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root/gclib/tophat_cpp/gff.cpp
Revision: 29
Committed: Tue Aug 2 21:24:54 2011 UTC (8 years, 9 months ago) by gpertea
File size: 64074 byte(s)
Log Message:
adding tophat source work

Line File contents
1 #include "gff.h"
2
3 //GffNames* GffReader::names=NULL;
4 GffNames* GffObj::names=NULL;
5 //global set of feature names, attribute names etc.
6 // -- common for all GffObjs in current application!
7
8 const uint GFF_MAX_LOCUS = 7000000; //longest known gene in human is ~2.2M, UCSC claims a gene for mouse of ~ 3.1 M
9 const uint GFF_MAX_EXON = 30000; //longest known exon in human is ~11K
10 const uint GFF_MAX_INTRON= 6000000;
11 bool gff_show_warnings = false; //global setting, set by GffReader->showWarnings()
12 const int gff_fid_mRNA=0;
13 const int gff_fid_transcript=1;
14 const int gff_fid_exon=2;
15 const int gff_fid_CDS=3; //never really used in GffObj ftype_id or subftype_id
16 const uint gfo_flag_HAS_ERRORS = 0x00000001;
17 const uint gfo_flag_CHILDREN_PROMOTED= 0x00000002;
18 const uint gfo_flag_IS_GENE = 0x00000004;
19 const uint gfo_flag_IS_TRANSCRIPT = 0x00000008;
20 const uint gfo_flag_FROM_GFF3 = 0x00000010;
21 const uint gfo_flag_BY_EXON = 0x00000020; //created by subfeature (exon) directly
22 const uint gfo_flag_DISCARDED = 0x00000100;
23 const uint gfo_flag_LST_KEEP = 0x00000200;
24 const uint gfo_flag_LEVEL_MSK = 0x00FF0000;
25 const byte gfo_flagShift_LEVEL = 16;
26
27 void gffnames_ref(GffNames* &n) {
28 if (n==NULL) n=new GffNames();
29 n->numrefs++;
30 }
31
32 void gffnames_unref(GffNames* &n) {
33 if (n==NULL) GError("Error: attempt to remove reference to null GffNames object!\n");
34 n->numrefs--;
35 if (n->numrefs==0) { delete n; n=NULL; }
36 }
37
38 int gfo_cmpByLoc(const pointer p1, const pointer p2) {
39
40 GffObj& g1=*((GffObj*)p1);
41 GffObj& g2=*((GffObj*)p2);
42 if (g1.gseq_id==g2.gseq_id) {
43 if (g1.start!=g2.start)
44 return (int)(g1.start-g2.start);
45 else if (g1.getLevel()!=g2.getLevel())
46 return (int)(g1.getLevel()-g2.getLevel());
47 else
48 if (g1.end!=g2.end)
49 return (int)(g1.end-g2.end);
50 else return strcmp(g1.getID(), g2.getID());
51 }
52 else return (int)(g1.gseq_id-g2.gseq_id);
53 }
54
55 char* GffLine::extractAttr(const char* pre, bool caseStrict, bool enforce_GTF2) {
56 //parse a key attribute and remove it from the info string
57 //(only works for attributes that have values following them after ' ' or '=')
58 static const char GTF2_ERR[]="Error parsing attribute %s ('\"' required) at GTF line:\n%s\n";
59 int lpre=strlen(pre);
60 char cend=pre[lpre-1];
61 char* pos = (caseStrict) ? strstr(info, pre) : strifind(info, pre);
62 if (pos==NULL) return NULL;
63 char* findstart=info;
64 //require word boundary on the left:
65 while (pos!=NULL && pos!=info && *(pos-1)!=';' && *(pos-1)!=' ') {
66 findstart=pos+lpre;
67 pos = (caseStrict) ? strstr(findstart, pre) : strifind(findstart, pre);
68 }
69 if (pos==NULL) return NULL;
70 if (cend!=' ' && cend!='=') {
71 //require word boundary on the right:
72 while (pos!=NULL && *(pos+lpre)!=' ' && *(pos+lpre)!='=') {
73 findstart=pos+lpre;
74 pos = (caseStrict) ? strstr(findstart, pre) : strifind(findstart, pre);
75 }
76 }
77 if (pos==NULL) return NULL;
78 char* vp=pos+lpre;
79 while (*vp==' ') vp++;
80 if (*vp==';' || *vp==0)
81 GError("Error parsing value of GFF attribute \"%s\", line:\n%s\n", pre, dupline);
82 bool dq_enclosed=false; //value string enclosed by double quotes
83 if (*vp=='"') {
84 dq_enclosed=true;
85 vp++;
86 }
87 if (enforce_GTF2 && !dq_enclosed)
88 GError(GTF2_ERR,pre, dupline);
89 char* vend=vp;
90 if (dq_enclosed) {
91 while (*vend!='"' && *vend!=';' && *vend!=0) vend++;
92 }
93 else {
94 while (*vend!=';' && *vend!=0) vend++;
95 }
96 if (enforce_GTF2 && *vend!='"')
97 GError(GTF2_ERR, pre, dupline);
98 char *r=Gstrdup(vp, vend-1);
99 //-- now remove this attribute from the info string
100 while (*vend!=0 && (*vend=='"' || *vend==';' || *vend==' ')) vend++;
101 if (*vend==0) vend--;
102 for (char *src=vend, *dest=pos;;src++,dest++) {
103 *dest=*src;
104 if (*src==0) break;
105 }
106 return r;
107 }
108
109 static char fnamelc[128];
110
111 GffLine::GffLine(GffReader* reader, const char* l) {
112 llen=strlen(l);
113 GMALLOC(line,llen+1);
114 memcpy(line, l, llen+1);
115 GMALLOC(dupline, llen+1);
116 memcpy(dupline, l, llen+1);
117 skip=true;
118 gseqname=NULL;
119 track=NULL;
120 ftype=NULL;
121 info=NULL;
122 _parents=NULL;
123 _parents_len=0;
124 num_parents=0;
125 parents=NULL;
126 is_gff3=false;
127 is_cds=false;
128 is_transcript=false;
129 is_exon=false;
130 is_gene=false;
131 exontype=0;
132 gene_id=NULL;
133 gene_name=NULL;
134 qstart=0;
135 qend=0;
136 qlen=0;
137 ID=NULL;
138 char* t[9];
139 int i=0;
140 int tidx=1;
141 t[0]=line;
142
143 while (line[i]!=0) {
144 if (line[i]=='\t') {
145 line[i]=0;
146 t[tidx]=line+i+1;
147 tidx++;
148 if (tidx>8) break;
149 }
150 i++;
151 }
152
153 if (tidx<8) { // ignore non-GFF lines
154 // GMessage("Warning: error parsing GFF/GTF line:\n%s\n", l);
155 return;
156 }
157 gseqname=t[0];
158 track=t[1];
159 ftype=t[2];
160 info=t[8];
161 char* p=t[3];
162 if (!parseUInt(p,fstart))
163 GError("Error parsing start coordinate from GFF line:\n%s\n",l);
164 p=t[4];
165 if (!parseUInt(p,fend))
166 GError("Error parsing end coordinate from GFF line:\n%s\n",l);
167 if (fend<fstart) swap(fend,fstart); //make sure fstart>=fend, always
168 p=t[5];
169 if (p[0]=='.' && p[1]==0) {
170 score=0;
171 }
172 else {
173 if (!parseDouble(p,score))
174 GError("Error parsing feature score from GFF line:\n%s\n",l);
175 }
176 strand=*t[6];
177 if (strand!='+' && strand!='-' && strand!='.')
178 GError("Error parsing strand (%c) from GFF line:\n%s\n",strand,l);
179 phase=*t[7]; // must be '.', '0', '1' or '2'
180 ID=NULL;
181 // exon/CDS/mrna filter
182 strncpy(fnamelc, ftype, 127);
183 fnamelc[127]=0;
184 strlower(fnamelc); //convert to lower case
185 bool is_t_data=false;
186 if (strstr(fnamelc, "utr")!=NULL) {
187 exontype=exgffUTR;
188 is_exon=true;
189 is_t_data=true;
190 }
191 else if (strstr(fnamelc, "exon")!=NULL) {
192 exontype=exgffExon;
193 is_exon=true;
194 is_t_data=true;
195 }
196 else if (strstr(fnamelc, "stop") &&
197 (strstr(fnamelc, "codon") || strstr(fnamelc, "cds"))){
198 exontype=exgffStop;
199 is_cds=true; //though some place it outside the last CDS segment
200 is_t_data=true;
201 }
202 else if (strstr(fnamelc, "start") &&
203 ((strstr(fnamelc, "codon")!=NULL) || strstr(fnamelc, "cds")!=NULL)){
204 exontype=exgffStart;
205 is_cds=true;
206 is_t_data=true;
207 }
208 else if (strcmp(fnamelc, "cds")==0) {
209 exontype=exgffCDS;
210 is_cds=true;
211 is_t_data=true;
212 }
213 else if (endsWith(fnamelc, "gene") || startsWith(fnamelc, "gene")) {
214 is_gene=true;
215 is_t_data=true; //because its name will be attached to parented transcripts
216 }
217 else if (endsWith(fnamelc,"rna") || endsWith(fnamelc,"transcript")) {
218 is_transcript=true;
219 is_t_data=true;
220 }
221
222 if (reader->transcriptsOnly && !is_t_data) {
223 char* id=extractAttr("ID=");
224 if (id==NULL) id=extractAttr("transcript_id");
225 //GMessage("Discarding non-transcript line:\n%s\n",l);
226 if (id!=NULL) {
227 reader->discarded_ids.Add(id, new int(1));
228 GFREE(id);
229 }
230 return; //skip this line, unwanted feature name
231 }
232 ID=extractAttr("ID=");
233 char* Parent=extractAttr("Parent=");
234 is_gff3=(ID!=NULL || Parent!=NULL);
235 if (is_gff3) {
236 //parse as GFF3
237 if (ID!=NULL) {
238 //has ID attr so it's likely to be a parent feature
239 //look for explicit gene name
240 gene_name=extractAttr("gene_name=",false);
241 if (gene_name==NULL) {
242 gene_name=extractAttr("geneName=",false);
243 if (gene_name==NULL) {
244 gene_name=extractAttr("gene_sym=",false);
245 if (gene_name==NULL) {
246 gene_name=extractAttr("gene=",false);
247 }
248 }
249 }
250 gene_id=extractAttr("geneID=",false);
251 if (gene_id==NULL) {
252 gene_id=extractAttr("gene_id=",false);
253 }
254 if (is_gene) {
255 //special case: keep the Name and ID attributes of the gene feature
256 if (gene_name==NULL)
257 gene_name=extractAttr("Name=");
258 if (gene_id==NULL) //the ID is also gene_id in this case
259 gene_id=Gstrdup(ID);
260 //skip=false;
261 //return;
262 GFREE(Parent); //TMI, we really don't care about gene Parents?
263 } //gene feature
264 }// has GFF3 ID
265 if (Parent!=NULL) {
266 //keep Parent attr
267 //parse multiple parents
268 num_parents=1;
269 p=Parent;
270 int last_delim_pos=-1;
271 while (*p!=';' && *p!=0) {
272 if (*p==',' && *(p+1)!=0 && *(p+1)!=';') {
273 num_parents++;
274 last_delim_pos=(p-Parent);
275 }
276 p++;
277 }
278 _parents_len=p-Parent+1;
279 _parents=Parent;
280 GMALLOC(parents, num_parents*sizeof(char*));
281 parents[0]=_parents;
282 int i=1;
283 if (last_delim_pos>0) {
284 for (p=_parents+1;p<=_parents+last_delim_pos;p++) {
285 if (*p==',') {
286 char* ep=p-1;
287 while (*ep==' ' && ep>_parents) ep--;
288 *(ep+1)=0; //end the string there
289 parents[i]=p+1;
290 i++;
291 }
292 }
293 }
294 } //has Parent field
295 } //GFF3
296 else { // GTF-like expected
297 Parent=extractAttr("transcript_id");
298 if (Parent!=NULL) { //GTF2 format detected
299 if (is_transcript) {
300 // atypical GTF with a parent transcript line declared
301 ID=Parent;
302 Parent=NULL;
303 }
304 gene_id=extractAttr("gene_id"); // for GTF this is the only attribute accepted as geneID
305 gene_name=extractAttr("gene_name");
306 if (gene_name==NULL) {
307 gene_name=extractAttr("gene_sym");
308 if (gene_name==NULL)
309 gene_name=extractAttr("gene");
310 }
311 //prepare for parseAttr by adding '=' character instead of spaces for all attributes
312 //after the attribute name
313 p=info;
314 bool noed=true; //not edited after the last delim
315 bool nsp=false; //non-space found after last delim
316 while (*p!=0) {
317 if (*p==' ') {
318 if (nsp && noed) {
319 *p='=';
320 noed=false;
321 p++;
322 continue;
323 }
324 }
325 else nsp=true; //non-space
326 if (*p==';') { noed=true; nsp=false; }
327 p++;
328 }
329 } //GTF2 detected (no parent line)
330 else {// Parent is NULL, check for jigsaw format or other pre-GTF2 format
331 //char* fexon=strstr(fnamelc, "exon");
332 //if (fexon!=NULL) {
333 if (exontype==exgffExon) {
334 if (startsWith(track,"jigsaw")) {
335 is_cds=true;
336 strcpy(track,"jigsaw");
337 p=strchr(info,';');
338 if (p==NULL) { Parent=Gstrdup(info); info=NULL; }
339 else { Parent=Gstrdup(info,p-1);
340 info=p+1;
341 }
342 }
343 } //exon feature?
344 if (Parent==NULL && exontype>=exgffCDS &&
345 (i=strcspn(info,"; \t\n\r"))<=(int)(strlen(info)+1)) {
346 //one word ID ? really desperate attempt to parse it here
347 Parent=Gstrdup(info,info+i-1);
348 info=NULL; //discard anything else on the line
349 }
350 }
351 if (Parent!=NULL) { //GTF transcript_id for exon/CDS feature
352 _parents=Parent;
353 GMALLOC(parents,sizeof(char*));
354 num_parents=1;
355 parents[0]=_parents;
356 }
357 } //GTF-like
358
359 //parse other potentially useful features
360 if (is_gff3) {
361 if ((p=strstr(info,"Target="))!=NULL) { //has Target attr
362 p+=7;
363 while (*p!=';' && *p!=0 && *p!=' ') p++;
364 if (*p!=' ') {
365 GError("Error parsing target coordinates from GFF line:\n%s\n",l);
366 }
367 if (!parseUInt(p,qstart))
368 GError("Error parsing target start coordinate from GFF line:\n%s\n",l);
369 if (*p!=' ') {
370 GError("Error parsing next target coordinate from GFF line:\n%s\n",l);
371 }
372 p++;
373 if (!parseUInt(p,qend))
374 GError("Error parsing target end coordinate from GFF line:\n%s\n",l);
375 }
376 if ((p=strifind(info,"Qreg="))!=NULL) { //has Qreg attr
377 p+=5;
378 if (!parseUInt(p,qstart))
379 GError("Error parsing target start coordinate from GFF line:\n%s\n",l);
380 if (*p!='-') {
381 GError("Error parsing next target coordinate from GFF line:\n%s\n",l);
382 }
383 p++;
384 if (!parseUInt(p,qend))
385 GError("Error parsing target end coordinate from GFF line:\n%s\n",l);
386 if (*p=='|' || *p==':') {
387 p++;
388 if (!parseUInt(p,qlen))
389 GError("Error parsing target length from GFF Qreg|: \n%s\n",l);
390 }
391 }//has Qreg attr
392 if (qlen==0 && (p=strifind(info,"Qlen="))!=NULL) {
393 p+=5;
394 if (!parseUInt(p,qlen))
395 GError("Error parsing target length from GFF Qlen:\n%s\n",l);
396 }
397 }//parsing some useful attributes in GFF3 records
398 if (ID==NULL && parents==NULL) {
399 if (reader->gff_warns)
400 GMessage("Warning: could not parse ID or Parent from GFF line:\n%s\n",dupline);
401 return; //skip
402 }
403 skip=false;
404 }
405
406 int GffObj::addExon(GffReader* reader, GffLine* gl, bool keepAttr, bool noExonAttr) {
407 //this will make sure we have the right subftype_id!
408 int subf_id=-1;
409 //if (ftype_id==gff_fid_mRNA) { //for mRNAs only parse known subfeatures!
410 if (isTranscript()) {
411 if (exon_ftype_id<0) {//exon_ftype_id=gff_fid_exon;
412 if (gl->exontype>0) exon_ftype_id=gff_fid_exon;
413 else exon_ftype_id=names->feats.addName(gl->ftype);
414 }
415 //any recognized mRNA segment gets the generic "exon" type (also applies to CDS)
416 if (gl->exontype==0 && !gl->is_transcript) {
417 //extraneous mRNA feature, discard
418 if (reader->gff_warns)
419 GMessage("Warning: discarding unrecognized transcript subfeature %s of %s\n",
420 gl->ftype, gffID);
421 return -1;
422 }
423 }
424 else { //non-mRNA parent feature, check this subf type
425 subf_id=names->feats.addName(gl->ftype);
426 if (exon_ftype_id<0 || exons.Count()==0) //never assigned a subfeature type before (e.g. first exon being added)
427 exon_ftype_id=subf_id;
428 else {
429 if (exon_ftype_id!=subf_id) {
430 //if (subftype_id==ftype_id && exons.Count()==1 && exons[0]->start==start && exons[0]->end==end) {
431 if (exon_ftype_id==ftype_id && exons.Count()==1 && exons[0]->start==start && exons[0]->end==end) {
432 //the existing exon was just a dummy one created by default, discard it
433 exons.Clear();
434 covlen=0;
435 exon_ftype_id=subf_id; //allow the new subfeature to completely takeover
436 }
437 else { //multiple subfeatures, prefer those with
438 if (reader->gff_warns)
439 GMessage("GFF Warning: multiple subfeatures (%s and %s) found for %s, discarding ",
440 names->feats.getName(subf_id), names->feats.getName(exon_ftype_id),gffID);
441 if (gl->exontype!=0) { //new feature is an exon, discard previously parsed subfeatures
442 if (reader->gff_warns) GMessage("%s.\n", names->feats.getName(exon_ftype_id));
443 exon_ftype_id=subf_id;
444 exons.Clear();
445 covlen=0;
446 }
447 else { //discard new feature
448 if (reader->gff_warns) GMessage("%s.\n", names->feats.getName(subf_id));
449 return -1; //skip this 2nd subfeature type for this parent!
450 }
451 }
452 } //incoming subfeature is of different type
453 } //new subfeature type
454 } //non-mRNA parent
455 int eidx=addExon(gl->fstart, gl->fend, gl->score, gl->phase,
456 gl->qstart,gl->qend, gl->is_cds, gl->exontype);
457 if (eidx<0) return eidx; //this should never happen
458 if (keepAttr) {
459 if (noExonAttr) {
460 if (attrs==NULL) //place the parsed attributes directly at transcript level
461 parseAttrs(attrs, gl->info);
462 }
463 else { //need all exon-level attributes
464 parseAttrs(exons[eidx]->attrs, gl->info, true);
465 }
466 }
467 return eidx;
468 }
469
470
471 int GffObj::addExon(uint segstart, uint segend, double sc, char fr, int qs, int qe, bool iscds, char exontype) {
472 if (exons.Count()==0) {
473 if (iscds) isCDS=true; //for now, assume CDS only if first "exon" given is a CDS
474 if (exon_ftype_id<0) {
475 exon_ftype_id = isTranscript() ? gff_fid_exon : ftype_id;
476 }
477 }
478 //special treatment of start/stop codon features, they might be broken/split between exons
479 //and in that case some providers will still give the wrong end coordinate as start+2 (e.g. UCSC)
480 //so we should not trust the end coordinate for such features
481 if (exontype==exgffStart || exontype==exgffStop) {
482 if (strand=='-') segstart=segend;
483 else segend=segstart;
484 if (exontype==exgffStart) {
485 if (CDstart==0 || segstart<CDstart) CDstart=segstart;
486 }
487 else {
488 if (segstart>CDend) CDend=segstart;
489 }
490 }
491 else if (iscds) { //update CDS anchors:
492 if (CDstart==0 || segstart<CDstart) {
493 CDstart=segstart;
494 if (exontype==exgffCDS && strand=='+') CDphase=fr;
495 }
496 if (segend>CDend) {
497 if (exontype==exgffCDS && strand=='-') CDphase=fr;
498 CDend=segend;
499 }
500 }
501 else { // not a CDS/start/stop
502 isCDS=false;
503 }
504 if (qs || qe) {
505 if (qs>qe) swap(qs,qe);
506 if (qs==0) qs=1;
507 }
508 if (exontype>0) { //check for overlaps between exon-type segments
509 int ovlen=0;
510 int oi=exonOverlapIdx(segstart, segend, &ovlen);
511 if (oi>=0) { //overlap existing segment
512 if (ovlen==0) {
513 //adjacent segments will be merged
514 if ((exons[oi]->exontype==exgffUTR && exontype==exgffCDS) ||
515 (exons[oi]->exontype==exgffCDS && exontype==exgffUTR)) {
516 expandExon(oi, segstart, segend, exgffCDSUTR, sc, fr, qs, qe);
517 return oi;
518 }
519 }
520 //only allow this for CDS within exon, stop_codon within exon, stop_codon within UTR,
521 // start_codon within CDS or stop_codon within CDS
522 if (exons[oi]->exontype>exontype &&
523 exons[oi]->start<=segstart && exons[oi]->end>=segend &&
524 !(exons[oi]->exontype==exgffUTR && exontype==exgffCDS)) {
525 //larger segment given first, now the smaller included one is redundant
526 return oi; //only used to store attributes from current GffLine
527 }
528 if (exontype>exons[oi]->exontype &&
529 segstart<=exons[oi]->start && segend>=exons[oi]->end &&
530 !(exontype==exgffUTR && exons[oi]->exontype==exgffCDS)) {
531 //smaller segment given first, so we have to enlarge it
532 expandExon(oi, segstart, segend, exontype, sc, fr, qs, qe);
533 //this should also check for overlapping next exon (oi+1) ?
534 return oi;
535 }
536 //there is also the special case of "ribosomal slippage exception" (programmed frameshift)
537 //where two CDS segments may actually overlap for 1 or 2 bases, but there should be only one encompassing exon
538 //if (ovlen>2 || exons[oi]->exontype!=exgffCDS || exontype!=exgffCDS) {
539 // --> had to relax this because of some weird UCSC annotations with exons partially overlapping the CDS segments
540 if (ovlen>2 && exons[oi]->exontype!=exgffUTR && exontype!=exgffUTR) {
541 //important structural warning, will always print:
542 if (gff_show_warnings)
543 GMessage("GFF Warning: discarding overlapping feature segment (%d-%d) (vs %d-%d (%s)) for GFF ID %s on %s\n",
544 segstart, segend, exons[oi]->start, exons[oi]->end, getSubfName(), gffID, getGSeqName());
545 hasErrors(true);
546 return -1; //segment NOT added
547 }
548 // else add the segment if the overlap is small and between two CDS segments
549 //TODO: we might want to add an attribute here with the slippage coordinate and size?
550 }//overlap of existing segment
551 } //check for overlap
552 // --- no overlap, or accepted micro-overlap (ribosomal slippage)
553 // create & add the new segment
554 GffExon* enew=new GffExon(segstart, segend, sc, fr, qs, qe, exontype);
555 int eidx=exons.Add(enew);
556 if (eidx<0) {
557 //this would actually be acceptable if the object is a "Gene" and "exons" are in fact isoforms
558 if (gff_show_warnings)
559 GMessage("GFF Warning: failed adding segment %d-%d for %s (discarded)!\n",
560 segstart, segend, gffID);
561 delete enew;
562 hasErrors(true);
563 return -1;
564 }
565 covlen+=(int)(exons[eidx]->end-exons[eidx]->start)+1;
566 start=exons.First()->start;
567 end=exons.Last()->end;
568 if (uptr!=NULL) { //collect stats about the underlying genomic sequence
569 GSeqStat* gsd=(GSeqStat*)uptr;
570 if (start<gsd->mincoord) gsd->mincoord=start;
571 if (end>gsd->maxcoord) gsd->maxcoord=end;
572 if (this->len()>gsd->maxfeat_len) {
573 gsd->maxfeat_len=this->len();
574 gsd->maxfeat=this;
575 }
576 }
577 return eidx;
578 }
579
580 void GffObj::expandExon(int oi, uint segstart, uint segend, char exontype, double sc, char fr, int qs, int qe) {
581 //oi is the index of the *first* overlapping segment found that must be enlarged
582 covlen-=exons[oi]->len();
583 if (segstart<exons[oi]->start)
584 exons[oi]->start=segstart;
585 if (qs && qs<exons[oi]->qstart) exons[oi]->qstart=qs;
586 if (segend>exons[oi]->end)
587 exons[oi]->end=segend;
588 if (qe && qe>exons[oi]->qend) exons[oi]->qend=qe;
589 //warning: score cannot be properly adjusted! e.g. if it's a p-value it's just going to get worse
590 if (sc!=0) exons[oi]->score=sc;
591 covlen+=exons[oi]->len();
592 //if (exons[oi]->exontype< exontype) -- always true
593 exons[oi]->exontype = exontype;
594 if (exontype==exgffCDS) exons[oi]->phase=fr;
595 //we must check if any more exons are also overlapping this
596 int ni=oi+1; //next exon index after oi
597 while (ni<exons.Count() && segend>=exons[ni]->start) { // next segment overlaps new enlarged segment
598 //only allow this if next segment is fully included, and a subordinate
599 if (exons[ni]->exontype<exontype && exons[ni]->end<=segend) {
600 /* I guess we have to relax this due to stupid UCSC hg18 files having a start_codon sticking out
601 chr1 hg18_knownGene start_codon 69806911 69806913 0.000000 + .
602 chr1 hg18_knownGene CDS 69806911 69806912 0.000000 + 0
603 chr1 hg18_knownGene exon 69805456 69806912 0.000000 + .
604 */
605 if (exons[ni]->qstart<exons[oi]->qstart) exons[oi]->qstart=exons[ni]->qstart;
606 if (exons[ni]->qend>exons[oi]->qend) exons[oi]->qend=exons[ni]->qend;
607 exons.Delete(ni);
608 }
609 else {
610 if (gff_show_warnings) GMessage("GFF Warning: overlapping existing exon(%d-%d) while expanding to %d-%d for GFF ID %s\n",
611 exons[ni]->start, exons[ni]->end, segstart, segend, gffID);
612 //hasErrors(true);
613 break;
614 }
615 }
616 // -- make sure any other related boundaries are updated:
617 start=exons.First()->start;
618 end=exons.Last()->end;
619 if (uptr!=NULL) { //collect stats about the underlying genomic sequence
620 GSeqStat* gsd=(GSeqStat*)uptr;
621 if (start<gsd->mincoord) gsd->mincoord=start;
622 if (end>gsd->maxcoord) gsd->maxcoord=end;
623 if (this->len()>gsd->maxfeat_len) {
624 gsd->maxfeat_len=this->len();
625 gsd->maxfeat=this;
626 }
627 }
628 }
629
630 void GffObj::removeExon(int idx) {
631 /*
632 if (idx==0 && segs[0].start==gstart)
633 gstart=segs[1].start;
634 if (idx==segcount && segs[segcount].end==gend)
635 gend=segs[segcount-1].end;
636 */
637 if (idx<0 || idx>=exons.Count()) return;
638 int segstart=exons[idx]->start;
639 int segend=exons[idx]->end;
640 exons.Delete(idx);
641 covlen -= (int)(segend-segstart)+1;
642 start=exons.First()->start;
643 end=exons.Last()->end;
644 if (isCDS) { CDstart=start; CDend=end; }
645 }
646
647 void GffObj::removeExon(GffExon* p) {
648 for (int idx=0;idx<exons.Count();idx++) {
649 if (exons[idx]==p) {
650 int segstart=exons[idx]->start;
651 int segend=exons[idx]->end;
652 exons.Delete(idx);
653 covlen -= (int)(segend-segstart)+1;
654 start=exons.First()->start;
655 end=exons.Last()->end;
656 if (isCDS) { CDstart=start; CDend=end; }
657 return;
658 }
659 }
660 }
661
662
663
664 GffObj::GffObj(GffReader *gfrd, GffLine* gffline, bool keepAttr, bool noExonAttr):
665 GSeg(0,0), exons(true,true,false), children(1,false) {
666 xstart=0;
667 xend=0;
668 xstatus=0;
669 partial=false;
670 isCDS=false;
671 uptr=NULL;
672 ulink=NULL;
673 parent=NULL;
674 udata=0;
675 flags=0;
676 CDstart=0;
677 CDend=0;
678 CDphase=0;
679 geneID=NULL;
680 gene_name=NULL;
681 attrs=NULL;
682 gffID=NULL;
683 track_id=-1;
684 gseq_id=-1;
685 ftype_id=-1;
686 exon_ftype_id=-1;
687 strand='.';
688 if (gfrd==NULL)
689 GError("Cannot use this GffObj constructor with a NULL GffReader!\n");
690 gffnames_ref(names);
691 if (gfrd->names==NULL) gfrd->names=names;
692 //qlen=0;qstart=0;qend=0;
693 gscore=0;
694 uscore=0;
695 covlen=0;
696 qcov=0;
697 start=gffline->fstart;
698 end=gffline->fend;
699 gseq_id=names->gseqs.addName(gffline->gseqname);
700 track_id=names->tracks.addName(gffline->track);
701 strand=gffline->strand;
702 qlen=gffline->qlen;
703 qstart=gffline->qstart;
704 qend=gffline->qend;
705 //setup flags from gffline
706 isCDS=gffline->is_cds; //for now
707 isGene(gffline->is_gene);
708 isTranscript(gffline->is_transcript || gffline->exontype!=0);
709 fromGff3(gffline->is_gff3);
710
711 if (gffline->parents!=NULL) {
712 //GTF style -- create a GffObj directly by subfeature
713 //(also possible orphan GFF3 exon line, or an exon given before its parent (chado))
714 if (gffline->exontype!=0) { //recognized exon-like feature
715 ftype_id=gff_fid_transcript; //so this is some sort of transcript
716 exon_ftype_id=gff_fid_exon; //subfeatures MUST be exons
717 }
718 else {//unrecognized subfeatures
719 //make this GffObj of the same feature type
720 ftype_id=names->feats.addName(gffline->ftype);
721 }
722 if (gffline->ID==NULL) { //typical GTF
723 gffID=Gstrdup(gffline->parents[0]);
724 this->createdByExon(true);
725 //this is likely the first exon/segment of the feature
726 addExon(gfrd, gffline, keepAttr, noExonAttr);
727 }
728 else { //a parented feature with an ID -- probably an orphan GFF3 line
729 if (gffline->is_gff3 && gffline->exontype!=0) {
730 //premature exon given before its parent transcript
731 //create the transcript entry here
732 gffID=Gstrdup(gffline->parents[0]);
733 this->createdByExon(true);
734 //this is the first exon/segment of the transcript
735 addExon(gfrd, gffline, keepAttr, noExonAttr);
736 }
737 else { //unrecognized non-exon feature ? use the ID instead
738 gffID=Gstrdup(gffline->ID);
739 if (keepAttr) this->parseAttrs(attrs, gffline->info);
740 }
741 }
742 } //subfeature given directly
743 else { //gffline->parents==NULL
744 //create a parent feature in its own right
745 gscore=gffline->score;
746 if (gffline->ID==NULL || gffline->ID[0]==0)
747 GError("Error: no ID found for GFF record start\n");
748 gffID=Gstrdup(gffline->ID); //there must be an ID here
749 //if (gffline->is_transcript) ftype_id=gff_fid_mRNA;
750 //else
751 ftype_id=names->feats.addName(gffline->ftype);
752 if (gffline->is_transcript)
753 exon_ftype_id=gff_fid_exon;
754
755 if (keepAttr) this->parseAttrs(attrs, gffline->info);
756 }//no parent
757
758 if (gffline->gene_name!=NULL) {
759 gene_name=Gstrdup(gffline->gene_name);
760 }
761 if (gffline->gene_id!=NULL) {
762 geneID=Gstrdup(gffline->gene_id);
763 }
764
765 GSeqStat* gsd=gfrd->gseqstats.AddIfNew(new GSeqStat(gseq_id,names->gseqs.lastNameUsed()),true);
766 uptr=gsd;
767 if (start<gsd->mincoord) gsd->mincoord=start;
768 if (end>gsd->maxcoord) gsd->maxcoord=end;
769 if (this->len()>gsd->maxfeat_len) {
770 gsd->maxfeat_len=this->len();
771 gsd->maxfeat=this;
772 }
773 }
774
775 GffLine* GffReader::nextGffLine() {
776 if (gffline!=NULL) return gffline; //caller should free gffline after processing
777 while (gffline==NULL) {
778 int llen=0;
779 buflen=GFF_LINELEN-1;
780 char* l=fgetline(linebuf, buflen, fh, &fpos, &llen);
781 if (l==NULL) {
782 return NULL; //end of file
783 }
784 int ns=0; //first nonspace position
785 while (l[ns]!=0 && isspace(l[ns])) ns++;
786 if (l[ns]=='#' || llen<10) continue;
787 gffline=new GffLine(this, l);
788 if (gffline->skip) {
789 delete gffline;
790 gffline=NULL;
791 continue;
792 }
793 if (gffline->ID==NULL && gffline->parents==NULL) { //it must have an ID
794 //this might not be needed, already checked in the GffLine constructor
795 if (gff_warns)
796 GMessage("Warning: malformed GFF line, no parent or record Id (kipping\n");
797 delete gffline;
798 gffline=NULL;
799 //continue;
800 }
801 }
802 return gffline;
803 }
804
805 char* GffReader::gfoBuildId(const char* id, const char* ctg) {
806 //caller must free the returned pointer
807 char* buf=NULL;
808 int idlen=strlen(id);
809 GMALLOC(buf, idlen+strlen(ctg)+2);
810 strcpy(buf, id);
811 buf[idlen]='~';
812 strcpy(buf+idlen+1, ctg);
813 return buf;
814 }
815
816 void GffReader::gfoRemove(const char* id, const char* ctg) {
817 char* buf=gfoBuildId(id,ctg);
818 phash.Remove(buf);
819 GFREE(buf);
820 }
821
822 //Warning: if gflst gets altered, idx becomes obsolete
823 GfoHolder* GffReader::gfoAdd(const char* id, const char* ctg, GffObj* gfo, int idx) {
824 char* buf=gfoBuildId(id,ctg);
825 GfoHolder* r=new GfoHolder(gfo,idx);
826 phash.Add(buf, r);
827 GFREE(buf);
828 return r;
829 }
830
831 GfoHolder* GffReader::gfoFind(const char* id, const char* ctg) {
832 char* buf=gfoBuildId(id,ctg);
833 GfoHolder* r=phash.Find(buf);
834 GFREE(buf);
835 return r;
836 }
837
838 GfoHolder* GffReader::replaceGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr, int replaceidx) {
839 GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
840 GfoHolder* r=NULL;
841 if (replaceidx>=0) {
842 gflst.Put(replaceidx,newgfo);
843 r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, replaceidx);
844 }
845 else {
846 int gfoidx=gflst.Add(newgfo);
847 r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, gfoidx);
848 }
849 if (gff_warns) {
850 int* pcount=tids.Find(newgfo->gffID);
851 if (pcount!=NULL) {
852 if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
853 (*pcount)++;
854 }
855 else {
856 tids.Add(newgfo->gffID,new int(1));
857 }
858 }
859 return r;
860 }
861
862 GfoHolder* GffReader::updateParent(GfoHolder* newgfh, GffObj* parent) {
863 //assert(parent);
864 //assert(newgfo);
865 parent->children.Add(newgfh->gffobj);
866 if (newgfh->gffobj->parent==NULL) newgfh->gffobj->parent=parent;
867 newgfh->gffobj->setLevel(parent->getLevel()+1);
868 if (parent->isGene()) {
869 if (parent->gene_name!=NULL && newgfh->gffobj->gene_name==NULL)
870 newgfh->gffobj->gene_name=Gstrdup(parent->gene_name);
871 if (parent->geneID!=NULL && newgfh->gffobj->geneID==NULL)
872 newgfh->gffobj->geneID=Gstrdup(parent->geneID);
873 }
874
875 return newgfh;
876 }
877
878 GfoHolder* GffReader::newGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr,
879 GffObj* parent, GffExon* pexon) {
880 GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
881 GfoHolder* r=NULL;
882 int gfoidx=gflst.Add(newgfo);
883 r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, gfoidx);
884 if (parent!=NULL) {
885 updateParent(r, parent);
886 if (pexon!=NULL) parent->removeExon(pexon);
887 }
888 if (gff_warns) {
889 int* pcount=tids.Find(newgfo->gffID);
890 if (pcount!=NULL) {
891 if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
892 (*pcount)++;
893 }
894 else {
895 tids.Add(newgfo->gffID,new int(1));
896 }
897 }
898 return r;
899 }
900
901 GfoHolder* GffReader::updateGffRec(GfoHolder* prevgfo, GffLine* gffline,
902 bool keepAttr) {
903 if (prevgfo==NULL) return NULL;
904 prevgfo->gffobj->createdByExon(false);
905 prevgfo->gffobj->ftype_id=prevgfo->gffobj->names->feats.addName(gffline->ftype);
906 prevgfo->gffobj->start=gffline->fstart;
907 prevgfo->gffobj->end=gffline->fend;
908 prevgfo->gffobj->isGene(gffline->is_gene);
909 prevgfo->gffobj->isTranscript(gffline->is_transcript || gffline->exontype!=0);
910 prevgfo->gffobj->fromGff3(gffline->is_gff3);
911 if (keepAttr) {
912 if (prevgfo->gffobj->attrs!=NULL) prevgfo->gffobj->attrs->Clear();
913 prevgfo->gffobj->parseAttrs(prevgfo->gffobj->attrs, gffline->info);
914 }
915 return prevgfo;
916 }
917
918
919 bool GffReader::addExonFeature(GfoHolder* prevgfo, GffLine* gffline, GHash<CNonExon>& pex, bool noExonAttr) {
920 bool r=true;
921 if (gffline->strand!=prevgfo->gffobj->strand) {
922 GMessage("GFF Error: duplicate GFF ID '%s' (exons found on different strands of %s)\n",
923 prevgfo->gffobj->gffID, prevgfo->gffobj->getGSeqName());
924 r=false;
925 }
926 int gdist=(gffline->fstart>prevgfo->gffobj->end) ? gffline->fstart-prevgfo->gffobj->end :
927 ((gffline->fend<prevgfo->gffobj->start)? prevgfo->gffobj->start-gffline->fend :
928 0 );
929 if (gdist>(int)GFF_MAX_LOCUS) { //too far apart, most likely this is a duplicate ID
930 GMessage("Error: duplicate GFF ID '%s' (or exons too far apart)!\n",prevgfo->gffobj->gffID);
931 //validation_errors = true;
932 r=false;
933 if (!gff_warns) exit(1);
934 }
935 int eidx=prevgfo->gffobj->addExon(this, gffline, !noExonAttr, noExonAttr);
936 if (eidx>=0 && gffline->ID!=NULL && gffline->exontype==0)
937 subfPoolAdd(pex, prevgfo);
938 return r;
939 }
940
941 CNonExon* GffReader::subfPoolCheck(GffLine* gffline, GHash<CNonExon>& pex, char*& subp_name) {
942 CNonExon* subp=NULL;
943 subp_name=NULL;
944 for (int i=0;i<gffline->num_parents;i++) {
945 if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
946 continue;
947 subp_name=gfoBuildId(gffline->parents[i], gffline->gseqname); //e.g. mRNA name
948 subp=pex.Find(subp_name);
949 if (subp!=NULL)
950 return subp;
951 GFREE(subp_name);
952 }
953 return NULL;
954 }
955
956 void GffReader::subfPoolAdd(GHash<CNonExon>& pex, GfoHolder* newgfo) {
957 //this might become a parent feature later
958 if (newgfo->gffobj->exons.Count()>0) {
959 char* xbuf=gfoBuildId(gffline->ID, gffline->gseqname);
960 pex.Add(xbuf, new CNonExon(newgfo->idx, newgfo->gffobj,
961 newgfo->gffobj->exons[0], gffline));
962 GFREE(xbuf);
963 }
964 }
965
966 GfoHolder* GffReader::promoteFeature(CNonExon* subp, char*& subp_name, GHash<CNonExon>& pex,
967 bool keepAttr, bool noExonAttr) {
968 GffObj* prevp=subp->parent; //grandparent of gffline (e.g. gene)
969 if (prevp!=gflst[subp->idx])
970 GError("Error promoting subfeature %s, gflst index mismatch?!\n", subp->gffline->ID);
971 subp->gffline->discardParent();
972 GfoHolder* gfoh=newGffRec(subp->gffline, keepAttr, noExonAttr, prevp, subp->exon);
973 pex.Remove(subp_name); //no longer a potential parent, moved it to phash already
974 prevp->promotedChildren(true);
975 return gfoh; //returns the holder of newly promoted feature
976 }
977
978 //have to parse the whole file because exons can be scattered all over
979 void GffReader::readAll(bool keepAttr, bool mergeCloseExons, bool noExonAttr) {
980 bool validation_errors = false;
981 //loc_debug=false;
982 GHash<CNonExon> pex; //keep track of any "exon"-like features that have an ID
983 //and thus could become promoted to parent features
984 while (nextGffLine()!=NULL) {
985 //seen this gff ID before?
986 GfoHolder* prevseen=NULL;
987 if (gffline->ID) //GFF3
988 prevseen=gfoFind(gffline->ID, gffline->gseqname);
989 if (prevseen!=NULL) {
990 if (prevseen->gffobj->createdByExon()) {
991 updateGffRec(prevseen, gffline, keepAttr);
992 }
993 else {
994 GMessage("Error: duplicate GFF ID '%s' encountered!\n",gffline->ID);
995 validation_errors = true;
996 if (gff_warns) {
997 delete gffline; gffline=NULL; continue;
998 }
999 else exit(1);
1000 }
1001 }
1002 if (gffline->parents==NULL) {//start GFF3-like record with no parent (mRNA, gene)
1003 if (!prevseen) newGffRec(gffline, keepAttr, noExonAttr);
1004 }
1005 else { //--- it's a parented feature (could still be a mRNA)
1006 bool found_parent=false;
1007 GfoHolder* newgfo=prevseen;
1008 for (int i=0;i<gffline->num_parents;i++) {
1009 if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
1010 continue; //skipping discarded parent feature
1011 GfoHolder* parentgfo=gfoFind(gffline->parents[i], gffline->gseqname);
1012 if (parentgfo!=NULL) { //parent GffObj parsed earlier
1013 found_parent=true;
1014 if (parentgfo->gffobj->isGene() && gffline->is_transcript
1015 && gffline->exontype==0) {
1016 //not an exon, but a transcript parented by a gene
1017 if (newgfo) {
1018 updateParent(newgfo, parentgfo->gffobj);
1019 }
1020 else {
1021 newgfo=newGffRec(gffline, keepAttr, noExonAttr, parentgfo->gffobj);
1022 }
1023 }
1024 else { //potential exon subfeature
1025 if (!addExonFeature(parentgfo, gffline, pex, noExonAttr))
1026 validation_errors=true;
1027 }
1028 }
1029 } //for each parsed parent Id
1030 if (!found_parent) { //new GTF-like record starting here with a subfeature directly
1031 //or it could be some chado GFF3 barf with exons declared BEFORE their parent :(
1032 //check if this feature isn't parented by a previously stored "exon" subfeature
1033 char* subp_name=NULL;
1034 CNonExon* subp=subfPoolCheck(gffline, pex, subp_name);
1035 if (subp!=NULL) { //found a subfeature that is the parent of this gffline
1036 //promote that subfeature to a full GffObj
1037 GfoHolder* gfoh=promoteFeature(subp, subp_name, pex, keepAttr, noExonAttr);
1038 //add current gffline as an exon of the newly promoted subfeature
1039 if (!addExonFeature(gfoh, gffline, pex, noExonAttr))
1040 validation_errors=true;
1041 }
1042 else { //no parent seen before, create one directly with this exon
1043 //loc_debug=true;
1044 GfoHolder* newgfo=prevseen ? prevseen : newGffRec(gffline, keepAttr, noExonAttr);
1045 if (gffline->ID!=NULL && gffline->exontype==0)
1046 subfPoolAdd(pex, newgfo);
1047 //even those with errors will be added here!
1048 }
1049 GFREE(subp_name);
1050 } //no previous parent found
1051 } //parented feature
1052 //--
1053 delete gffline;
1054 gffline=NULL;
1055 }//while gff lines
1056 gflst.finalize(this, mergeCloseExons, keepAttr, noExonAttr); //force sorting by locus if so constructed
1057 // all gff records are now loaded in GList gflst
1058 // so we can free the hash
1059 phash.Clear();
1060 tids.Clear();
1061 if (validation_errors) {
1062 exit(1);
1063 }
1064 }
1065
1066 GffObj* GffObj::finalize(GffReader* gfr, bool mergeCloseExons, bool keepAttrs, bool noExonAttr) {
1067 //merge
1068 //always merge adjacent or overlapping segments
1069 //but if mergeCloseExons then merge even when distance is up to 5 bases
1070 udata=0;
1071 uptr=NULL;
1072 if (gfr->transcriptsOnly && !(isTranscript() || (isGene() && children.Count()==0))) {
1073 isDiscarded(true);
1074 }
1075 if (ftype_id==gff_fid_transcript && CDstart>0) {
1076 ftype_id=gff_fid_mRNA;
1077 //exon_ftype_id=gff_fid_exon;
1078 }
1079 //if (ftype_id==gff_fid_mRNA || exon_ftype_id==gff_fid_exon || mergeCloseExons) {
1080 if (isTranscript() || exon_ftype_id==gff_fid_exon || mergeCloseExons) {
1081 int mindist=mergeCloseExons ? 5:1;
1082 for (int i=0;i<exons.Count()-1;i++) {
1083 int ni=i+1;
1084 uint mend=exons[i]->end;
1085 while (ni<exons.Count()) {
1086 int dist=(int)(exons[ni]->start-mend);
1087 if (dist>mindist) break; //no merging with next segment
1088 if (gfr!=NULL && gfr->gff_warns && dist!=0 && (exons[ni]->exontype!=exgffUTR && exons[i]->exontype!=exgffUTR)) {
1089 GMessage("GFF warning: merging adjacent/overlapping segments of %s on %s (%d-%d, %d-%d)\n",
1090 gffID, getGSeqName(), exons[i]->start, exons[i]->end,exons[ni]->start, exons[ni]->end);
1091 }
1092 mend=exons[ni]->end;
1093 covlen-=exons[i]->len();
1094 exons[i]->end=mend;
1095 covlen+=exons[i]->len();
1096 covlen-=exons[ni]->len();
1097 if (exons[ni]->attrs!=NULL && (exons[i]->attrs==NULL ||
1098 exons[i]->attrs->Count()<exons[ni]->attrs->Count())) {
1099 //use the other exon attributes, if more
1100 delete(exons[i]->attrs);
1101 exons[i]->attrs=exons[ni]->attrs;
1102 exons[ni]->attrs=NULL;
1103 }
1104 exons.Delete(ni);
1105 } //check for merge with next exon
1106 } //for each exon
1107 }
1108 //attribute reduction for GTF records
1109 if (keepAttrs && !noExonAttr && !fromGff3()
1110 && exons.Count()>0 && exons[0]->attrs!=NULL) {
1111 bool attrs_discarded=false;
1112 for (int a=0;a<exons[0]->attrs->Count();a++) {
1113 int attr_name_id=exons[0]->attrs->Get(a)->attr_id;
1114 char* attr_name=names->attrs.getName(attr_name_id);
1115 char* attr_val =exons[0]->attrs->Get(a)->attr_val;
1116 bool sameExonAttr=true;
1117 for (int i=1;i<exons.Count();i++) {
1118 char* ov=exons[i]->getAttr(attr_name_id);
1119 if (ov==NULL || (strcmp(ov,attr_val)!=0)) {
1120 sameExonAttr=false;
1121 break;
1122 }
1123 }
1124 if (sameExonAttr) {
1125 //delete this attribute from exons level
1126 attrs_discarded=true;
1127 this->addAttr(attr_name, attr_val);
1128 for (int i=1;i<exons.Count();i++) {
1129 removeExonAttr(*(exons[i]), attr_name_id);
1130 }
1131 exons[0]->attrs->freeItem(a);
1132 }
1133 }
1134 if (attrs_discarded) exons[0]->attrs->Pack();
1135 }
1136 return this;
1137 }
1138
1139 void GffObj::parseAttrs(GffAttrs*& atrlist, char* info, bool isExon) {
1140 if (names==NULL)
1141 GError(ERR_NULL_GFNAMES, "parseAttrs()");
1142 if (atrlist==NULL)
1143 atrlist=new GffAttrs();
1144 char* endinfo=info+strlen(info);
1145 char* start=info;
1146 char* pch=start;
1147 while (start<endinfo) {
1148 //skip spaces
1149 while (*start==' ' && start<endinfo) start++;
1150 pch=strchr(start, ';');
1151 if (pch==NULL) pch=endinfo;
1152 else {
1153 *pch='\0';
1154 pch++;
1155 }
1156 char* ech=strchr(start,'=');
1157 if (ech!=NULL) { // attr=value format found
1158 *ech='\0';
1159 //if (noExonAttr && (strcmp(start, "exon_number")==0 || strcmp(start, "exon")==0)) { start=pch; continue; }
1160 if (strcmp(start, "exon_number")==0 || strcmp(start, "exon")==0 ||
1161 strcmp(start, "exon_id")==0)
1162 { start=pch; continue; }
1163 ech++;
1164 while (*ech==' ' && ech<endinfo) ech++;//skip extra spaces after the '='
1165 //atrlist->Add(new GffAttr(names->attrs.addName(start),ech));
1166 //make sure we don't add the same attribute more than once
1167 if (isExon && (strcmp(start, "protein_id")==0)) {
1168 //Ensembl special case
1169 this->addAttr(start, ech);
1170 start=pch;
1171 continue;
1172 }
1173 atrlist->add_or_update(names, start, ech);
1174 }
1175 /*
1176 else { //not an attr=value format
1177 atrlist->Add(new GffAttr(names->attrs.addName(start),"1"));
1178 }
1179 */
1180 start=pch;
1181 }
1182 if (atrlist->Count()==0) { delete atrlist; atrlist=NULL; }
1183 }
1184
1185 void GffObj::addAttr(const char* attrname, const char* attrvalue) {
1186 if (this->attrs==NULL)
1187 this->attrs=new GffAttrs();
1188 //this->attrs->Add(new GffAttr(names->attrs.addName(attrname),attrvalue));
1189 this->attrs->add_or_update(names, attrname, attrvalue);
1190 }
1191
1192
1193 void GffObj::setFeatureName(const char* feature) {
1194 //change the feature name/type for a transcript
1195 int fid=names->feats.addName(feature);
1196 if (monoFeature() && exons.Count()>0)
1197 this->exon_ftype_id=fid;
1198 this->ftype_id=fid;
1199 }
1200
1201 void GffObj::setRefName(const char* newname) {
1202 //change the feature name/type for a transcript
1203 int rid=names->gseqs.addName(newname);
1204 this->gseq_id=rid;
1205 }
1206
1207
1208
1209 int GffObj::removeAttr(const char* attrname, const char* attrval) {
1210 if (this->attrs==NULL || attrname==NULL || attrname[0]==0) return 0;
1211 int aid=this->names->attrs.getId(attrname);
1212 if (aid<0) return 0;
1213 int delcount=0; //could be more than one ?
1214 for (int i=0;i<this->attrs->Count();i++) {
1215 if (aid==this->attrs->Get(i)->attr_id) {
1216 if (attrval==NULL ||
1217 strcmp(attrval, this->attrs->Get(i)->attr_val)==0) {
1218 delcount++;
1219 this->attrs->freeItem(i);
1220 }
1221 }
1222 }
1223 if (delcount>0) this->attrs->Pack();
1224 return delcount;
1225 }
1226
1227 int GffObj::removeAttr(int aid, const char* attrval) {
1228 if (this->attrs==NULL || aid<0) return 0;
1229 int delcount=0; //could be more than one ?
1230 for (int i=0;i<this->attrs->Count();i++) {
1231 if (aid==this->attrs->Get(i)->attr_id) {
1232 if (attrval==NULL ||
1233 strcmp(attrval, this->attrs->Get(i)->attr_val)==0) {
1234 delcount++;
1235 this->attrs->freeItem(i);
1236 }
1237 }
1238 }
1239 if (delcount>0) this->attrs->Pack();
1240 return delcount;
1241 }
1242
1243
1244 int GffObj::removeExonAttr(GffExon& exon, const char* attrname, const char* attrval) {
1245 if (exon.attrs==NULL || attrname==NULL || attrname[0]==0) return 0;
1246 int aid=this->names->attrs.getId(attrname);
1247 if (aid<0) return 0;
1248 int delcount=0; //could be more than one
1249 for (int i=0;i<exon.attrs->Count();i++) {
1250 if (aid==exon.attrs->Get(i)->attr_id) {
1251 if (attrval==NULL ||
1252 strcmp(attrval, exon.attrs->Get(i)->attr_val)==0) {
1253 delcount++;
1254 exon.attrs->freeItem(i);
1255 }
1256 }
1257 }
1258 if (delcount>0) exon.attrs->Pack();
1259 return delcount;
1260 }
1261
1262 int GffObj::removeExonAttr(GffExon& exon, int aid, const char* attrval) {
1263 if (exon.attrs==NULL || aid<0) return 0;
1264 int delcount=0; //could be more than one
1265 for (int i=0;i<exon.attrs->Count();i++) {
1266 if (aid==exon.attrs->Get(i)->attr_id) {
1267 if (attrval==NULL ||
1268 strcmp(attrval, exon.attrs->Get(i)->attr_val)==0) {
1269 delcount++;
1270 exon.attrs->freeItem(i);
1271 }
1272 }
1273 }
1274 if (delcount>0) exon.attrs->Pack();
1275 return delcount;
1276 }
1277
1278
1279 void GffObj::getCDS_ends(uint& cds_start, uint& cds_end) {
1280 cds_start=0;
1281 cds_end=0;
1282 if (CDstart==0 || CDend==0) return; //no CDS info
1283 int cdsadj=0;
1284 if (CDphase=='1' || CDphase=='2') {
1285 cdsadj=CDphase-'0';
1286 }
1287 cds_start=CDstart;
1288 cds_end=CDend;
1289 if (strand=='-') cds_end-=cdsadj;
1290 else cds_start+=cdsadj;
1291 }
1292
1293 void GffObj::mRNA_CDS_coords(uint& cds_mstart, uint& cds_mend) {
1294 //sets cds_start and cds_end to the CDS start,end coordinates on the spliced mRNA transcript
1295 cds_mstart=0;
1296 cds_mend=0;
1297 if (CDstart==0 || CDend==0) return; //no CDS info
1298 //restore normal coordinates, just in case
1299 unxcoord();
1300 int cdsadj=0;
1301 if (CDphase=='1' || CDphase=='2') {
1302 cdsadj=CDphase-'0';
1303 }
1304 /*
1305 uint seqstart=CDstart;
1306 uint seqend=CDend;
1307 */
1308 uint seqstart=exons.First()->start;
1309 uint seqend=exons.Last()->end;
1310 int s=0; //resulting nucleotide counter
1311 if (strand=='-') {
1312 for (int x=exons.Count()-1;x>=0;x--) {
1313 uint sgstart=exons[x]->start;
1314 uint sgend=exons[x]->end;
1315 if (seqend<sgstart || seqstart>sgend) continue;
1316 if (seqstart>=sgstart && seqstart<=sgend)
1317 sgstart=seqstart; //seqstart within this segment
1318 if (seqend>=sgstart && seqend<=sgend)
1319 sgend=seqend; //seqend within this segment
1320 s+=(int)(sgend-sgstart)+1;
1321 if (CDstart>=sgstart && CDstart<=sgend) {
1322 //CDstart in this segment
1323 //and we are getting the whole transcript
1324 cds_mend=s-(int)(CDstart-sgstart);
1325 }
1326 if (CDend>=sgstart && CDend<=sgend) {
1327 //CDstart in this segment
1328 //and we are getting the whole transcript
1329 cds_mstart=s-(int)(CDend-cdsadj-sgstart);
1330 }
1331 } //for each exon
1332 } // - strand
1333 else { // + strand
1334 for (int x=0;x<exons.Count();x++) {
1335 uint sgstart=exons[x]->start;
1336 uint sgend=exons[x]->end;
1337 if (seqend<sgstart || seqstart>sgend) continue;
1338 if (seqstart>=sgstart && seqstart<=sgend)
1339 sgstart=seqstart; //seqstart within this segment
1340 if (seqend>=sgstart && seqend<=sgend)
1341 sgend=seqend; //seqend within this segment
1342 s+=(int)(sgend-sgstart)+1;
1343 /* for (uint i=sgstart;i<=sgend;i++) {
1344 spliced[s]=gsubseq[i-gstart];
1345 s++;
1346 }//for each nt
1347 */
1348 if (CDstart>=sgstart && CDstart<=sgend) {
1349 //CDstart in this segment
1350 cds_mstart=s-(int)(sgend-CDstart-cdsadj);
1351 }
1352 if (CDend>=sgstart && CDend<=sgend) {
1353 //CDend in this segment
1354 cds_mend=s-(int)(sgend-CDend);
1355 }
1356 } //for each exon
1357 } // + strand
1358 //spliced[s]=0;
1359 //if (rlen!=NULL) *rlen=s;
1360 //return spliced;
1361 }
1362
1363 char* GffObj::getUnspliced(GFaSeqGet* faseq, int* rlen, GList<GSeg>* seglst)
1364 {
1365 if (faseq==NULL) { GMessage("Warning: getUnspliced(NULL,.. ) called!\n");
1366 return NULL;
1367 }
1368 //restore normal coordinates:
1369 unxcoord();
1370 if (exons.Count()==0) return NULL;
1371 int fspan=end-start+1;
1372 const char* gsubseq=faseq->subseq(start, fspan);
1373 if (gsubseq==NULL) {
1374 GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1375 }
1376 char* unspliced=NULL;
1377
1378 int seqstart=exons.First()->start;
1379 int seqend=exons.Last()->end;
1380
1381 int unsplicedlen = 0;
1382
1383 unsplicedlen += seqend - seqstart + 1;
1384
1385 GMALLOC(unspliced, unsplicedlen+1); //allocate more here
1386 //uint seqstart, seqend;
1387
1388 int s = 0; //resulting nucleotide counter
1389 if (strand=='-')
1390 {
1391 if (seglst!=NULL)
1392 seglst->Add(new GSeg(s+1,s+1+seqend-seqstart));
1393 for (int i=seqend;i>=seqstart;i--)
1394 {
1395 unspliced[s] = ntComplement(gsubseq[i-start]);
1396 s++;
1397 }//for each nt
1398 } // - strand
1399 else
1400 { // + strand
1401 if (seglst!=NULL)
1402 seglst->Add(new GSeg(s+1,s+1+seqend-seqstart));
1403 for (int i=seqstart;i<=seqend;i++)
1404 {
1405 unspliced[s]=gsubseq[i-start];
1406 s++;
1407 }//for each nt
1408 } // + strand
1409 //assert(s <= unsplicedlen);
1410 unspliced[s]=0;
1411 if (rlen!=NULL) *rlen=s;
1412 return unspliced;
1413 }
1414
1415 char* GffObj::getSpliced(GFaSeqGet* faseq, bool CDSonly, int* rlen, uint* cds_start, uint* cds_end,
1416 GList<GSeg>* seglst) {
1417 if (CDSonly && CDstart==0) return NULL;
1418 if (faseq==NULL) { GMessage("Warning: getSpliced(NULL,.. ) called!\n");
1419 return NULL;
1420 }
1421 //restore normal coordinates:
1422 unxcoord();
1423 if (exons.Count()==0) return NULL;
1424 int fspan=end-start+1;
1425 const char* gsubseq=faseq->subseq(start, fspan);
1426 if (gsubseq==NULL) {
1427 GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1428 }
1429 if (fspan<(int)(end-start+1)) { //special case: stop coordinate was extended past the gseq length, must adjust
1430 int endadj=end-start+1-fspan;
1431 uint prevend=end;
1432 end-=endadj;
1433 if (CDend>end) CDend=end;
1434 if (exons.Last()->end>end) {
1435 exons.Last()->end=end; //this could get us into trouble if exon start is also > end
1436 if (exons.Last()->start>exons.Last()->end) {
1437 GError("GffObj::getSpliced() error: improper genomic coordinate %d on %s for %s\n",
1438 prevend,getGSeqName(), getID());
1439 }
1440 covlen-=endadj;
1441 }
1442 }
1443 char* spliced=NULL;
1444 GMALLOC(spliced, covlen+1); //allocate more here
1445 uint seqstart, seqend;
1446 int cdsadj=0;
1447 if (CDphase=='1' || CDphase=='2') {
1448 cdsadj=CDphase-'0';
1449 }
1450 if (CDSonly) {
1451 seqstart=CDstart;
1452 seqend=CDend;
1453 if (strand=='-') seqend-=cdsadj;
1454 else seqstart+=cdsadj;
1455 }
1456 else {
1457 seqstart=exons.First()->start;
1458 seqend=exons.Last()->end;
1459 }
1460 int s=0; //resulting nucleotide counter
1461 if (strand=='-') {
1462 for (int x=exons.Count()-1;x>=0;x--) {
1463 uint sgstart=exons[x]->start;
1464 uint sgend=exons[x]->end;
1465 if (seqend<sgstart || seqstart>sgend) continue;
1466 if (seqstart>=sgstart && seqstart<=sgend)
1467 sgstart=seqstart; //seqstart within this segment
1468 if (seqend>=sgstart && seqend<=sgend)
1469 sgend=seqend; //seqend within this segment
1470 if (seglst!=NULL)
1471 seglst->Add(new GSeg(s+1,s+1+sgend-sgstart));
1472 for (uint i=sgend;i>=sgstart;i--) {
1473 spliced[s] = ntComplement(gsubseq[i-start]);
1474 s++;
1475 }//for each nt
1476
1477 if (!CDSonly && cds_start!=NULL && CDstart>0) {
1478 if (CDstart>=sgstart && CDstart<=sgend) {
1479 //CDstart in this segment
1480 //and we are getting the whole transcript
1481 *cds_end=s-(CDstart-sgstart);
1482 }
1483 if (CDend>=sgstart && CDend<=sgend) {
1484 //CDstart in this segment
1485 //and we are getting the whole transcript
1486 *cds_start=s-(CDend-cdsadj-sgstart);
1487 }
1488 }//update local CDS coordinates
1489 } //for each exon
1490 } // - strand
1491 else { // + strand
1492 for (int x=0;x<exons.Count();x++) {
1493 uint sgstart=exons[x]->start;
1494 uint sgend=exons[x]->end;
1495 if (seqend<sgstart || seqstart>sgend) continue;
1496 if (seqstart>=sgstart && seqstart<=sgend)
1497 sgstart=seqstart; //seqstart within this segment
1498 if (seqend>=sgstart && seqend<=sgend)
1499 sgend=seqend; //seqend within this segment
1500 if (seglst!=NULL)
1501 seglst->Add(new GSeg(s+1,s+1+sgend-sgstart));
1502 for (uint i=sgstart;i<=sgend;i++) {
1503 spliced[s]=gsubseq[i-start];
1504 s++;
1505 }//for each nt
1506 if (!CDSonly && cds_start!=NULL && CDstart>0) {
1507 if (CDstart>=sgstart && CDstart<=sgend) {
1508 //CDstart in this segment
1509 //and we are getting the whole transcript
1510 *cds_start=s-(sgend-CDstart-cdsadj);
1511 }
1512 if (CDend>=sgstart && CDend<=sgend) {
1513 //CDstart in this segment
1514 //and we are getting the whole transcript
1515 *cds_end=s-(sgend-CDend);
1516 }
1517 }//update local CDS coordinates
1518 } //for each exon
1519 } // + strand
1520 spliced[s]=0;
1521 if (rlen!=NULL) *rlen=s;
1522 return spliced;
1523 }
1524
1525 char* GffObj::getSplicedTr(GFaSeqGet* faseq, bool CDSonly, int* rlen) {
1526 if (CDSonly && CDstart==0) return NULL;
1527 //restore normal coordinates:
1528 unxcoord();
1529 if (exons.Count()==0) return NULL;
1530 int fspan=end-start+1;
1531 const char* gsubseq=faseq->subseq(start, fspan);
1532 if (gsubseq==NULL) {
1533 GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1534 }
1535
1536 char* translation=NULL;
1537 GMALLOC(translation, (int)(covlen/3)+1);
1538 uint seqstart, seqend;
1539 int cdsadj=0;
1540 if (CDphase=='1' || CDphase=='2') {
1541 cdsadj=CDphase-'0';
1542 }
1543 if (CDSonly) {
1544 seqstart=CDstart;
1545 seqend=CDend;
1546 if (strand=='-') seqend-=cdsadj;
1547 else seqstart+=cdsadj;
1548 }
1549 else {
1550 seqstart=exons.First()->start;
1551 seqend=exons.Last()->end;
1552 }
1553 Codon codon;
1554 int nt=0; //codon nucleotide counter (0..2)
1555 int aa=0; //aminoacid count
1556 if (strand=='-') {
1557 for (int x=exons.Count()-1;x>=0;x--) {
1558 uint sgstart=exons[x]->start;
1559 uint sgend=exons[x]->end;
1560 if (seqend<sgstart || seqstart>sgend) continue;
1561 if (seqstart>=sgstart && seqstart<=sgend)
1562 sgstart=seqstart; //seqstart within this segment
1563 if (seqend>=sgstart && seqend<=sgend) {
1564 sgend=seqend; //seqend within this segment
1565 }
1566 for (uint i=sgend;i>=sgstart;i--) {
1567 codon.nuc[nt]=ntComplement(gsubseq[i-start]);
1568 nt++;
1569 if (nt==3) {
1570 nt=0;
1571 translation[aa]=codon.translate();
1572 aa++;
1573 }
1574 }//for each nt
1575 } //for each exon
1576 } // - strand
1577 else { // + strand
1578 for (int x=0;x<exons.Count();x++) {
1579 uint sgstart=exons[x]->start;
1580 uint sgend=exons[x]->end;
1581 if (seqend<sgstart || seqstart>sgend) continue;
1582 if (seqstart>=sgstart && seqstart<=sgend)
1583 sgstart=seqstart; //seqstart within this segment
1584 if (seqend>=sgstart && seqend<=sgend)
1585 sgend=seqend; //seqend within this segment
1586 for (uint i=sgstart;i<=sgend;i++) {
1587 codon.nuc[nt]=gsubseq[i-start];
1588 nt++;
1589 if (nt==3) {
1590 nt=0;
1591 translation[aa]=codon.translate();
1592 aa++;
1593 }
1594 }//for each nt
1595 } //for each exon
1596 } // + strand
1597 translation[aa]=0;
1598 if (rlen!=NULL) *rlen=aa;
1599 return translation;
1600 }
1601
1602 void GffObj::printSummary(FILE* fout) {
1603 if (fout==NULL) fout=stdout;
1604 fprintf(fout, "%s\t%c\t%d\t%d\t%4.2f\t%4.1f\n", gffID,
1605 strand, start, end, gscore, (float)qcov/10.0);
1606 }
1607
1608 void GffObj::printGxfLine(FILE* fout, const char* tlabel, const char* gseqname, bool iscds,
1609 uint segstart, uint segend, int exidx, char phase, bool gff3) {
1610 static char scorestr[14];
1611 strcpy(scorestr,".");
1612 GffAttrs* xattrs=NULL;
1613 if (exidx>=0) {
1614 if (exons[exidx]->score) sprintf(scorestr,"%.2f", exons[exidx]->score);
1615 xattrs=exons[exidx]->attrs;
1616 }
1617 if (phase==0 || !iscds) phase='.';
1618 const char* ftype=iscds ? "CDS" : getSubfName();
1619 if (gff3) {
1620 fprintf(fout,
1621 "%s\t%s\t%s\t%d\t%d\t%s\t%c\t%c\tParent=%s",
1622 gseqname, tlabel, ftype, segstart, segend, scorestr, strand,
1623 phase, gffID);
1624 if (xattrs!=NULL) {
1625 for (int i=0;i<xattrs->Count();i++)
1626 fprintf(fout, ";%s=%s",names->attrs.getName(xattrs->Get(i)->attr_id),
1627 xattrs->Get(i)->attr_val);
1628 }
1629 fprintf(fout, "\n");
1630 } //GFF
1631 else {//for GTF -- we print only transcripts
1632 //if (isValidTranscript())
1633 fprintf(fout, "%s\t%s\t%s\t%d\t%d\t%s\t%c\t%c\ttranscript_id \"%s\";",
1634 gseqname, tlabel, ftype, segstart, segend, scorestr, strand, phase, gffID);
1635 //char* geneid=(geneID!=NULL)? geneID : gffID;
1636 if (geneID)
1637 fprintf(fout," gene_id \"%s\";",geneID);
1638 if (gene_name!=NULL) {
1639 //fprintf(fout, " gene_name ");
1640 //if (gene_name[0]=='"') fprintf (fout, "%s;",gene_name);
1641 // else fprintf(fout, "\"%s\";",gene_name);
1642 fprintf(fout," gene_name \"%s\";",gene_name);
1643 }
1644 if (xattrs!=NULL) {
1645 for (int i=0;i<xattrs->Count();i++) {
1646 if (xattrs->Get(i)->attr_val==NULL) continue;
1647 const char* attrname=names->attrs.getName(xattrs->Get(i)->attr_id);
1648 fprintf(fout, " %s ",attrname);
1649 if (xattrs->Get(i)->attr_val[0]=='"')
1650 fprintf(fout, "%s;",xattrs->Get(i)->attr_val);
1651 else fprintf(fout, "\"%s\";",xattrs->Get(i)->attr_val);
1652 }
1653 }
1654 //for GTF, also append the GffObj attributes to each exon line
1655 if ((xattrs=this->attrs)!=NULL) {
1656 for (int i=0;i<xattrs->Count();i++) {
1657 if (xattrs->Get(i)->attr_val==NULL) continue;
1658 const char* attrname=names->attrs.getName(xattrs->Get(i)->attr_id);
1659 fprintf(fout, " %s ",attrname);
1660 if (xattrs->Get(i)->attr_val[0]=='"')
1661 fprintf(fout, "%s;",xattrs->Get(i)->attr_val);
1662 else fprintf(fout, "\"%s\";",xattrs->Get(i)->attr_val);
1663 }
1664 }
1665 fprintf(fout, "\n");
1666 }//GTF
1667 }
1668
1669 void GffObj::printGxf(FILE* fout, GffPrintMode gffp,
1670 const char* tlabel, const char* gfparent) {
1671 static char tmpstr[255];
1672 if (tlabel==NULL) {
1673 tlabel=track_id>=0 ? names->tracks.Get(track_id)->name :
1674 (char*)"gffobj" ;
1675 }
1676 unxcoord();
1677 //if (exons.Count()==0) return;
1678 const char* gseqname=names->gseqs.Get(gseq_id)->name;
1679 bool gff3 = (gffp>=pgffAny);
1680 bool showCDS = (gffp==pgtfAny || gffp==pgtfCDS || gffp==pgffCDS || gffp==pgffAny || gffp==pgffBoth);
1681 bool showExon = (gffp<=pgtfExon || gffp==pgffAny || gffp==pgffExon || gffp==pgffBoth);
1682 if (gff3) {
1683 //print GFF3 mRNA line:
1684 if (gscore>0.0) sprintf(tmpstr,"%.2f", gscore);
1685 else strcpy(tmpstr,".");
1686 uint pstart, pend;
1687 if (gffp==pgffCDS) {
1688 pstart=CDstart;
1689 pend=CDend;
1690 }
1691 else { pstart=start;pend=end; }
1692 //const char* ftype=isTranscript() ? "mRNA" : getFeatureName();
1693 const char* ftype=getFeatureName();
1694 fprintf(fout,
1695 "%s\t%s\t%s\t%d\t%d\t%s\t%c\t.\tID=%s",
1696 gseqname, tlabel, ftype, pstart, pend, tmpstr, strand, gffID);
1697 if (CDstart>0 && !showCDS && !isCDS) fprintf(fout,";CDS=%d-%d",CDstart,CDend);
1698 if (gfparent!=NULL) {
1699 //parent override
1700 fprintf(fout, ";Parent=%s",gfparent);
1701 }
1702 else {
1703 if (parent!=NULL && !parent->isDiscarded())
1704 fprintf(fout, ";Parent=%s",parent->getID());
1705 }
1706 if (geneID!=NULL)
1707 fprintf(fout, ";geneID=%s",geneID);
1708 if (gene_name!=NULL)
1709 fprintf(fout, ";gene_name=%s",gene_name);
1710 if (attrs!=NULL) {
1711 for (int i=0;i<attrs->Count();i++) {
1712 const char* attrname=names->attrs.getName(attrs->Get(i)->attr_id);
1713 fprintf(fout,";%s=%s", attrname,
1714 attrs->Get(i)->attr_val);
1715 }
1716 }
1717 fprintf(fout,"\n");
1718 }// gff3 mRNA line
1719 if (showExon) {
1720 //print exons
1721 if (isCDS && exons.Count()>0 &&
1722 ((strand=='-' && exons.Last()->phase<'0') || (strand=='+' && exons.Last()->phase<'0')))
1723 updateExonPhase();
1724
1725 for (int i=0;i<exons.Count();i++) {
1726 printGxfLine(fout, tlabel, gseqname, isCDS, exons[i]->start, exons[i]->end, i, exons[i]->phase, gff3);
1727 }
1728 }//printing exons
1729 if (showCDS && !isCDS && CDstart>0) {
1730 GArray<GffCDSeg> cds(true,true);
1731 getCDSegs(cds);
1732 for (int i=0;i<cds.Count();i++) {
1733 printGxfLine(fout, tlabel, gseqname, true, cds[i].start, cds[i].end, -1, cds[i].phase, gff3);
1734 }
1735 } //showCDS
1736 }
1737
1738 void GffObj::updateExonPhase() {
1739 if (!isCDS) return;
1740 int cdsacc=0;
1741 if (CDphase=='1' || CDphase=='2') {
1742 cdsacc+= 3-(CDphase-'0');
1743 }
1744 if (strand=='-') { //reverse strand
1745 for (int i=exons.Count()-1;i>=0;i--) {
1746 exons[i]->phase='0'+ (3-cdsacc%3)%3;
1747 cdsacc+=exons[i]->end-exons[i]->start+1;
1748 }
1749 }
1750 else { //forward strand
1751 for (int i=0;i<exons.Count();i++) {
1752 exons[i]->phase='0'+ (3-cdsacc%3)%3;
1753 cdsacc+=exons[i]->end-exons[i]->start+1;
1754 }
1755 }
1756 }
1757
1758
1759 void GffObj::getCDSegs(GArray<GffCDSeg>& cds) {
1760 GffCDSeg cdseg;
1761 int cdsacc=0;
1762 if (CDphase=='1' || CDphase=='2') {
1763 cdsacc+= 3-(CDphase-'0');
1764 }
1765 if (strand=='-') {
1766 for (int x=exons.Count()-1;x>=0;x--) {
1767 uint sgstart=exons[x]->start;
1768 uint sgend=exons[x]->end;
1769 if (CDend<sgstart || CDstart>sgend) continue;
1770 if (CDstart>=sgstart && CDstart<=sgend)
1771 sgstart=CDstart; //cdstart within this segment
1772 if (CDend>=sgstart && CDend<=sgend)
1773 sgend=CDend; //cdend within this segment
1774 cdseg.start=sgstart;
1775 cdseg.end=sgend;
1776 cdseg.exonidx=x;
1777 //cdseg.phase='0'+(cdsacc>0 ? (3-cdsacc%3)%3 : 0);
1778 cdseg.phase='0'+ (3-cdsacc%3)%3;
1779 cdsacc+=sgend-sgstart+1;
1780 cds.Add(cdseg);
1781 } //for each exon
1782 } // - strand
1783 else { // + strand
1784 for (int x=0;x<exons.Count();x++) {
1785 uint sgstart=exons[x]->start;
1786 uint sgend=exons[x]->end;
1787 if (CDend<sgstart || CDstart>sgend) continue;
1788 if (CDstart>=sgstart && CDstart<=sgend)
1789 sgstart=CDstart; //seqstart within this segment
1790 if (CDend>=sgstart && CDend<=sgend)
1791 sgend=CDend; //seqend within this segment
1792 cdseg.start=sgstart;
1793 cdseg.end=sgend;
1794 cdseg.exonidx=x;
1795 //cdseg.phase='0'+(cdsacc>0 ? (3-cdsacc%3)%3 : 0);
1796 cdseg.phase='0' + (3-cdsacc%3)%3 ;
1797 cdsacc+=sgend-sgstart+1;
1798 cds.Add(cdseg);
1799 } //for each exon
1800 } // + strand
1801 }