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root/gclib/gclib/gff.cpp
Revision: 16
Committed: Mon Jul 18 20:56:02 2011 UTC (8 years ago) by gpertea
File size: 64545 byte(s)
Log Message:
sync with local source

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 int ovlen=0;
509 if (exontype>0) { //check for overlaps between exon-type segments
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 //e.g. CDS to (UTR|exon)
515 if ((exons[oi]->exontype>=exgffUTR && exontype==exgffCDS) ||
516 (exons[oi]->exontype==exgffCDS && exontype>=exgffUTR)) {
517 expandExon(oi, segstart, segend, exgffCDSUTR, sc, fr, qs, qe);
518 return oi;
519 }
520 //CDS adjacent to stop_codon: UCSC does (did?) this
521 if ((exons[oi]->exontype==exgffStop && exontype==exgffCDS) ||
522 (exons[oi]->exontype==exgffCDS && exontype==exgffStop)) {
523 expandExon(oi, segstart, segend, exgffCDS, sc, fr, qs, qe);
524 return oi;
525 }
526 }
527 //only allow this for CDS within exon, stop_codon within (CDS|UTR|exon),
528 // start_codon within (CDS|exon)
529 if (exons[oi]->exontype>exontype &&
530 exons[oi]->start<=segstart && exons[oi]->end>=segend &&
531 !(exons[oi]->exontype==exgffUTR && exontype==exgffCDS)) {
532 //larger segment given first, now the smaller included one is redundant
533 return oi; //only used to store attributes from current GffLine
534 }
535 if (exontype>exons[oi]->exontype &&
536 segstart<=exons[oi]->start && segend>=exons[oi]->end &&
537 !(exontype==exgffUTR && exons[oi]->exontype==exgffCDS)) {
538 //smaller segment given first, so we have to enlarge it
539 expandExon(oi, segstart, segend, exontype, sc, fr, qs, qe);
540 //this should also check for overlapping next exon (oi+1) ?
541 return oi;
542 }
543 //there is also the special case of "ribosomal slippage exception" (programmed frameshift)
544 //where two CDS segments may actually overlap for 1 or 2 bases, but there should be only one encompassing exon
545 //if (ovlen>2 || exons[oi]->exontype!=exgffCDS || exontype!=exgffCDS) {
546 // had to relax this because of some weird UCSC annotations with exons partially overlapping the CDS segments
547 /*
548 if (ovlen>2 && exons[oi]->exontype!=exgffUTR && exontype!=exgffUTR) {
549 if (gff_show_warnings)
550 GMessage("GFF Warning: discarding overlapping feature segment (%d-%d) (vs %d-%d (%s)) for GFF ID %s on %s\n",
551 segstart, segend, exons[oi]->start, exons[oi]->end, getSubfName(), gffID, getGSeqName());
552 hasErrors(true);
553 return -1; //segment NOT added
554 }
555 */
556
557 if ((ovlen>2 || ovlen==0) || exons[oi]->exontype!=exgffCDS || exontype!=exgffCDS) {
558 if (gff_show_warnings)
559 GMessage("GFF Warning: merging overlapping/adjacent feature segment (%d-%d) into (%d-%d) (%s) for GFF ID %s on %s\n",
560 segstart, segend, exons[oi]->start, exons[oi]->end, getSubfName(), gffID, getGSeqName());
561 expandExon(oi, segstart, segend, exontype, sc, fr, qs, qe);
562 return oi;
563 }
564 // else add the segment if the overlap is small and between two CDS segments
565 //TODO: we might want to add an attribute here with the slippage coordinate and size?
566 covlen-=ovlen;
567 }//overlap or adjacent to existing segment
568 } //check for overlap
569 // --- no overlap, or accepted micro-overlap (ribosomal slippage)
570 // create & add the new segment
571 GffExon* enew=new GffExon(segstart, segend, sc, fr, qs, qe, exontype);
572 int eidx=exons.Add(enew);
573 if (eidx<0) {
574 //this would actually be acceptable if the object is a "Gene" and "exons" are in fact isoforms
575 if (gff_show_warnings)
576 GMessage("GFF Warning: failed adding segment %d-%d for %s (discarded)!\n",
577 segstart, segend, gffID);
578 delete enew;
579 hasErrors(true);
580 return -1;
581 }
582 covlen+=(int)(exons[eidx]->end-exons[eidx]->start)+1;
583 start=exons.First()->start;
584 end=exons.Last()->end;
585 if (uptr!=NULL) { //collect stats about the underlying genomic sequence
586 GSeqStat* gsd=(GSeqStat*)uptr;
587 if (start<gsd->mincoord) gsd->mincoord=start;
588 if (end>gsd->maxcoord) gsd->maxcoord=end;
589 if (this->len()>gsd->maxfeat_len) {
590 gsd->maxfeat_len=this->len();
591 gsd->maxfeat=this;
592 }
593 }
594 return eidx;
595 }
596
597 void GffObj::expandExon(int oi, uint segstart, uint segend, char exontype, double sc, char fr, int qs, int qe) {
598 //oi is the index of the *first* overlapping segment found that must be enlarged
599 covlen-=exons[oi]->len();
600 if (segstart<exons[oi]->start)
601 exons[oi]->start=segstart;
602 if (qs && qs<exons[oi]->qstart) exons[oi]->qstart=qs;
603 if (segend>exons[oi]->end)
604 exons[oi]->end=segend;
605 if (qe && qe>exons[oi]->qend) exons[oi]->qend=qe;
606 //warning: score cannot be properly adjusted! e.g. if it's a p-value it's just going to get worse
607 if (sc!=0) exons[oi]->score=sc;
608 covlen+=exons[oi]->len();
609 //if (exons[oi]->exontype< exontype) -- always true
610 exons[oi]->exontype = exontype;
611 if (exontype==exgffCDS) exons[oi]->phase=fr;
612 //we must check if any more exons are also overlapping this
613 int ni=oi+1; //next exon index after oi
614 while (ni<exons.Count() && segend>=exons[ni]->start) { // next segment overlaps new enlarged segment
615 //only allow this if next segment is fully included, and a subordinate
616 if (exons[ni]->exontype<exontype && exons[ni]->end<=segend) {
617 /* I guess we have to relax this due to stupid UCSC hg18 files having a start_codon sticking out
618 chr1 hg18_knownGene start_codon 69806911 69806913 0.000000 + .
619 chr1 hg18_knownGene CDS 69806911 69806912 0.000000 + 0
620 chr1 hg18_knownGene exon 69805456 69806912 0.000000 + .
621 */
622 if (exons[ni]->qstart<exons[oi]->qstart) exons[oi]->qstart=exons[ni]->qstart;
623 if (exons[ni]->qend>exons[oi]->qend) exons[oi]->qend=exons[ni]->qend;
624 exons.Delete(ni);
625 }
626 else {
627 if (gff_show_warnings) GMessage("GFF Warning: overlapping existing exon(%d-%d) while expanding to %d-%d for GFF ID %s\n",
628 exons[ni]->start, exons[ni]->end, segstart, segend, gffID);
629 //hasErrors(true);
630 break;
631 }
632 }
633 // -- make sure any other related boundaries are updated:
634 start=exons.First()->start;
635 end=exons.Last()->end;
636 if (uptr!=NULL) { //collect stats about the underlying genomic sequence
637 GSeqStat* gsd=(GSeqStat*)uptr;
638 if (start<gsd->mincoord) gsd->mincoord=start;
639 if (end>gsd->maxcoord) gsd->maxcoord=end;
640 if (this->len()>gsd->maxfeat_len) {
641 gsd->maxfeat_len=this->len();
642 gsd->maxfeat=this;
643 }
644 }
645 }
646
647 void GffObj::removeExon(int idx) {
648 /*
649 if (idx==0 && segs[0].start==gstart)
650 gstart=segs[1].start;
651 if (idx==segcount && segs[segcount].end==gend)
652 gend=segs[segcount-1].end;
653 */
654 if (idx<0 || idx>=exons.Count()) return;
655 int segstart=exons[idx]->start;
656 int segend=exons[idx]->end;
657 exons.Delete(idx);
658 covlen -= (int)(segend-segstart)+1;
659 start=exons.First()->start;
660 end=exons.Last()->end;
661 if (isCDS) { CDstart=start; CDend=end; }
662 }
663
664 void GffObj::removeExon(GffExon* p) {
665 for (int idx=0;idx<exons.Count();idx++) {
666 if (exons[idx]==p) {
667 int segstart=exons[idx]->start;
668 int segend=exons[idx]->end;
669 exons.Delete(idx);
670 covlen -= (int)(segend-segstart)+1;
671 start=exons.First()->start;
672 end=exons.Last()->end;
673 if (isCDS) { CDstart=start; CDend=end; }
674 return;
675 }
676 }
677 }
678
679
680
681 GffObj::GffObj(GffReader *gfrd, GffLine* gffline, bool keepAttr, bool noExonAttr):
682 GSeg(0,0), exons(true,true,false), children(1,false) {
683 xstart=0;
684 xend=0;
685 xstatus=0;
686 partial=false;
687 isCDS=false;
688 uptr=NULL;
689 ulink=NULL;
690 parent=NULL;
691 udata=0;
692 flags=0;
693 CDstart=0;
694 CDend=0;
695 CDphase=0;
696 geneID=NULL;
697 gene_name=NULL;
698 attrs=NULL;
699 gffID=NULL;
700 track_id=-1;
701 gseq_id=-1;
702 ftype_id=-1;
703 exon_ftype_id=-1;
704 strand='.';
705 if (gfrd==NULL)
706 GError("Cannot use this GffObj constructor with a NULL GffReader!\n");
707 gffnames_ref(names);
708 if (gfrd->names==NULL) gfrd->names=names;
709 //qlen=0;qstart=0;qend=0;
710 gscore=0;
711 uscore=0;
712 covlen=0;
713 qcov=0;
714 start=gffline->fstart;
715 end=gffline->fend;
716 gseq_id=names->gseqs.addName(gffline->gseqname);
717 track_id=names->tracks.addName(gffline->track);
718 strand=gffline->strand;
719 qlen=gffline->qlen;
720 qstart=gffline->qstart;
721 qend=gffline->qend;
722 //setup flags from gffline
723 isCDS=gffline->is_cds; //for now
724 isGene(gffline->is_gene);
725 isTranscript(gffline->is_transcript || gffline->exontype!=0);
726 fromGff3(gffline->is_gff3);
727
728 if (gffline->parents!=NULL) {
729 //GTF style -- create a GffObj directly by subfeature
730 //(also possible orphan GFF3 exon line, or an exon given before its parent (chado))
731 if (gffline->exontype!=0) { //recognized exon-like feature
732 ftype_id=gff_fid_transcript; //so this is some sort of transcript
733 exon_ftype_id=gff_fid_exon; //subfeatures MUST be exons
734 }
735 else {//unrecognized subfeatures
736 //make this GffObj of the same feature type
737 ftype_id=names->feats.addName(gffline->ftype);
738 }
739 if (gffline->ID==NULL) { //typical GTF
740 gffID=Gstrdup(gffline->parents[0]);
741 this->createdByExon(true);
742 //this is likely the first exon/segment of the feature
743 addExon(gfrd, gffline, keepAttr, noExonAttr);
744 }
745 else { //a parented feature with an ID -- probably an orphan GFF3 line
746 if (gffline->is_gff3 && gffline->exontype!=0) {
747 //premature exon given before its parent transcript
748 //create the transcript entry here
749 gffID=Gstrdup(gffline->parents[0]);
750 this->createdByExon(true);
751 //this is the first exon/segment of the transcript
752 addExon(gfrd, gffline, keepAttr, noExonAttr);
753 }
754 else { //unrecognized non-exon feature ? use the ID instead
755 gffID=Gstrdup(gffline->ID);
756 if (keepAttr) this->parseAttrs(attrs, gffline->info);
757 }
758 }
759 } //subfeature given directly
760 else { //gffline->parents==NULL
761 //create a parent feature in its own right
762 gscore=gffline->score;
763 if (gffline->ID==NULL || gffline->ID[0]==0)
764 GError("Error: no ID found for GFF record start\n");
765 gffID=Gstrdup(gffline->ID); //there must be an ID here
766 //if (gffline->is_transcript) ftype_id=gff_fid_mRNA;
767 //else
768 ftype_id=names->feats.addName(gffline->ftype);
769 if (gffline->is_transcript)
770 exon_ftype_id=gff_fid_exon;
771
772 if (keepAttr) this->parseAttrs(attrs, gffline->info);
773 }//no parent
774
775 if (gffline->gene_name!=NULL) {
776 gene_name=Gstrdup(gffline->gene_name);
777 }
778 if (gffline->gene_id!=NULL) {
779 geneID=Gstrdup(gffline->gene_id);
780 }
781
782 GSeqStat* gsd=gfrd->gseqstats.AddIfNew(new GSeqStat(gseq_id,names->gseqs.lastNameUsed()),true);
783 uptr=gsd;
784 if (start<gsd->mincoord) gsd->mincoord=start;
785 if (end>gsd->maxcoord) gsd->maxcoord=end;
786 if (this->len()>gsd->maxfeat_len) {
787 gsd->maxfeat_len=this->len();
788 gsd->maxfeat=this;
789 }
790 }
791
792 GffLine* GffReader::nextGffLine() {
793 if (gffline!=NULL) return gffline; //caller should free gffline after processing
794 while (gffline==NULL) {
795 int llen=0;
796 buflen=GFF_LINELEN-1;
797 char* l=fgetline(linebuf, buflen, fh, &fpos, &llen);
798 if (l==NULL) {
799 return NULL; //end of file
800 }
801 int ns=0; //first nonspace position
802 while (l[ns]!=0 && isspace(l[ns])) ns++;
803 if (l[ns]=='#' || llen<10) continue;
804 gffline=new GffLine(this, l);
805 if (gffline->skip) {
806 delete gffline;
807 gffline=NULL;
808 continue;
809 }
810 if (gffline->ID==NULL && gffline->parents==NULL) { //it must have an ID
811 //this might not be needed, already checked in the GffLine constructor
812 if (gff_warns)
813 GMessage("Warning: malformed GFF line, no parent or record Id (kipping\n");
814 delete gffline;
815 gffline=NULL;
816 //continue;
817 }
818 }
819 return gffline;
820 }
821
822 char* GffReader::gfoBuildId(const char* id, const char* ctg) {
823 //caller must free the returned pointer
824 char* buf=NULL;
825 int idlen=strlen(id);
826 GMALLOC(buf, idlen+strlen(ctg)+2);
827 strcpy(buf, id);
828 buf[idlen]='~';
829 strcpy(buf+idlen+1, ctg);
830 return buf;
831 }
832
833 void GffReader::gfoRemove(const char* id, const char* ctg) {
834 char* buf=gfoBuildId(id,ctg);
835 phash.Remove(buf);
836 GFREE(buf);
837 }
838
839 //Warning: if gflst gets altered, idx becomes obsolete
840 GfoHolder* GffReader::gfoAdd(const char* id, const char* ctg, GffObj* gfo, int idx) {
841 char* buf=gfoBuildId(id,ctg);
842 GfoHolder* r=new GfoHolder(gfo,idx);
843 phash.Add(buf, r);
844 GFREE(buf);
845 return r;
846 }
847
848 GfoHolder* GffReader::gfoFind(const char* id, const char* ctg) {
849 char* buf=gfoBuildId(id,ctg);
850 GfoHolder* r=phash.Find(buf);
851 GFREE(buf);
852 return r;
853 }
854
855 GfoHolder* GffReader::replaceGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr, int replaceidx) {
856 GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
857 GfoHolder* r=NULL;
858 if (replaceidx>=0) {
859 gflst.Put(replaceidx,newgfo);
860 r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, replaceidx);
861 }
862 else {
863 int gfoidx=gflst.Add(newgfo);
864 r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, gfoidx);
865 }
866 if (gff_warns) {
867 int* pcount=tids.Find(newgfo->gffID);
868 if (pcount!=NULL) {
869 if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
870 (*pcount)++;
871 }
872 else {
873 tids.Add(newgfo->gffID,new int(1));
874 }
875 }
876 return r;
877 }
878
879 GfoHolder* GffReader::updateParent(GfoHolder* newgfh, GffObj* parent) {
880 //assert(parent);
881 //assert(newgfo);
882 parent->children.Add(newgfh->gffobj);
883 if (newgfh->gffobj->parent==NULL) newgfh->gffobj->parent=parent;
884 newgfh->gffobj->setLevel(parent->getLevel()+1);
885 if (parent->isGene()) {
886 if (parent->gene_name!=NULL && newgfh->gffobj->gene_name==NULL)
887 newgfh->gffobj->gene_name=Gstrdup(parent->gene_name);
888 if (parent->geneID!=NULL && newgfh->gffobj->geneID==NULL)
889 newgfh->gffobj->geneID=Gstrdup(parent->geneID);
890 }
891
892 return newgfh;
893 }
894
895 GfoHolder* GffReader::newGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr,
896 GffObj* parent, GffExon* pexon) {
897 GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
898 GfoHolder* r=NULL;
899 int gfoidx=gflst.Add(newgfo);
900 r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, gfoidx);
901 if (parent!=NULL) {
902 updateParent(r, parent);
903 if (pexon!=NULL) parent->removeExon(pexon);
904 }
905 if (gff_warns) {
906 int* pcount=tids.Find(newgfo->gffID);
907 if (pcount!=NULL) {
908 if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
909 (*pcount)++;
910 }
911 else {
912 tids.Add(newgfo->gffID,new int(1));
913 }
914 }
915 return r;
916 }
917
918 GfoHolder* GffReader::updateGffRec(GfoHolder* prevgfo, GffLine* gffline,
919 bool keepAttr) {
920 if (prevgfo==NULL) return NULL;
921 prevgfo->gffobj->createdByExon(false);
922 prevgfo->gffobj->ftype_id=prevgfo->gffobj->names->feats.addName(gffline->ftype);
923 prevgfo->gffobj->start=gffline->fstart;
924 prevgfo->gffobj->end=gffline->fend;
925 prevgfo->gffobj->isGene(gffline->is_gene);
926 prevgfo->gffobj->isTranscript(gffline->is_transcript || gffline->exontype!=0);
927 prevgfo->gffobj->fromGff3(gffline->is_gff3);
928 if (keepAttr) {
929 if (prevgfo->gffobj->attrs!=NULL) prevgfo->gffobj->attrs->Clear();
930 prevgfo->gffobj->parseAttrs(prevgfo->gffobj->attrs, gffline->info);
931 }
932 return prevgfo;
933 }
934
935
936 bool GffReader::addExonFeature(GfoHolder* prevgfo, GffLine* gffline, GHash<CNonExon>& pex, bool noExonAttr) {
937 bool r=true;
938 if (gffline->strand!=prevgfo->gffobj->strand) {
939 GMessage("GFF Error: duplicate GFF ID '%s' (exons found on different strands of %s)\n",
940 prevgfo->gffobj->gffID, prevgfo->gffobj->getGSeqName());
941 r=false;
942 }
943 int gdist=(gffline->fstart>prevgfo->gffobj->end) ? gffline->fstart-prevgfo->gffobj->end :
944 ((gffline->fend<prevgfo->gffobj->start)? prevgfo->gffobj->start-gffline->fend :
945 0 );
946 if (gdist>(int)GFF_MAX_LOCUS) { //too far apart, most likely this is a duplicate ID
947 GMessage("Error: duplicate GFF ID '%s' (or exons too far apart)!\n",prevgfo->gffobj->gffID);
948 //validation_errors = true;
949 r=false;
950 if (!gff_warns) exit(1);
951 }
952 int eidx=prevgfo->gffobj->addExon(this, gffline, !noExonAttr, noExonAttr);
953 if (eidx>=0 && gffline->ID!=NULL && gffline->exontype==0)
954 subfPoolAdd(pex, prevgfo);
955 return r;
956 }
957
958 CNonExon* GffReader::subfPoolCheck(GffLine* gffline, GHash<CNonExon>& pex, char*& subp_name) {
959 CNonExon* subp=NULL;
960 subp_name=NULL;
961 for (int i=0;i<gffline->num_parents;i++) {
962 if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
963 continue;
964 subp_name=gfoBuildId(gffline->parents[i], gffline->gseqname); //e.g. mRNA name
965 subp=pex.Find(subp_name);
966 if (subp!=NULL)
967 return subp;
968 GFREE(subp_name);
969 }
970 return NULL;
971 }
972
973 void GffReader::subfPoolAdd(GHash<CNonExon>& pex, GfoHolder* newgfo) {
974 //this might become a parent feature later
975 if (newgfo->gffobj->exons.Count()>0) {
976 char* xbuf=gfoBuildId(gffline->ID, gffline->gseqname);
977 pex.Add(xbuf, new CNonExon(newgfo->idx, newgfo->gffobj,
978 newgfo->gffobj->exons[0], gffline));
979 GFREE(xbuf);
980 }
981 }
982
983 GfoHolder* GffReader::promoteFeature(CNonExon* subp, char*& subp_name, GHash<CNonExon>& pex,
984 bool keepAttr, bool noExonAttr) {
985 GffObj* prevp=subp->parent; //grandparent of gffline (e.g. gene)
986 if (prevp!=gflst[subp->idx])
987 GError("Error promoting subfeature %s, gflst index mismatch?!\n", subp->gffline->ID);
988 subp->gffline->discardParent();
989 GfoHolder* gfoh=newGffRec(subp->gffline, keepAttr, noExonAttr, prevp, subp->exon);
990 pex.Remove(subp_name); //no longer a potential parent, moved it to phash already
991 prevp->promotedChildren(true);
992 return gfoh; //returns the holder of newly promoted feature
993 }
994
995 //have to parse the whole file because exons can be scattered all over
996 void GffReader::readAll(bool keepAttr, bool mergeCloseExons, bool noExonAttr) {
997 bool validation_errors = false;
998 //loc_debug=false;
999 GHash<CNonExon> pex; //keep track of any "exon"-like features that have an ID
1000 //and thus could become promoted to parent features
1001 while (nextGffLine()!=NULL) {
1002 //seen this gff ID before?
1003 GfoHolder* prevseen=NULL;
1004 if (gffline->ID) //GFF3
1005 prevseen=gfoFind(gffline->ID, gffline->gseqname);
1006 if (prevseen!=NULL) {
1007 if (prevseen->gffobj->createdByExon()) {
1008 updateGffRec(prevseen, gffline, keepAttr);
1009 }
1010 else {
1011 GMessage("Error: duplicate GFF ID '%s' encountered!\n",gffline->ID);
1012 validation_errors = true;
1013 if (gff_warns) {
1014 delete gffline; gffline=NULL; continue;
1015 }
1016 else exit(1);
1017 }
1018 }
1019 if (gffline->parents==NULL) {//start GFF3-like record with no parent (mRNA, gene)
1020 if (!prevseen) newGffRec(gffline, keepAttr, noExonAttr);
1021 }
1022 else { //--- it's a parented feature (could still be a mRNA)
1023 bool found_parent=false;
1024 GfoHolder* newgfo=prevseen;
1025 for (int i=0;i<gffline->num_parents;i++) {
1026 if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
1027 continue; //skipping discarded parent feature
1028 GfoHolder* parentgfo=gfoFind(gffline->parents[i], gffline->gseqname);
1029 if (parentgfo!=NULL) { //parent GffObj parsed earlier
1030 found_parent=true;
1031 if (parentgfo->gffobj->isGene() && gffline->is_transcript
1032 && gffline->exontype==0) {
1033 //not an exon, but a transcript parented by a gene
1034 if (newgfo) {
1035 updateParent(newgfo, parentgfo->gffobj);
1036 }
1037 else {
1038 newgfo=newGffRec(gffline, keepAttr, noExonAttr, parentgfo->gffobj);
1039 }
1040 }
1041 else { //potential exon subfeature
1042 if (!addExonFeature(parentgfo, gffline, pex, noExonAttr))
1043 validation_errors=true;
1044 }
1045 }
1046 } //for each parsed parent Id
1047 if (!found_parent) { //new GTF-like record starting here with a subfeature directly
1048 //or it could be some chado GFF3 barf with exons declared BEFORE their parent :(
1049 //check if this feature isn't parented by a previously stored "exon" subfeature
1050 char* subp_name=NULL;
1051 CNonExon* subp=subfPoolCheck(gffline, pex, subp_name);
1052 if (subp!=NULL) { //found a subfeature that is the parent of this gffline
1053 //promote that subfeature to a full GffObj
1054 GfoHolder* gfoh=promoteFeature(subp, subp_name, pex, keepAttr, noExonAttr);
1055 //add current gffline as an exon of the newly promoted subfeature
1056 if (!addExonFeature(gfoh, gffline, pex, noExonAttr))
1057 validation_errors=true;
1058 }
1059 else { //no parent seen before, create one directly with this exon
1060 //loc_debug=true;
1061 GfoHolder* newgfo=prevseen ? prevseen : newGffRec(gffline, keepAttr, noExonAttr);
1062 if (gffline->ID!=NULL && gffline->exontype==0)
1063 subfPoolAdd(pex, newgfo);
1064 //even those with errors will be added here!
1065 }
1066 GFREE(subp_name);
1067 } //no previous parent found
1068 } //parented feature
1069 //--
1070 delete gffline;
1071 gffline=NULL;
1072 }//while gff lines
1073 gflst.finalize(this, mergeCloseExons, keepAttr, noExonAttr); //force sorting by locus if so constructed
1074 // all gff records are now loaded in GList gflst
1075 // so we can free the hash
1076 phash.Clear();
1077 tids.Clear();
1078 if (validation_errors) {
1079 exit(1);
1080 }
1081 }
1082
1083 GffObj* GffObj::finalize(GffReader* gfr, bool mergeCloseExons, bool keepAttrs, bool noExonAttr) {
1084 //merge
1085 //always merge adjacent or overlapping segments
1086 //but if mergeCloseExons then merge even when distance is up to 5 bases
1087 udata=0;
1088 uptr=NULL;
1089 if (gfr->transcriptsOnly && !(isTranscript() || (isGene() && children.Count()==0))) {
1090 isDiscarded(true);
1091 }
1092 if (ftype_id==gff_fid_transcript && CDstart>0) {
1093 ftype_id=gff_fid_mRNA;
1094 //exon_ftype_id=gff_fid_exon;
1095 }
1096 //if (ftype_id==gff_fid_mRNA || exon_ftype_id==gff_fid_exon || mergeCloseExons) {
1097 if (isTranscript() || exon_ftype_id==gff_fid_exon || mergeCloseExons) {
1098 int mindist=mergeCloseExons ? 5:1;
1099 for (int i=0;i<exons.Count()-1;i++) {
1100 int ni=i+1;
1101 uint mend=exons[i]->end;
1102 while (ni<exons.Count()) {
1103 int dist=(int)(exons[ni]->start-mend);
1104 if (dist>mindist) break; //no merging with next segment
1105 if (gfr!=NULL && gfr->gff_warns && dist!=0 && (exons[ni]->exontype!=exgffUTR && exons[i]->exontype!=exgffUTR)) {
1106 GMessage("GFF warning: merging adjacent/overlapping segments of %s on %s (%d-%d, %d-%d)\n",
1107 gffID, getGSeqName(), exons[i]->start, exons[i]->end,exons[ni]->start, exons[ni]->end);
1108 }
1109 mend=exons[ni]->end;
1110 covlen-=exons[i]->len();
1111 exons[i]->end=mend;
1112 covlen+=exons[i]->len();
1113 covlen-=exons[ni]->len();
1114 if (exons[ni]->attrs!=NULL && (exons[i]->attrs==NULL ||
1115 exons[i]->attrs->Count()<exons[ni]->attrs->Count())) {
1116 //use the other exon attributes, if more
1117 delete(exons[i]->attrs);
1118 exons[i]->attrs=exons[ni]->attrs;
1119 exons[ni]->attrs=NULL;
1120 }
1121 exons.Delete(ni);
1122 } //check for merge with next exon
1123 } //for each exon
1124 }
1125 //attribute reduction for GTF records
1126 if (keepAttrs && !noExonAttr && !fromGff3()
1127 && exons.Count()>0 && exons[0]->attrs!=NULL) {
1128 bool attrs_discarded=false;
1129 for (int a=0;a<exons[0]->attrs->Count();a++) {
1130 int attr_name_id=exons[0]->attrs->Get(a)->attr_id;
1131 char* attr_name=names->attrs.getName(attr_name_id);
1132 char* attr_val =exons[0]->attrs->Get(a)->attr_val;
1133 bool sameExonAttr=true;
1134 for (int i=1;i<exons.Count();i++) {
1135 char* ov=exons[i]->getAttr(attr_name_id);
1136 if (ov==NULL || (strcmp(ov,attr_val)!=0)) {
1137 sameExonAttr=false;
1138 break;
1139 }
1140 }
1141 if (sameExonAttr) {
1142 //delete this attribute from exons level
1143 attrs_discarded=true;
1144 this->addAttr(attr_name, attr_val);
1145 for (int i=1;i<exons.Count();i++) {
1146 removeExonAttr(*(exons[i]), attr_name_id);
1147 }
1148 exons[0]->attrs->freeItem(a);
1149 }
1150 }
1151 if (attrs_discarded) exons[0]->attrs->Pack();
1152 }
1153 return this;
1154 }
1155
1156 void GffObj::parseAttrs(GffAttrs*& atrlist, char* info, bool isExon) {
1157 if (names==NULL)
1158 GError(ERR_NULL_GFNAMES, "parseAttrs()");
1159 if (atrlist==NULL)
1160 atrlist=new GffAttrs();
1161 char* endinfo=info+strlen(info);
1162 char* start=info;
1163 char* pch=start;
1164 while (start<endinfo) {
1165 //skip spaces
1166 while (*start==' ' && start<endinfo) start++;
1167 pch=strchr(start, ';');
1168 if (pch==NULL) pch=endinfo;
1169 else {
1170 *pch='\0';
1171 pch++;
1172 }
1173 char* ech=strchr(start,'=');
1174 if (ech!=NULL) { // attr=value format found
1175 *ech='\0';
1176 //if (noExonAttr && (strcmp(start, "exon_number")==0 || strcmp(start, "exon")==0)) { start=pch; continue; }
1177 if (strcmp(start, "exon_number")==0 || strcmp(start, "exon")==0 ||
1178 strcmp(start, "exon_id")==0)
1179 { start=pch; continue; }
1180 ech++;
1181 while (*ech==' ' && ech<endinfo) ech++;//skip extra spaces after the '='
1182 //atrlist->Add(new GffAttr(names->attrs.addName(start),ech));
1183 //make sure we don't add the same attribute more than once
1184 if (isExon && (strcmp(start, "protein_id")==0)) {
1185 //Ensembl special case
1186 this->addAttr(start, ech);
1187 start=pch;
1188 continue;
1189 }
1190 atrlist->add_or_update(names, start, ech);
1191 }
1192 /*
1193 else { //not an attr=value format
1194 atrlist->Add(new GffAttr(names->attrs.addName(start),"1"));
1195 }
1196 */
1197 start=pch;
1198 }
1199 if (atrlist->Count()==0) { delete atrlist; atrlist=NULL; }
1200 }
1201
1202 void GffObj::addAttr(const char* attrname, const char* attrvalue) {
1203 if (this->attrs==NULL)
1204 this->attrs=new GffAttrs();
1205 //this->attrs->Add(new GffAttr(names->attrs.addName(attrname),attrvalue));
1206 this->attrs->add_or_update(names, attrname, attrvalue);
1207 }
1208
1209
1210 void GffObj::setFeatureName(const char* feature) {
1211 //change the feature name/type for a transcript
1212 int fid=names->feats.addName(feature);
1213 if (monoFeature() && exons.Count()>0)
1214 this->exon_ftype_id=fid;
1215 this->ftype_id=fid;
1216 }
1217
1218 void GffObj::setRefName(const char* newname) {
1219 //change the feature name/type for a transcript
1220 int rid=names->gseqs.addName(newname);
1221 this->gseq_id=rid;
1222 }
1223
1224
1225
1226 int GffObj::removeAttr(const char* attrname, const char* attrval) {
1227 if (this->attrs==NULL || attrname==NULL || attrname[0]==0) return 0;
1228 int aid=this->names->attrs.getId(attrname);
1229 if (aid<0) return 0;
1230 int delcount=0; //could be more than one ?
1231 for (int i=0;i<this->attrs->Count();i++) {
1232 if (aid==this->attrs->Get(i)->attr_id) {
1233 if (attrval==NULL ||
1234 strcmp(attrval, this->attrs->Get(i)->attr_val)==0) {
1235 delcount++;
1236 this->attrs->freeItem(i);
1237 }
1238 }
1239 }
1240 if (delcount>0) this->attrs->Pack();
1241 return delcount;
1242 }
1243
1244 int GffObj::removeAttr(int aid, const char* attrval) {
1245 if (this->attrs==NULL || aid<0) return 0;
1246 int delcount=0; //could be more than one ?
1247 for (int i=0;i<this->attrs->Count();i++) {
1248 if (aid==this->attrs->Get(i)->attr_id) {
1249 if (attrval==NULL ||
1250 strcmp(attrval, this->attrs->Get(i)->attr_val)==0) {
1251 delcount++;
1252 this->attrs->freeItem(i);
1253 }
1254 }
1255 }
1256 if (delcount>0) this->attrs->Pack();
1257 return delcount;
1258 }
1259
1260
1261 int GffObj::removeExonAttr(GffExon& exon, const char* attrname, const char* attrval) {
1262 if (exon.attrs==NULL || attrname==NULL || attrname[0]==0) return 0;
1263 int aid=this->names->attrs.getId(attrname);
1264 if (aid<0) return 0;
1265 int delcount=0; //could be more than one
1266 for (int i=0;i<exon.attrs->Count();i++) {
1267 if (aid==exon.attrs->Get(i)->attr_id) {
1268 if (attrval==NULL ||
1269 strcmp(attrval, exon.attrs->Get(i)->attr_val)==0) {
1270 delcount++;
1271 exon.attrs->freeItem(i);
1272 }
1273 }
1274 }
1275 if (delcount>0) exon.attrs->Pack();
1276 return delcount;
1277 }
1278
1279 int GffObj::removeExonAttr(GffExon& exon, int aid, const char* attrval) {
1280 if (exon.attrs==NULL || aid<0) return 0;
1281 int delcount=0; //could be more than one
1282 for (int i=0;i<exon.attrs->Count();i++) {
1283 if (aid==exon.attrs->Get(i)->attr_id) {
1284 if (attrval==NULL ||
1285 strcmp(attrval, exon.attrs->Get(i)->attr_val)==0) {
1286 delcount++;
1287 exon.attrs->freeItem(i);
1288 }
1289 }
1290 }
1291 if (delcount>0) exon.attrs->Pack();
1292 return delcount;
1293 }
1294
1295
1296 void GffObj::getCDS_ends(uint& cds_start, uint& cds_end) {
1297 cds_start=0;
1298 cds_end=0;
1299 if (CDstart==0 || CDend==0) return; //no CDS info
1300 int cdsadj=0;
1301 if (CDphase=='1' || CDphase=='2') {
1302 cdsadj=CDphase-'0';
1303 }
1304 cds_start=CDstart;
1305 cds_end=CDend;
1306 if (strand=='-') cds_end-=cdsadj;
1307 else cds_start+=cdsadj;
1308 }
1309
1310 void GffObj::mRNA_CDS_coords(uint& cds_mstart, uint& cds_mend) {
1311 //sets cds_start and cds_end to the CDS start,end coordinates on the spliced mRNA transcript
1312 cds_mstart=0;
1313 cds_mend=0;
1314 if (CDstart==0 || CDend==0) return; //no CDS info
1315 //restore normal coordinates, just in case
1316 unxcoord();
1317 int cdsadj=0;
1318 if (CDphase=='1' || CDphase=='2') {
1319 cdsadj=CDphase-'0';
1320 }
1321 /*
1322 uint seqstart=CDstart;
1323 uint seqend=CDend;
1324 */
1325 uint seqstart=exons.First()->start;
1326 uint seqend=exons.Last()->end;
1327 int s=0; //resulting nucleotide counter
1328 if (strand=='-') {
1329 for (int x=exons.Count()-1;x>=0;x--) {
1330 uint sgstart=exons[x]->start;
1331 uint sgend=exons[x]->end;
1332 if (seqend<sgstart || seqstart>sgend) continue;
1333 if (seqstart>=sgstart && seqstart<=sgend)
1334 sgstart=seqstart; //seqstart within this segment
1335 if (seqend>=sgstart && seqend<=sgend)
1336 sgend=seqend; //seqend within this segment
1337 s+=(int)(sgend-sgstart)+1;
1338 if (CDstart>=sgstart && CDstart<=sgend) {
1339 //CDstart in this segment
1340 //and we are getting the whole transcript
1341 cds_mend=s-(int)(CDstart-sgstart);
1342 }
1343 if (CDend>=sgstart && CDend<=sgend) {
1344 //CDstart in this segment
1345 //and we are getting the whole transcript
1346 cds_mstart=s-(int)(CDend-cdsadj-sgstart);
1347 }
1348 } //for each exon
1349 } // - strand
1350 else { // + strand
1351 for (int x=0;x<exons.Count();x++) {
1352 uint sgstart=exons[x]->start;
1353 uint sgend=exons[x]->end;
1354 if (seqend<sgstart || seqstart>sgend) continue;
1355 if (seqstart>=sgstart && seqstart<=sgend)
1356 sgstart=seqstart; //seqstart within this segment
1357 if (seqend>=sgstart && seqend<=sgend)
1358 sgend=seqend; //seqend within this segment
1359 s+=(int)(sgend-sgstart)+1;
1360 /* for (uint i=sgstart;i<=sgend;i++) {
1361 spliced[s]=gsubseq[i-gstart];
1362 s++;
1363 }//for each nt
1364 */
1365 if (CDstart>=sgstart && CDstart<=sgend) {
1366 //CDstart in this segment
1367 cds_mstart=s-(int)(sgend-CDstart-cdsadj);
1368 }
1369 if (CDend>=sgstart && CDend<=sgend) {
1370 //CDend in this segment
1371 cds_mend=s-(int)(sgend-CDend);
1372 }
1373 } //for each exon
1374 } // + strand
1375 //spliced[s]=0;
1376 //if (rlen!=NULL) *rlen=s;
1377 //return spliced;
1378 }
1379
1380 char* GffObj::getUnspliced(GFaSeqGet* faseq, int* rlen, GList<GSeg>* seglst)
1381 {
1382 if (faseq==NULL) { GMessage("Warning: getUnspliced(NULL,.. ) called!\n");
1383 return NULL;
1384 }
1385 //restore normal coordinates:
1386 unxcoord();
1387 if (exons.Count()==0) return NULL;
1388 int fspan=end-start+1;
1389 const char* gsubseq=faseq->subseq(start, fspan);
1390 if (gsubseq==NULL) {
1391 GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1392 }
1393 char* unspliced=NULL;
1394
1395 int seqstart=exons.First()->start;
1396 int seqend=exons.Last()->end;
1397
1398 int unsplicedlen = 0;
1399
1400 unsplicedlen += seqend - seqstart + 1;
1401
1402 GMALLOC(unspliced, unsplicedlen+1); //allocate more here
1403 //uint seqstart, seqend;
1404
1405 int s = 0; //resulting nucleotide counter
1406 if (strand=='-')
1407 {
1408 if (seglst!=NULL)
1409 seglst->Add(new GSeg(s+1,s+1+seqend-seqstart));
1410 for (int i=seqend;i>=seqstart;i--)
1411 {
1412 unspliced[s] = ntComplement(gsubseq[i-start]);
1413 s++;
1414 }//for each nt
1415 } // - strand
1416 else
1417 { // + strand
1418 if (seglst!=NULL)
1419 seglst->Add(new GSeg(s+1,s+1+seqend-seqstart));
1420 for (int i=seqstart;i<=seqend;i++)
1421 {
1422 unspliced[s]=gsubseq[i-start];
1423 s++;
1424 }//for each nt
1425 } // + strand
1426 //assert(s <= unsplicedlen);
1427 unspliced[s]=0;
1428 if (rlen!=NULL) *rlen=s;
1429 return unspliced;
1430 }
1431
1432 char* GffObj::getSpliced(GFaSeqGet* faseq, bool CDSonly, int* rlen, uint* cds_start, uint* cds_end,
1433 GList<GSeg>* seglst) {
1434 if (CDSonly && CDstart==0) return NULL;
1435 if (faseq==NULL) { GMessage("Warning: getSpliced(NULL,.. ) called!\n");
1436 return NULL;
1437 }
1438 //restore normal coordinates:
1439 unxcoord();
1440 if (exons.Count()==0) return NULL;
1441 int fspan=end-start+1;
1442 const char* gsubseq=faseq->subseq(start, fspan);
1443 if (gsubseq==NULL) {
1444 GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1445 }
1446 if (fspan<(int)(end-start+1)) { //special case: stop coordinate was extended past the gseq length, must adjust
1447 int endadj=end-start+1-fspan;
1448 uint prevend=end;
1449 end-=endadj;
1450 if (CDend>end) CDend=end;
1451 if (exons.Last()->end>end) {
1452 exons.Last()->end=end; //this could get us into trouble if exon start is also > end
1453 if (exons.Last()->start>exons.Last()->end) {
1454 GError("GffObj::getSpliced() error: improper genomic coordinate %d on %s for %s\n",
1455 prevend,getGSeqName(), getID());
1456 }
1457 covlen-=endadj;
1458 }
1459 }
1460 char* spliced=NULL;
1461 GMALLOC(spliced, covlen+1); //allocate more here
1462 uint seqstart, seqend;
1463 int cdsadj=0;
1464 if (CDphase=='1' || CDphase=='2') {
1465 cdsadj=CDphase-'0';
1466 }
1467 if (CDSonly) {
1468 seqstart=CDstart;
1469 seqend=CDend;
1470 if (strand=='-') seqend-=cdsadj;
1471 else seqstart+=cdsadj;
1472 }
1473 else {
1474 seqstart=exons.First()->start;
1475 seqend=exons.Last()->end;
1476 }
1477 int s=0; //resulting nucleotide counter
1478 if (strand=='-') {
1479 for (int x=exons.Count()-1;x>=0;x--) {
1480 uint sgstart=exons[x]->start;
1481 uint sgend=exons[x]->end;
1482 if (seqend<sgstart || seqstart>sgend) continue;
1483 if (seqstart>=sgstart && seqstart<=sgend)
1484 sgstart=seqstart; //seqstart within this segment
1485 if (seqend>=sgstart && seqend<=sgend)
1486 sgend=seqend; //seqend within this segment
1487 if (seglst!=NULL)
1488 seglst->Add(new GSeg(s+1,s+1+sgend-sgstart));
1489 for (uint i=sgend;i>=sgstart;i--) {
1490 spliced[s] = ntComplement(gsubseq[i-start]);
1491 s++;
1492 }//for each nt
1493
1494 if (!CDSonly && cds_start!=NULL && CDstart>0) {
1495 if (CDstart>=sgstart && CDstart<=sgend) {
1496 //CDstart in this segment
1497 //and we are getting the whole transcript
1498 *cds_end=s-(CDstart-sgstart);
1499 }
1500 if (CDend>=sgstart && CDend<=sgend) {
1501 //CDstart in this segment
1502 //and we are getting the whole transcript
1503 *cds_start=s-(CDend-cdsadj-sgstart);
1504 }
1505 }//update local CDS coordinates
1506 } //for each exon
1507 } // - strand
1508 else { // + strand
1509 for (int x=0;x<exons.Count();x++) {
1510 uint sgstart=exons[x]->start;
1511 uint sgend=exons[x]->end;
1512 if (seqend<sgstart || seqstart>sgend) continue;
1513 if (seqstart>=sgstart && seqstart<=sgend)
1514 sgstart=seqstart; //seqstart within this segment
1515 if (seqend>=sgstart && seqend<=sgend)
1516 sgend=seqend; //seqend within this segment
1517 if (seglst!=NULL)
1518 seglst->Add(new GSeg(s+1,s+1+sgend-sgstart));
1519 for (uint i=sgstart;i<=sgend;i++) {
1520 spliced[s]=gsubseq[i-start];
1521 s++;
1522 }//for each nt
1523 if (!CDSonly && cds_start!=NULL && CDstart>0) {
1524 if (CDstart>=sgstart && CDstart<=sgend) {
1525 //CDstart in this segment
1526 //and we are getting the whole transcript
1527 *cds_start=s-(sgend-CDstart-cdsadj);
1528 }
1529 if (CDend>=sgstart && CDend<=sgend) {
1530 //CDstart in this segment
1531 //and we are getting the whole transcript
1532 *cds_end=s-(sgend-CDend);
1533 }
1534 }//update local CDS coordinates
1535 } //for each exon
1536 } // + strand
1537 spliced[s]=0;
1538 if (rlen!=NULL) *rlen=s;
1539 return spliced;
1540 }
1541
1542 char* GffObj::getSplicedTr(GFaSeqGet* faseq, bool CDSonly, int* rlen) {
1543 if (CDSonly && CDstart==0) return NULL;
1544 //restore normal coordinates:
1545 unxcoord();
1546 if (exons.Count()==0) return NULL;
1547 int fspan=end-start+1;
1548 const char* gsubseq=faseq->subseq(start, fspan);
1549 if (gsubseq==NULL) {
1550 GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1551 }
1552
1553 char* translation=NULL;
1554 GMALLOC(translation, (int)(covlen/3)+1);
1555 uint seqstart, seqend;
1556 int cdsadj=0;
1557 if (CDphase=='1' || CDphase=='2') {
1558 cdsadj=CDphase-'0';
1559 }
1560 if (CDSonly) {
1561 seqstart=CDstart;
1562 seqend=CDend;
1563 if (strand=='-') seqend-=cdsadj;
1564 else seqstart+=cdsadj;
1565 }
1566 else {
1567 seqstart=exons.First()->start;
1568 seqend=exons.Last()->end;
1569 }
1570 Codon codon;
1571 int nt=0; //codon nucleotide counter (0..2)
1572 int aa=0; //aminoacid count
1573 if (strand=='-') {
1574 for (int x=exons.Count()-1;x>=0;x--) {
1575 uint sgstart=exons[x]->start;
1576 uint sgend=exons[x]->end;
1577 if (seqend<sgstart || seqstart>sgend) continue;
1578 if (seqstart>=sgstart && seqstart<=sgend)
1579 sgstart=seqstart; //seqstart within this segment
1580 if (seqend>=sgstart && seqend<=sgend) {
1581 sgend=seqend; //seqend within this segment
1582 }
1583 for (uint i=sgend;i>=sgstart;i--) {
1584 codon.nuc[nt]=ntComplement(gsubseq[i-start]);
1585 nt++;
1586 if (nt==3) {
1587 nt=0;
1588 translation[aa]=codon.translate();
1589 aa++;
1590 }
1591 }//for each nt
1592 } //for each exon
1593 } // - strand
1594 else { // + strand
1595 for (int x=0;x<exons.Count();x++) {
1596 uint sgstart=exons[x]->start;
1597 uint sgend=exons[x]->end;
1598 if (seqend<sgstart || seqstart>sgend) continue;
1599 if (seqstart>=sgstart && seqstart<=sgend)
1600 sgstart=seqstart; //seqstart within this segment
1601 if (seqend>=sgstart && seqend<=sgend)
1602 sgend=seqend; //seqend within this segment
1603 for (uint i=sgstart;i<=sgend;i++) {
1604 codon.nuc[nt]=gsubseq[i-start];
1605 nt++;
1606 if (nt==3) {
1607 nt=0;
1608 translation[aa]=codon.translate();
1609 aa++;
1610 }
1611 }//for each nt
1612 } //for each exon
1613 } // + strand
1614 translation[aa]=0;
1615 if (rlen!=NULL) *rlen=aa;
1616 return translation;
1617 }
1618
1619 void GffObj::printSummary(FILE* fout) {
1620 if (fout==NULL) fout=stdout;
1621 fprintf(fout, "%s\t%c\t%d\t%d\t%4.2f\t%4.1f\n", gffID,
1622 strand, start, end, gscore, (float)qcov/10.0);
1623 }
1624
1625 void GffObj::printGxfLine(FILE* fout, const char* tlabel, const char* gseqname, bool iscds,
1626 uint segstart, uint segend, int exidx, char phase, bool gff3) {
1627 static char scorestr[14];
1628 strcpy(scorestr,".");
1629 GffAttrs* xattrs=NULL;
1630 if (exidx>=0) {
1631 if (exons[exidx]->score) sprintf(scorestr,"%.2f", exons[exidx]->score);
1632 xattrs=exons[exidx]->attrs;
1633 }
1634 if (phase==0 || !iscds) phase='.';
1635 const char* ftype=iscds ? "CDS" : getSubfName();
1636 if (gff3) {
1637 fprintf(fout,
1638 "%s\t%s\t%s\t%d\t%d\t%s\t%c\t%c\tParent=%s",
1639 gseqname, tlabel, ftype, segstart, segend, scorestr, strand,
1640 phase, gffID);
1641 if (xattrs!=NULL) {
1642 for (int i=0;i<xattrs->Count();i++)
1643 fprintf(fout, ";%s=%s",names->attrs.getName(xattrs->Get(i)->attr_id),
1644 xattrs->Get(i)->attr_val);
1645 }
1646 fprintf(fout, "\n");
1647 } //GFF
1648 else {//for GTF -- we print only transcripts
1649 //if (isValidTranscript())
1650 fprintf(fout, "%s\t%s\t%s\t%d\t%d\t%s\t%c\t%c\ttranscript_id \"%s\";",
1651 gseqname, tlabel, ftype, segstart, segend, scorestr, strand, phase, gffID);
1652 //char* geneid=(geneID!=NULL)? geneID : gffID;
1653 if (geneID)
1654 fprintf(fout," gene_id \"%s\";",geneID);
1655 if (gene_name!=NULL) {
1656 //fprintf(fout, " gene_name ");
1657 //if (gene_name[0]=='"') fprintf (fout, "%s;",gene_name);
1658 // else fprintf(fout, "\"%s\";",gene_name);
1659 fprintf(fout," gene_name \"%s\";",gene_name);
1660 }
1661 if (xattrs!=NULL) {
1662 for (int i=0;i<xattrs->Count();i++) {
1663 if (xattrs->Get(i)->attr_val==NULL) continue;
1664 const char* attrname=names->attrs.getName(xattrs->Get(i)->attr_id);
1665 fprintf(fout, " %s ",attrname);
1666 if (xattrs->Get(i)->attr_val[0]=='"')
1667 fprintf(fout, "%s;",xattrs->Get(i)->attr_val);
1668 else fprintf(fout, "\"%s\";",xattrs->Get(i)->attr_val);
1669 }
1670 }
1671 //for GTF, also append the GffObj attributes to each exon line
1672 if ((xattrs=this->attrs)!=NULL) {
1673 for (int i=0;i<xattrs->Count();i++) {
1674 if (xattrs->Get(i)->attr_val==NULL) continue;
1675 const char* attrname=names->attrs.getName(xattrs->Get(i)->attr_id);
1676 fprintf(fout, " %s ",attrname);
1677 if (xattrs->Get(i)->attr_val[0]=='"')
1678 fprintf(fout, "%s;",xattrs->Get(i)->attr_val);
1679 else fprintf(fout, "\"%s\";",xattrs->Get(i)->attr_val);
1680 }
1681 }
1682 fprintf(fout, "\n");
1683 }//GTF
1684 }
1685
1686 void GffObj::printGxf(FILE* fout, GffPrintMode gffp,
1687 const char* tlabel, const char* gfparent) {
1688 static char tmpstr[255];
1689 if (tlabel==NULL) {
1690 tlabel=track_id>=0 ? names->tracks.Get(track_id)->name :
1691 (char*)"gffobj" ;
1692 }
1693 unxcoord();
1694 //if (exons.Count()==0) return;
1695 const char* gseqname=names->gseqs.Get(gseq_id)->name;
1696 bool gff3 = (gffp>=pgffAny);
1697 bool showCDS = (gffp==pgtfAny || gffp==pgtfCDS || gffp==pgffCDS || gffp==pgffAny || gffp==pgffBoth);
1698 bool showExon = (gffp<=pgtfExon || gffp==pgffAny || gffp==pgffExon || gffp==pgffBoth);
1699 if (gff3) {
1700 //print GFF3 mRNA line:
1701 if (gscore>0.0) sprintf(tmpstr,"%.2f", gscore);
1702 else strcpy(tmpstr,".");
1703 uint pstart, pend;
1704 if (gffp==pgffCDS) {
1705 pstart=CDstart;
1706 pend=CDend;
1707 }
1708 else { pstart=start;pend=end; }
1709 //const char* ftype=isTranscript() ? "mRNA" : getFeatureName();
1710 const char* ftype=getFeatureName();
1711 fprintf(fout,
1712 "%s\t%s\t%s\t%d\t%d\t%s\t%c\t.\tID=%s",
1713 gseqname, tlabel, ftype, pstart, pend, tmpstr, strand, gffID);
1714 if (CDstart>0 && !showCDS && !isCDS) fprintf(fout,";CDS=%d-%d",CDstart,CDend);
1715 if (gfparent!=NULL) {
1716 //parent override
1717 fprintf(fout, ";Parent=%s",gfparent);
1718 }
1719 else {
1720 if (parent!=NULL && !parent->isDiscarded())
1721 fprintf(fout, ";Parent=%s",parent->getID());
1722 }
1723 if (geneID!=NULL)
1724 fprintf(fout, ";geneID=%s",geneID);
1725 if (gene_name!=NULL)
1726 fprintf(fout, ";gene_name=%s",gene_name);
1727 if (attrs!=NULL) {
1728 for (int i=0;i<attrs->Count();i++) {
1729 const char* attrname=names->attrs.getName(attrs->Get(i)->attr_id);
1730 fprintf(fout,";%s=%s", attrname,
1731 attrs->Get(i)->attr_val);
1732 }
1733 }
1734 fprintf(fout,"\n");
1735 }// gff3 mRNA line
1736 if (showExon) {
1737 //print exons
1738 if (isCDS && exons.Count()>0 &&
1739 ((strand=='-' && exons.Last()->phase<'0') || (strand=='+' && exons.Last()->phase<'0')))
1740 updateExonPhase();
1741
1742 for (int i=0;i<exons.Count();i++) {
1743 printGxfLine(fout, tlabel, gseqname, isCDS, exons[i]->start, exons[i]->end, i, exons[i]->phase, gff3);
1744 }
1745 }//printing exons
1746 if (showCDS && !isCDS && CDstart>0) {
1747 GArray<GffCDSeg> cds(true,true);
1748 getCDSegs(cds);
1749 for (int i=0;i<cds.Count();i++) {
1750 printGxfLine(fout, tlabel, gseqname, true, cds[i].start, cds[i].end, -1, cds[i].phase, gff3);
1751 }
1752 } //showCDS
1753 }
1754
1755 void GffObj::updateExonPhase() {
1756 if (!isCDS) return;
1757 int cdsacc=0;
1758 if (CDphase=='1' || CDphase=='2') {
1759 cdsacc+= 3-(CDphase-'0');
1760 }
1761 if (strand=='-') { //reverse strand
1762 for (int i=exons.Count()-1;i>=0;i--) {
1763 exons[i]->phase='0'+ (3-cdsacc%3)%3;
1764 cdsacc+=exons[i]->end-exons[i]->start+1;
1765 }
1766 }
1767 else { //forward strand
1768 for (int i=0;i<exons.Count();i++) {
1769 exons[i]->phase='0'+ (3-cdsacc%3)%3;
1770 cdsacc+=exons[i]->end-exons[i]->start+1;
1771 }
1772 }
1773 }
1774
1775
1776 void GffObj::getCDSegs(GArray<GffCDSeg>& cds) {
1777 GffCDSeg cdseg;
1778 int cdsacc=0;
1779 if (CDphase=='1' || CDphase=='2') {
1780 cdsacc+= 3-(CDphase-'0');
1781 }
1782 if (strand=='-') {
1783 for (int x=exons.Count()-1;x>=0;x--) {
1784 uint sgstart=exons[x]->start;
1785 uint sgend=exons[x]->end;
1786 if (CDend<sgstart || CDstart>sgend) continue;
1787 if (CDstart>=sgstart && CDstart<=sgend)
1788 sgstart=CDstart; //cdstart within this segment
1789 if (CDend>=sgstart && CDend<=sgend)
1790 sgend=CDend; //cdend within this segment
1791 cdseg.start=sgstart;
1792 cdseg.end=sgend;
1793 cdseg.exonidx=x;
1794 //cdseg.phase='0'+(cdsacc>0 ? (3-cdsacc%3)%3 : 0);
1795 cdseg.phase='0'+ (3-cdsacc%3)%3;
1796 cdsacc+=sgend-sgstart+1;
1797 cds.Add(cdseg);
1798 } //for each exon
1799 } // - strand
1800 else { // + strand
1801 for (int x=0;x<exons.Count();x++) {
1802 uint sgstart=exons[x]->start;
1803 uint sgend=exons[x]->end;
1804 if (CDend<sgstart || CDstart>sgend) continue;
1805 if (CDstart>=sgstart && CDstart<=sgend)
1806 sgstart=CDstart; //seqstart within this segment
1807 if (CDend>=sgstart && CDend<=sgend)
1808 sgend=CDend; //seqend within this segment
1809 cdseg.start=sgstart;
1810 cdseg.end=sgend;
1811 cdseg.exonidx=x;
1812 //cdseg.phase='0'+(cdsacc>0 ? (3-cdsacc%3)%3 : 0);
1813 cdseg.phase='0' + (3-cdsacc%3)%3 ;
1814 cdsacc+=sgend-sgstart+1;
1815 cds.Add(cdseg);
1816 } //for each exon
1817 } // + strand
1818 }