
71 e0c6654
72
73 }
74 if ($sum_meth eq "mean"){
75 $header=<<e0c6654;
76 \# annotation_file: $file_ann
77 \# wt_file: $file_wt
78 \# treat_file: $file_treat
79 \# p-value cutoff: $pv_cut
80 \# raw data cutoff cutoff: $media_cut
81 \# summary method: $sum_meth
82 \# fold change cutoff: $FC_cut
83 \# type of analysis: $tipo
84 \# headers: name RefSeq Chr txStart txEnd strand mean_chip1 mean_chip2 FC_mean num_probes_in_gene p-value FDR(q-value)
85 e0c6654
86
87 }
88 if ($sum_meth eq "median"){
89 $header=<<e0c6654;
90 \# annotation_file: $file_ann
91 \# wt_file: $file_wt
92 \# treat_file: $file_treat
93 \# p-value cutoff: $pv_cut
94 \# raw data cutoff cutoff: $media_cut
95 \# summary method: $sum_meth
96 \# fold change cutoff: $FC_cut
97 \# type of analysis: $tipo
98 \# headers: name RefSeq Chr txStart txEnd strand median_chip1 median_chip2 FC_median num_probes_in_gene p-value FDR(q-value)
99 e0c6654
100
101 }
102
103
104
105 # "usage" se non ci sono opzioni
106 if (!$file_ann || !$file_wt || !$file_treat) {
107 &printusage()
108 }
109
110 #if ($pv_cut == 1){$pv_cut=0.9999;}
111 if (!$media_cut){$media_cut=0;}
112 if (!$FC_cut){$FC_cut=0;}
113
114 my @r1=();
115 my @r2=();
116
117 #my $confident=(1-$pv_cut)*100;
118 #inserire nell'ordine: tabella annotazione, tabella valori wt, tabella valori treated, p-value cutoff, raw signal cutoff
119
120
121 open (annotation,"<$file_ann") || die "file_ann not open:$!\n";
122 open (wt,"<$file_wt") || die "$file_wt not open:$!\n";
123 open (treated,"<$file_treat") || die "$file_treat not open:$!\n";
124 open (output,">$file_output") || die "bed_$file_wt not open:$!\n";
125
126 print output "$header";
127
128 print "Comparison --> probe_selection=$tipo, Normalization=$normalization_q, summary method=$sum_meth Filters: p-value=$pv_cut, raw value=$media_cut, FC=$FC_cut";
129
130 while (defined (my $line_down = <annotation>)) {
131 chomp $line_down;
132 my @tmp_down = split("\t", $line_down);
133 my @probe_match=split("\,", $tmp_down[9]);
134 foreach $probes (@probe_match){
135 my @coord=split("-", $probes);
136 $tab_tot{$tmp_down[0]}{"$coord[0]\t$coord[1]"}.="$tmp_down[1]\n$tmp_down[7]\n$tmp_down[0]\n$tmp_down[2]\n$tmp_down[3]\n$tmp_down[4]\n$tmp_down[5]\n$tmp_down[6]\n";
137 push(@ciclo,"$tmp_down[0]\t$coord[0]\t$coord[1]");
138 }
139 }
140
141 while (defined (my $line_down = <wt>)) {
142 chomp $line_down;
143 my @tmp_down = split("\t", $line_down);
144 chomp $tmp_down[0];
145 $tab_tot_wt{"$tmp_down[0]\t$tmp_down[3]"}=$tmp_down[5];
146 }
147
148
149 while (defined (my $line_down = <treated>)) {
150 chomp $line_down;
151 my @tmp_down = split("\t", $line_down);
152 chomp $tmp_down[0];
153 $tab_tot_treat{"$tmp_down[0]\t$tmp_down[3]"}=$tmp_down[5];
154 }
155
156 if($normalization_q eq "yes"){
157
158 @sort_wt=sort{$tab_tot_wt{$a} <=> $tab_tot_wt{$b}} keys %tab_tot_wt;
159 @sort_treat=sort{$tab_tot_treat{$a} <=> $tab_tot_treat{$b}} (keys %tab_tot_treat);
160
161 for($i=0;$i<=$#sort_wt;$i++){
162 $media=($tab_tot_wt{$sort_wt[$i]}+$tab_tot_treat{$sort_treat[$i]})/2;
163 $tab_tot_value{$sort_wt[$i]}.="$media\n";
164 }
165
166 for($i=0;$i<=$#sort_treat;$i++){
167 $media=($tab_tot_wt{$sort_wt[$i]}+$tab_tot_treat{$sort_treat[$i]})/2;
168 $tab_tot_value{$sort_treat[$i]}.="$media\n";
169 }
170
171 }
172
173
174 foreach $key_value(@ciclo){
175
176 @keys_values=split("\t",$key_value);
177 @array1= split("\n",$tab_tot{$keys_values[0]}{"$keys_values[1]\t$keys_values[2]"});
178 if($normalization_q eq "yes"){
179 @array2= split("\n",$tab_tot_value{"$keys_values[1]\t$keys_values[2]"});
180 $value1=$array2[0];
181 $value2=$array2[1];
182 }
183 else{
184 $value1=$tab_tot_wt{"$keys_values[1]\t$keys_values[2]"};
185 $value2=$tab_tot_treat{"$keys_values[1]\t$keys_values[2]"};
186 }
187 if ($tipo eq "internal_exon"){
188 $prendo = "^exon";
189 }
190 if ($tipo eq "all_exon"){
191 $prendo = "exon";
192 }
193 if ($tipo eq "last_exon"){
194 $prendo = "exon last";
195 }
196
197 if ((!($array1[0] eq "")) && ($array1[1] =~ /$prendo/g)) {
198 if ($data_log eq "no_log"){
199 $log1=log($value1)/log(2);
200 $log2=log($value2)/log(2);
201 }
202 if ($data_log eq "log"){
203 $log1=$value1;
204 $log2=$value2;
205 }
206 $tab_gene_wt{"$array1[0]\t$array1[2]\t$array1[3]\t$array1[4]\t$array1[5]\t$array1[6]"}.="$log1\n";
207 $tab_gene_tratted{"$array1[0]\t$array1[2]\t$array1[3]\t$array1[4]\t$array1[5]\t$array1[6]"}.="$log2\n";
208 }
209
210 }
211
212 foreach $key (keys %tab_gene_wt) {
213 @r1=split("\n",$tab_gene_wt{$key});
214 @r2=split("\n",$tab_gene_tratted{$key});
215
216 sort {$a <=> $b} (@r1);
217 sort {$a <=> $b} (@r2);
218
219 if ($#r1>0){
220 my $ttest = new Statistics::TTest;
221 $ttest->set_significance(95);
222 $ttest->load_data(\@r1,\@r2);
223 my $s1=$ttest->{s1};
224 my $s2=$ttest->{s2};
225 $media1=$s1->{mean};
226 $media2=$s2->{mean};
227 $total_probes=$#r1+1;
228 $potenza_a=$media2-$media1;
229 $FCa=((2)**$potenza_a);
230 if( (@r1 % 2) == 1 ) {
231 $median1 = $r1[((@r1+1) / 2)-1];
232 $median2 = $r2[((@r2+1) / 2)-1];
233 } else {
234 $median1 = ($r1[(@r1 / 2)-1] + $r1[@r1 / 2]) / 2;
235 $median2 = ($r2[(@r2 / 2)-1] + $r2[@r2 / 2]) / 2;
236 }
237 $potenza_m=$median2-$median1;
238 $FCm=((2)**$potenza_m);
239
240
241 if ($FCa<1){
242 $FCa=(-(1/$FCa));
243 }
244
245
246 if ($FCm<1){
247 $FCm=(-(1/$FCm));
248 }
249 if ($sum_meth eq "mean"){
250 if ((($media1<$media_cut) && ($media2<$media_cut)) || ($FC_cut>=abs($FCa))){
251 next;
252 }
253 $p_value{"$key\t$media1\t$media2\t$FCa\t$total_probes"}=$ttest->{t_prob};
254
255 #print output "$key\t$media1\t$media2\t$FCa\t",$ttest->{t_prob},"\t$total_probes\n";
256 }
257 if ($sum_meth eq "median"){
258 if ((($media1<$media_cut) && ($media2<$media_cut)) || ($FC_cut>=abs($FCm))){
259 next;
260 }
261 #print output "$key\t$median1\t$median2\t$FCm\t",$ttest->{t_prob},"\t$total_probes\n";
262 $p_value{"$key\t$median1\t$median2\t$FCm\t$total_probes"}=$ttest->{t_prob};
263 }
264 if ($sum_meth eq "both"){
265 if (($media1<$media_cut) && ($media2<$media_cut)){
266 next;
267 }
268 #print output "$key\t$media1\t$media2\t$FCa\t$median1\t$median2\t$FCm\t",$ttest->{t_prob},"\t$total_probes\n";
269 $p_value{"$key\t$media1\t$media2\t$FCa\t$median1\t$median2\t$FCm\t$total_probes"}=$ttest->{t_prob};
270 }
271 }
272 if ($#r1==0){
273 $media1=$r1[0];
274 $media2=$r2[0];
275 $median1=$r1[0];
276 $median2=$r2[0];
277 $potenza=$media2-$media1;
278 $FCa=((2)**$potenza);
279 $FCm=((2)**$potenza);
280 if ($FCa<1){
281 $FCa=(-(1/$FCa));
282 }
283 if ($FCm<1){
284 $FCm=(-(1/$FCm));
285 }
286
287 if ($sum_meth eq "both"){
288 if (($media1<$media_cut) && ($media2<$media_cut)){
289 next;
290 }
291 $p_value{"$key\t$media1\t$media2\t$FCa\t$median1\t$median2\t$FCm\t$total_probes"}=1;
292 }
293 if ($sum_meth eq "mean"){
294 if ((($media1<$media_cut) && ($media2<$media_cut)) || ($FC_cut>=abs($FCa))){
295 next;
296 }
297 $p_value{"$key\t$media1\t$media2\t$FCa\t$total_probes"}=1;
298 }
299 if ($sum_meth eq "median"){
300 if ((($media1<$media_cut) && ($media2<$media_cut)) || ($FC_cut>=abs($FCm))){
301 next;
302 }
303 $p_value{"$key\t$median1\t$median2\t$FCm\t$total_probes"}=1;
304 }
305 }
306 }
307
308 @sort_pvalue=sort{$p_value{$a} <=> $p_value{$b}} keys %p_value;
309
310 if($corretction eq "yes"){
311 for($i=0;$i<=$#sort_pvalue;$i++){
312 $qvalue=$p_value{$sort_pvalue[$i]}*(($#sort_pvalue+1)/($i+1));
313 push(@QVALUE, $qvalue);
314 }
315
316 @qvalue_sort = sort {$a <=> $b} @QVALUE;
317
318 for($i=0;$i<=$#sort_pvalue;$i++){
319 #$FDR=((($i+1)*0.05)/($#sort_pvalue+1));
320 $qvalue=shift(@qvalue_sort);
321 if($qvalue>1){$qvalue=1;}
322 if($pv_cut>=$qvalue){
323 print output "$sort_pvalue[$i]\t$p_value{$sort_pvalue[$i]}\t$qvalue\n";
324 }
325 }
326 }
327 if($corretction eq "no"){
328 for($i=0;$i<=$#sort_pvalue;$i++){
329 if($pv_cut>=$qvalue){
330 print output "$sort_pvalue[$i]\t$p_value{$sort_pvalue[$i]}\n";
331 }
332 }
333 }
334
335
336
337
338
339 }
340 if($option eq "expr"){
341 if ($sum_meth eq "median"){
342 $header=<<e0c6654;
343 \# annotation_file: $file_ann
344 \# expression_file: $file_wt
345 \# type of analysis: $tipo
346 \# summary method: $sum_meth
347 \# headers: name RefSeq Chr txStart txEnd strand median_chip num_probes_in_gene
348 e0c6654
349
350 }
351 if ($sum_meth eq "mean"){
352 $header=<<e0c6654;
353 \# annotation_file: $file_ann
354 \# expression_file: $file_wt
355 \# type of analysis: $tipo
356 \# summary method: $sum_meth
357 \# headers: name RefSeq Chr txStart txEnd strand mean_chip num_probes_in_gene
358 e0c6654
359
360 }
361 if ($sum_meth eq "both"){
362 $header=<<e0c6654;
363 \# annotation_file: $file_ann
364 \# expression_file: $file_wt
365 \# type of analysis: $tipo
366 \# summary method: $sum_meth
367 \# headers: name RefSeq Chr txStart txEnd strand mean_chip median_chip num_probes_in_gene
368 e0c6654
369
370 }
371 if (!$file_ann || !$file_wt) {
372 &printusage()
373 }
374 my @r1=();
375 my @r2=();
376
377
378 open (annotation,"<$file_ann") || die "file_ann not open:$!\n";
379 open (wt,"<$file_wt") || die "$file_wt not open:$!\n";
380 open (output,">$file_output") || die "bed_$file_wt not open:$!\n";
381
382 print output "$header";
383
384 print "Expression --> probe_selection=$tipo summary method=$sum_meth";
385
386 while (defined (my $line_down = <annotation>)) {
387 chomp $line_down;
388 my @tmp_down = split("\t", $line_down);
389 my @probe_match=split("\,", $tmp_down[9]);
390 foreach $probes (@probe_match){
391 my @coord=split("-", $probes);
392 $tab_tot{$tmp_down[0]}{"$coord[0]\t$coord[1]"}.="$tmp_down[1]\n$tmp_down[7]\n$tmp_down[0]\n$tmp_down[2]\n$tmp_down[3]\n$tmp_down[4]\n$tmp_down[5]\n$tmp_down[6]\n";
393 push(@ciclo,"$tmp_down[0]\t$coord[0]\t$coord[1]");
394 }
395 }
396
397 while (defined (my $line_down = <wt>)) {
398 chomp $line_down;
399 $line_down=~ s/ //g;
400 my @tmp_down = split("\t", $line_down);
401 chomp $tmp_down[0];
402 $tab_tot_wt{"$tmp_down[0]\t$tmp_down[3]"}=$tmp_down[5];
403 }
404 #@sort_wt=sort{$tab_tot_wt{$a} <=> $tab_tot_wt{$b}} keys %tab_tot_wt;
405
406
407 #print "ciclo = $ciclo[0]\t$ciclo[1]\n";
408
409 foreach $key_value(@ciclo){
410
411 @keys_values=split("\t",$key_value);
412 @array1= split("\n",$tab_tot{$keys_values[0]}{"$keys_values[1]\t$keys_values[2]"});
413 @array2= split("\n",$tab_tot_wt{"$keys_values[1]\t$keys_values[2]"});
414
415 if ($tipo eq "internal_exon"){
416 $prendo = "^exon";
417 }
418 if ($tipo eq "all_exon"){
419 $prendo = "exon";
420 }
421 if ($tipo eq "last_exon"){
422 $prendo = "exon last";
423 }
424
425 if ((!($array1[0] eq "")) && ($array1[1] =~ /$prendo/g)) {
426
427 if ($data_log eq "no_log"){
428 $log1=log($array2[0])/log(2);
429 }
430 if ($data_log eq "log"){
431 $log1=$array2[0];
432 }
433
434 $tab_gene_wt{"$array1[0]\t$array1[2]\t$array1[3]\t$array1[4]\t$array1[5]\t$array1[6]"}.="$log1\n";
435 }
436 if ((!($array1[0] eq "")) && ($array1[1] =~ /intron/g)) {
437 if ($data_log eq "no_log"){
438 $log1=log($array2[0])/log(2);
439 }
440 if ($data_log eq "log"){
441 $log1=$array2[0];
442 }
443 $tab_intron_wt{"$array1[0]\t$array1[2]\t$array1[3]\t$array1[4]\t$array1[5]\t$array1[6]"}.="$log1\n";
444 }
445
446 }
447
448
449 foreach $key (keys %tab_gene_wt) {
450 @r1=split("\n",$tab_gene_wt{$key});
451 if (exists $tab_intron_wt{$key}){
452 @r2=split("\n",$tab_intron_wt{$key});
453 sort {$a <=> $b} (@r2);
454 }else{
455 @r2=("no");
456 }
457 sort {$a <=> $b} (@r1);
458 if ($#r2>0) {
459 if ($#r1>0) {
460 my $ttest = new Statistics::TTest;
461 $ttest->set_significance(95);
462 $ttest->load_data(\@r1,\@r2);
463 my $s1=$ttest->{s1};
464 my $s2=$ttest->{s2};
465 $media1=$s1->{mean};
466 $media2=$s2->{mean};
467 $total_probes=$#r1+1;
468 $total_probes2=$#r2+1;
469 if( (@r1 % 2) == 1 ) {
470 $median1 = $r1[((@r1+1) / 2)-1];
471 } else {
472 $median1 = ($r1[(@r1 / 2)-1] + $r1[@r1 / 2]) / 2;
473 }
474 if( (@r2 % 2) == 1 ) {
475 $median2 = $r2[((@r2+1) / 2)-1];
476 } else {
477 $median2 = ($r2[(@r2 / 2)-1] + $r2[@r2 / 2]) / 2;
478 }
479 if($media1>=$media2){
480 $pvalue=$ttest->{t_prob};
481 }
482 if($media1<$media2){
483 $pvalue=1;
484 }
485 if ($sum_meth eq "mean"){
486 print output "$key\t$media1\t$media2\t$pvalue\t$total_probes\t$total_probes2\n";
487 #print output "$key\t$media1\t$total_probes\n";
488 }
489 if ($sum_meth eq "median"){
490 print output "$key\t$median1\t$median2\t$pvalue\t$total_probes\t$total_probes2\n";
491 #print output "$key\t$median1\t$total_probes\n";
492 }
493 if ($sum_meth eq "both"){
494 print output "$key\t$media1\t$media2\t$median1\t$median2\t$pvalue\t$total_probes\t$total_probes2\n";
495 #print output "$key\t$media1\t$median1\t$total_probes\n";
496 }
497 }
498 if ($#r1==0) {
499 @r1=@r2;
500 my $ttest = new Statistics::TTest;
501 $ttest->set_significance(95);
502 $ttest->load_data(\@r1,\@r2);
503 my $s2=$ttest->{s2};
504 $media2=$s2->{mean};
505 $total_probes=1;
506 $total_probes2=$#r2+1;
507 $media1=$r1[0];
508 $median1=$r1[0];
509 if( (@r2 % 2) == 1 ) {
510 $median2 = $r2[((@r2+1) / 2)-1];
511 } else {
512 $median2 = ($r2[(@r2 / 2)-1] + $r2[@r2 / 2]) / 2;
513 }
514 if ($sum_meth eq "mean"){
515 print output "$key\t$media1\t$media2\tNA\t$total_probes\t$total_probes2\n";
516 #print output "$key\t$media1\t$total_probes\n";
517 }
518 if ($sum_meth eq "median"){
519 print output "$key\t$median1\t$median2\tNA\t$total_probes\t$total_probes2\n";
520 #print output "$key\t$median1\t$total_probes\n";
521 }
522 if ($sum_meth eq "both"){
523 print output "$key\t$media1\t$media2\t$median1\t$median2\tNA\t$total_probes\t$total_probes2\n";
524 #print output "$key\t$media1\t$median1\t$total_probes\n";
525 }
526 }
527
528
529 }
530
531 if ($r2[0] eq "no") {
532 if ($#r1>0) {
533 @r2=@r1;
534 my $ttest = new Statistics::TTest;
535 $ttest->set_significance(95);
536 $ttest->load_data(\@r1,\@r2);
537 my $s1=$ttest->{s1};
538 $media1=$s1->{mean};
539 $total_probes=$#r1+1;
540 if( (@r1 % 2) == 1 ) {
541 $median1 = $r1[((@r1+1) / 2)-1];
542 } else {
543 $median1 = ($r1[(@r1 / 2)-1] + $r1[@r1 / 2]) / 2;
544 }
545 }
546 if ($#r==0){
547 $media1=$r1[0];
548 $median1=$r1[0];
549 $total_probes=$#r1+1;
550 }
551 $media2=0;
552 $median2=0;
553 if ($sum_meth eq "both"){
554 print output "$key\t$media1\t$media2\t$median1\t$median2\tNA\t$total_probes\t0\n";
555 #print output "$key\t$media1\t$median1\t$total_probes\n";
556 }
557 if ($sum_meth eq "mean"){
558 print output "$key\t$media1\t$media2\tNA\t$total_probes\t0\n";
559 #print output "$key\t$media1\t$total_probes\n";
560 }
561 if ($sum_meth eq "median"){
562 print output "$key\t$median1\t$median2\tNA\t$total_probes\t0\n";
563 #print output "$key\t$median1\t$total_probes\n";
564 }
565 }
566 if (($#r2 == 0) && ($r2[0] ne "no") && ($#r1==0)){
567 $media1=$r1[0];
568 $media2=$r2[0];
569 $median1=$r1[0];
570 $median2=$r2[0];
571 if ($sum_meth eq "both"){
572 print output "$key\t$media1\t$media2\t$median1\t$median2\tNA\t1\t1\n";
573 #print output "$key\t$media1\t$median1\t1\n";
574 }
575 if ($sum_meth eq "mean"){
576 print output "$key\t$media1\t$media2\tNA\t1\t1\n";
577 #print output "$key\t$media1\t1\n";
578 }
579 if ($sum_meth eq "median"){
580 print output "$key\t$median1\t$median2\tNA\t1\t1\n";
581 #print output "$key\t$median1\t1\n";
582 }
583 }
584 }
585
586
587
588
589 }
590
591
592
593
594
595 ####################################################################################################################################
596
597 sub printusage {
598
599 print<<eoc22334;
600
601
602
603 ***************************************************************
604 :: N i m b l e G e n E x p r e s s i o n A n a l y s i s ::
605 ***************************************************************
606
607
608 USAGE SUMMARY
609 ---------------------------------------------------------------------------------
610 This program utilizes NimbleGen ratio files in gff format as INPUT FILE and
611 provides a table of the computed picks in the same gff file format.
612
613
614 --ann annotation file
615 --wt wild type file
616 --treat treated file
617 --pv p-value cut-off
618 --rc raw signal cut-off
619 --fc fold change cut-toff
620
621 -----------------------------------------------------------------------------------------
622 EXAMPLES:
623
624 perl program.pl --in 75340_ratio.gff --perc 0.98 --t s --num 3 --dist 250 --w 500
625 OR
626 perl program.pl --in 75340_ratio.gff --perc 0.98 --t p --log 5 --num 3 --dist 250 --w 500
627
628 -----------------------------------------------------------------------------------------
629
630 eoc22334
631 exit 0;
632
633 }
634
635
636