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comparison rapsodyn/mpileupfilterandstat.pl @ 0:442a7c88b886 draft

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author mcharles
date Wed, 10 Sep 2014 09:18:15 -0400
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-1:000000000000 0:442a7c88b886
1 #!/usr/bin/perl
2 use strict;
3 use Getopt::Long;
4
5 #
6 # Filter a pileup file on forward/reverse presence and %read having the variant
7 # The error code
8 # 1 : multiple variant type detected insertion/deletion/mutation
9 # 1i : inconsistency in insertion
10 # 1d : inconsistency in deletion
11 # 1m : inconsistency in mutation
12 # 2 : insufficient depth
13 # 3 : insufficient variant frequency
14 # 4 : variant position not covered by forward and reverse reads
15 # 5 : variant with other variant in neighbourhood
16 # 6 : too much depth
17 # 8 : parsing error (couldn't parse the mpileup line correctly)
18 # 9 : parsing error (couldn't parse the readbase string correctly)
19
20
21 my $inputfile;
22 my $logfile;
23 my $MIN_DISTANCE=0;
24 my $MIN_VARIANTFREQUENCY=0;
25 my $MIN_FORWARDREVERSE=0;
26 my $MIN_DEPTH=0;
27 my $MAX_DEPTH=500;
28 my $VERBOSE=0;
29 my $ONLY_UNFILTERED_VARIANT="OFF";
30 my $DO_STAT="NO";
31
32
33 my $STAT_MIN_DEPTH_MIN = 2;
34 my $STAT_MIN_DEPTH_MAX = 10;
35 my $STAT_MIN_DEPTH_STEP = 2;
36 my $STAT_MAX_DEPTH_MIN = 100;
37 my $STAT_MAX_DEPTH_MAX = 200;
38 my $STAT_MAX_DEPTH_STEP = 100;
39 my $STAT_FREQ_MIN = 0.8;
40 my $STAT_FREQ_MAX = 1;
41 my $STAT_FREQ_STEP = 0.1;
42 my $STAT_DIST_MIN = 0;
43 my $STAT_DIST_MAX = 50;
44 my $STAT_DIST_STEP = 50;
45
46 GetOptions (
47 "input_file=s" => \$inputfile,
48 "log_file=s" => \$logfile,
49 "min_depth=i" => \$MIN_DEPTH,
50 "max_depth=i" => \$MAX_DEPTH,
51 "min_frequency=f" => \$MIN_VARIANTFREQUENCY,
52 "min_distance=i" => \$MIN_DISTANCE,
53 "min_forward_and_reverse=i" => \$MIN_FORWARDREVERSE,
54 "variant_only=s" => \$ONLY_UNFILTERED_VARIANT,
55 "v=i" => \$VERBOSE,
56 "do_stat=s" => \$DO_STAT,
57 "stat_min_depth_min=i" => \$STAT_MIN_DEPTH_MIN,
58 "stat_min_depth_max=i" => \$STAT_MIN_DEPTH_MAX,
59 "stat_min_depth_step=i" => \$STAT_MIN_DEPTH_STEP,
60 "stat_max_depth_min=i" => \$STAT_MAX_DEPTH_MIN,
61 "stat_max_depth_max=i" => \$STAT_MAX_DEPTH_MAX,
62 "stat_max_depth_step=i" => \$STAT_MAX_DEPTH_STEP,
63 "stat_freq_min=f" => \$STAT_FREQ_MIN,
64 "stat_freq_max=f" => \$STAT_FREQ_MAX,
65 "stat_freq_step=f" => \$STAT_FREQ_STEP,
66 "stat_dist_min=i" => \$STAT_DIST_MIN,
67 "stat_dist_max=i" => \$STAT_DIST_MAX,
68 "stat_dist_step=i" => \$STAT_DIST_STEP
69 ) or die("Error in command line arguments\n");
70
71 open(IF, $inputfile) or die("Can't open $inputfile\n");
72
73 my @tbl_line;
74 my %USR_PARAM;
75 $USR_PARAM{"min_depth"} = $MIN_DEPTH;
76 $USR_PARAM{"max_depth"} = $MAX_DEPTH;
77 $USR_PARAM{"min_freq"} = $MIN_VARIANTFREQUENCY;
78 $USR_PARAM{"min_dist"} = $MIN_DISTANCE;
79 $USR_PARAM{"min_fr"} = $MIN_FORWARDREVERSE;
80
81
82
83 #Extraction des variants
84 my $nb_line=0;
85 while (my $line=<IF>){
86 $nb_line++;
87 if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){
88 print "$nb_line\n";
89 }
90 my $error_code=0;
91 if ($line=~/(.*?)\s+(\d+)\s+([ATGCN])\s+(\d+)\s+(.*?)\s+(.*?)$/){
92 my $current_chromosome = $1;
93 my $current_position = $2;
94 my $current_refbase = $3;
95 my $current_coverage = $4;
96 my $current_readbase_string = $5;
97 my $current_quality_string = $6;
98
99 #Suppression of mPileUp special character
100 $current_readbase_string =~ s/\$//g; #the read start at this position
101 $current_readbase_string =~ s/\^.//g; #the read end at this position followed by quality char
102
103 if ($current_readbase_string =~ /[ATGCNatgcn\d]/){
104 my %variant;
105 $variant{"line"} = $line;
106 $variant{"chr"} = $current_chromosome;
107 $variant{"pos"} = $current_position;
108 $variant{"refbase"} = $current_refbase;
109 $variant{"coverage"} = $current_coverage;
110 $variant{"readbase"} = $current_readbase_string;
111 $variant{"quality"} = $current_quality_string;
112 push(@tbl_line,\%variant);
113
114 if ($ONLY_UNFILTERED_VARIANT eq "ON"){
115 print $line;
116 }
117
118 }
119 else {
120 #Position with no variant
121 }
122
123 }
124 else {
125 #Error Parsing
126 print STDERR "$line #8";
127 }
128 }
129 close(IF);
130
131 if ($ONLY_UNFILTERED_VARIANT eq "ON"){
132 exit(0);
133 }
134
135 ####Checking the distance between variant and other filter
136
137
138 my @error;
139 for (my $i=0;$i<=$#tbl_line;$i++){
140 # print "ligne : $tbl_line[$i]\n";
141 my $before="";
142 my $after="";
143 my %line = %{$tbl_line[$i]};
144
145 if ($tbl_line[$i-1]){
146 $before = $tbl_line[$i-1];
147 }
148 if ($tbl_line[$i+1]){
149 $after = $tbl_line[$i+1];
150 }
151 my $error_code = check_error($tbl_line[$i],$before,$after,\%USR_PARAM);
152 if ($error_code == 0){
153 print $line{"line"};
154 }
155 else {
156 push(@error,$error_code,"\t",$line{"line"});
157 }
158 }
159
160 ### LOG
161 open(LF,">$logfile") or die ("Can't open $logfile\n");
162
163 if ($DO_STAT eq "YES"){
164 for (my $idx_min_depth=$STAT_MIN_DEPTH_MIN;$idx_min_depth<=$STAT_MIN_DEPTH_MAX;$idx_min_depth = $idx_min_depth + $STAT_MIN_DEPTH_STEP ){
165 for (my $idx_max_depth=$STAT_MAX_DEPTH_MIN;$idx_max_depth<=$STAT_MAX_DEPTH_MAX;$idx_max_depth = $idx_max_depth + $STAT_MAX_DEPTH_STEP ){
166 for (my $idx_freq = $STAT_FREQ_MIN;$idx_freq<=$STAT_FREQ_MAX;$idx_freq= $idx_freq+$STAT_FREQ_STEP){
167 for (my $idx_dist=$STAT_DIST_MIN;$idx_dist<=$STAT_DIST_MAX;$idx_dist = $idx_dist + $STAT_DIST_STEP){
168 for (my $idx_fr=0;$idx_fr<=1;$idx_fr++){
169 my %stat_param;
170 $stat_param{"min_depth"}=$idx_min_depth;
171 $stat_param{"max_depth"}=$idx_max_depth;
172 $stat_param{"min_freq"}=$idx_freq;
173 $stat_param{"min_fr"}=$idx_fr;
174 $stat_param{"min_dist"}=$idx_dist;
175
176 print LF "#SNP = ",&test_check(\@tbl_line,\%stat_param),"\tdepth (min/max) = ",$stat_param{"min_depth"}," / ",$stat_param{"max_depth"},"\tmin_dist=",$stat_param{"min_dist"},"\tmin_freq=",$stat_param{"min_freq"},"\tmin_forwardreverse = ",$stat_param{"min_fr"},"\n";
177 }
178 }
179 }
180 print "\n";
181 }
182 }
183 }
184
185
186 for (my $i=0;$i<=$#error;$i++){
187 print LF $error[$i];
188 }
189 close (LF);
190
191
192
193
194 sub test_check{
195 my $ref_tbl_line = shift;
196 my $ref_param = shift;
197 my @tbl_line = @$ref_tbl_line;
198 my %param = %$ref_param;
199 my $nb=0;
200
201 for (my $i=0;$i<=$#tbl_line;$i++){
202 my $before="";
203 my $after="";
204 my %line = %{$tbl_line[$i]};
205
206 if ($tbl_line[$i-1]){
207 $before = $tbl_line[$i-1];
208 }
209 if ($tbl_line[$i+1]){
210 $after = $tbl_line[$i+1];
211 }
212 my $error_code = check_error($tbl_line[$i],$before,$after,\%param);
213 if ($error_code == 0){
214 $nb++;
215 }
216 }
217
218 return $nb;
219 }
220
221 sub check_error{
222 my $refline = shift;
223 my %line = %$refline;
224 my $refbefore = shift;
225 my $refafter = shift;
226 my $refparam = shift;
227 my %param = %$refparam;
228
229
230 my $current_chromosome = $line{"chr"};
231 my $current_position = $line{"pos"};
232 my $current_refbase = $line{"refbase"};
233 my $current_coverage = $line{"coverage"};
234 my $current_readbase_string = $line{"readbase"};
235
236
237 my $min_depth = $param{"min_depth"};
238 my $max_depth = $param{"max_depth"};
239 my $min_variant_frequency = $param{"min_freq"};
240 my $min_forward_reverse = $param{"min_fr"};
241 my $min_dist = $param{"min_dist"};
242
243 #Verification of neightbourhood
244 if ($refbefore){
245 my %compareline = %$refbefore;
246 my $compare_chromosome = $compareline{"chr"};
247 my $compare_position = $compareline{"pos"};
248 my $compare_refbase = $compareline{"refbase"};
249 my $compare_coverage = $compareline{"coverage"};
250 my $compare_readbase_string = $compareline{"readbase"};
251
252 if (($current_chromosome eq $compare_chromosome )&&($compare_position + $min_dist >= $current_position)){
253 return 5;
254 }
255 }
256
257 if ($refafter){
258 my %compareline = %$refafter;
259 my $compare_chromosome = $compareline{"chr"};
260 my $compare_position = $compareline{"pos"};
261 my $compare_refbase = $compareline{"refbase"};
262 my $compare_coverage = $compareline{"coverage"};
263 my $compare_readbase_string = $compareline{"readbase"};
264
265 if (($current_chromosome eq $compare_chromosome )&&($current_position + $min_dist >= $compare_position)){
266 return 5;
267 }
268 }
269
270
271
272
273 #Extraction of insertions
274
275 ##################################################################
276 # my @IN = $current_readbase_string =~ m/\+[0-9]+[ACGTNacgtn]+/g;
277 # my @DEL = $current_readbase_string =~ m/\-[0-9]+[ACGTNacgtn]+/g;
278 # print "IN : @IN\n";
279 # print "DEL :@DEL\n";
280 #$current_readbase_string=~s/[\+\-][0-9]+[ACGTNacgtn]+//g;
281 ##################################################################
282 #!!! marche pas : exemple .+1Ct. correspond a . / +1C / t /. mais le match de l'expression vire +1Ct
283 ##################################################################
284
285 # => parcours de boucle
286 my @readbase = split(//,$current_readbase_string);
287 my $cleaned_readbase_string="";
288 my @IN;
289 my @DEL;
290 my $current_IN="";
291 my $current_DEL="";
292 my $current_size=0;
293
294 for (my $i=0;$i<=$#readbase;$i++){
295 if ($readbase[$i] eq "+"){
296 #Ouverture de IN
297 $current_IN="+";
298
299 #Recuperation de la taille
300 my $sub = substr $current_readbase_string,$i;
301 if ($sub=~/^\+(\d+)/){
302 $current_size = $1;
303 }
304 my $remaining_size = $current_size;
305 while (($remaining_size>0)&&($i<=$#readbase)){
306 $i++;
307 $current_IN.=$readbase[$i];
308 if ($readbase[$i]=~ /[ATGCNatgcn]/){
309 $remaining_size--;
310 }
311 }
312 push(@IN,$current_IN);
313 }
314 elsif ($readbase[$i] eq "-"){
315 #Ouverture de DEL
316 $current_DEL="-";
317
318 #Recuperation de la taille
319 my $sub = substr $current_readbase_string,$i;
320 if ($sub=~/^\-(\d+)/){
321 $current_size = $1;
322 }
323 my $remaining_size = $current_size;
324 while (($remaining_size>0)&&($i<=$#readbase)){
325 $i++;
326 $current_DEL.=$readbase[$i];
327 if ($readbase[$i]=~ /[ATGCNatgcn]/){
328 $remaining_size--;
329 }
330 }
331 push(@DEL,$current_DEL);
332
333 }
334 else {
335 #Ajout a la string
336 $cleaned_readbase_string .= $readbase[$i];
337 }
338 }
339
340
341 # print "IN : @IN\n";
342 # print "DEL :@DEL\n";
343 # print "$cleaned_readbase_string\n";
344
345 my @current_readbase_array = split(//,$cleaned_readbase_string);
346
347 #Filtering : error detection
348
349 if ($#current_readbase_array+1 != $current_coverage){
350 return 9;
351 #parsing error (couldn't parse the readbase string correctly)
352 }
353 elsif ($current_coverage<$min_depth){
354 return 2;
355 # 2 : insufficient depth
356 }
357 elsif ($current_coverage>$max_depth){
358 return 6;
359 # 6 : too much depth
360 }
361 else {
362 if ($#IN>=0){
363 if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){
364 return 1;
365 # 1 : variant type overload (multiple variant type detected insertion/deletion/mutation)
366 }
367 else {
368 ########## TEST de coherence des insertions ################
369 # for (my $i=0;$i<=$#IN;$i++){
370 # if (uc($IN[0]) ne uc($IN[$i])){
371 # print uc($IN[0]),"\n";
372 # print uc($IN[$i]),"\n";
373 # return "1i";
374 # }
375 # }
376 ###########################################################
377
378 if($#IN+1 < $current_coverage*$min_variant_frequency ){
379 return 3;
380 # 3 : insufficient variant frequency
381 }
382 }
383 }
384 elsif ($#DEL>=0){
385 if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){
386 return 1;
387 # 1 : variant type overload (multiple variant type detected insertion/deletion/mutation)
388 }
389 else {
390 ########## TEST de coherence des deletions ################
391 # for (my $i=0;$i<=$#DEL;$i++){
392 # if (uc($DEL[0]) ne uc($DEL[$i])){
393 # print uc($DEL[0]),"\n";
394 # print uc($DEL[$i]),"\n";
395 # return "1d";
396 # }
397 # }
398 ###########################################################
399
400 if($#DEL+1 < $current_coverage*$min_variant_frequency){
401 return 3;
402 # 3 : insufficient variant frequency
403 }
404 }
405 }
406 else {
407 my $nbA=0;
408 $nbA++ while ($current_readbase_string =~ m/A/g);
409 my $nbC=0;
410 $nbC++ while ($current_readbase_string =~ m/C/g);
411 my $nbT=0;
412 $nbT++ while ($current_readbase_string =~ m/T/g);
413 my $nbG=0;
414 $nbG++ while ($current_readbase_string =~ m/G/g);
415 my $nbN=0;
416 $nbN++ while ($current_readbase_string =~ m/N/g);
417 my $nba=0;
418 $nba++ while ($current_readbase_string =~ m/a/g);
419 my $nbc=0;
420 $nbc++ while ($current_readbase_string =~ m/c/g);
421 my $nbt=0;
422 $nbt++ while ($current_readbase_string =~ m/t/g);
423 my $nbg=0;
424 $nbg++ while ($current_readbase_string =~ m/g/g);
425 my $nbn=0;
426 $nbn++ while ($current_readbase_string =~ m/n/g);
427
428 if (($nbA+$nba>0)&&($nbT+$nbt+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){
429 return "1m";
430 }
431 if (($nbT+$nbt>0)&&($nbA+$nba+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){
432 return "1m";
433 }
434 if (($nbG+$nbg>0)&&($nbA+$nba+$nbT+$nbt+$nbC+$nbc+$nbN+$nbn>0)){
435 return "1m";
436 }
437 if (($nbC+$nbc>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbN+$nbn>0)){
438 return "1m";
439 }
440 if (($nbN+$nbn>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbC+$nbc>0)){
441 return "1m";
442 }
443
444 if ($nbA+$nba >= $current_coverage*$min_variant_frequency){
445 if (($nbA<$min_forward_reverse)||($nba<$min_forward_reverse)){
446 return 4;
447 # 4 : variant position not covered by forward and reverse reads
448 }
449 }
450 elsif ($nbT+$nbt >= $current_coverage*$min_variant_frequency){
451 if (($nbT<$min_forward_reverse)||($nbt<$min_forward_reverse)){
452 return 4;
453 # 4 : variant position not covered by forward and reverse reads
454 }
455 }
456 elsif ($nbG+$nbg >= $current_coverage*$min_variant_frequency){
457 if (($nbG<$min_forward_reverse)||($nbg<$min_forward_reverse)){
458 return 4;
459 # 4 : variant position not covered by forward and reverse reads
460 }
461 }
462 elsif ($nbC+$nbc >= $current_coverage*$min_variant_frequency){
463 if (($nbC<$min_forward_reverse)||($nbc<$min_forward_reverse)){
464 return 4;
465 # 4 : variant position not covered by forward and reverse reads
466 }
467 }
468 elsif ($nbN+$nbn >= $current_coverage*$min_variant_frequency){
469 if (($nbN<$min_forward_reverse)||($nbn<$min_forward_reverse)){
470 return 4;
471 # 4 : variant position not covered by forward and reverse reads
472 }
473 }
474 else {
475 return 3;
476 # 3 : insufficient variant frequency
477 }
478 }
479 }
480
481 return 0;
482 }