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root/gclib/gclib/gff.cpp
Revision: 50
Committed: Thu Sep 8 00:47:22 2011 UTC (8 years, 1 month ago) by gpertea
File size: 64571 byte(s)
Log Message:
fixed a loading bug when a CDS was given to a monoFeature() with a self-exon

Line User Rev File contents
1 gpertea 2 #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 gpertea 16 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 gpertea 2 const int gff_fid_mRNA=0;
13 gpertea 16 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 gpertea 2
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 gpertea 16 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 gpertea 2 }
54    
55 gpertea 16 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 gpertea 2
109 gpertea 16 static char fnamelc[128];
110    
111 gpertea 2 GffLine::GffLine(GffReader* reader, const char* l) {
112 gpertea 16 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 gpertea 2 skip=true;
118     gseqname=NULL;
119     track=NULL;
120     ftype=NULL;
121     info=NULL;
122 gpertea 16 _parents=NULL;
123     _parents_len=0;
124     num_parents=0;
125     parents=NULL;
126     is_gff3=false;
127 gpertea 2 is_cds=false;
128 gpertea 16 is_transcript=false;
129 gpertea 2 is_exon=false;
130 gpertea 16 is_gene=false;
131 gpertea 2 exontype=0;
132 gpertea 16 gene_id=NULL;
133     gene_name=NULL;
134 gpertea 2 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 gpertea 16 if (fend<fstart) swap(fend,fstart); //make sure fstart>=fend, always
168 gpertea 2 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 gpertea 16 phase=*t[7]; // must be '.', '0', '1' or '2'
180 gpertea 2 ID=NULL;
181     // exon/CDS/mrna filter
182 gpertea 16 strncpy(fnamelc, ftype, 127);
183     fnamelc[127]=0;
184 gpertea 2 strlower(fnamelc); //convert to lower case
185 gpertea 16 bool is_t_data=false;
186 gpertea 2 if (strstr(fnamelc, "utr")!=NULL) {
187     exontype=exgffUTR;
188     is_exon=true;
189 gpertea 16 is_t_data=true;
190 gpertea 2 }
191     else if (strstr(fnamelc, "exon")!=NULL) {
192     exontype=exgffExon;
193     is_exon=true;
194 gpertea 16 is_t_data=true;
195 gpertea 2 }
196 gpertea 16 else if (strstr(fnamelc, "stop") &&
197     (strstr(fnamelc, "codon") || strstr(fnamelc, "cds"))){
198 gpertea 2 exontype=exgffStop;
199 gpertea 16 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 gpertea 2 is_cds=true;
206 gpertea 16 is_t_data=true;
207 gpertea 2 }
208     else if (strcmp(fnamelc, "cds")==0) {
209     exontype=exgffCDS;
210     is_cds=true;
211 gpertea 16 is_t_data=true;
212 gpertea 2 }
213 gpertea 16 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 gpertea 2 }
217 gpertea 16 else if (endsWith(fnamelc,"rna") || endsWith(fnamelc,"transcript")) {
218     is_transcript=true;
219     is_t_data=true;
220     }
221 gpertea 2
222 gpertea 16 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 gpertea 2 }
232 gpertea 16 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 gpertea 2 //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 gpertea 16 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 gpertea 2 if (startsWith(track,"jigsaw")) {
335 gpertea 16 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 gpertea 2 Parent=Gstrdup(info,info+i-1);
348 gpertea 16 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 gpertea 2
359 gpertea 16 //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 gpertea 2 }
376 gpertea 16 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 gpertea 2 }
397 gpertea 16 }//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 gpertea 2 }
403     skip=false;
404     }
405    
406 gpertea 16 int GffObj::addExon(GffReader* reader, GffLine* gl, bool keepAttr, bool noExonAttr) {
407 gpertea 2 //this will make sure we have the right subftype_id!
408     int subf_id=-1;
409 gpertea 50 if (!isTranscript() && gl->is_cds && monoFeature()) {
410     isTranscript(true);
411     exon_ftype_id=gff_fid_exon;
412     if (exons.Count()==1) exons[0]->exontype=exgffExon;
413     }
414 gpertea 16 if (isTranscript()) {
415     if (exon_ftype_id<0) {//exon_ftype_id=gff_fid_exon;
416     if (gl->exontype>0) exon_ftype_id=gff_fid_exon;
417     else exon_ftype_id=names->feats.addName(gl->ftype);
418     }
419 gpertea 2 //any recognized mRNA segment gets the generic "exon" type (also applies to CDS)
420 gpertea 16 if (gl->exontype==0 && !gl->is_transcript) {
421     //extraneous mRNA feature, discard
422     if (reader->gff_warns)
423     GMessage("Warning: discarding unrecognized transcript subfeature %s of %s\n",
424     gl->ftype, gffID);
425 gpertea 2 return -1;
426 gpertea 16 }
427 gpertea 2 }
428 gpertea 16 else { //non-mRNA parent feature, check this subf type
429 gpertea 2 subf_id=names->feats.addName(gl->ftype);
430 gpertea 16 if (exon_ftype_id<0 || exons.Count()==0) //never assigned a subfeature type before (e.g. first exon being added)
431     exon_ftype_id=subf_id;
432     else {
433     if (exon_ftype_id!=subf_id) {
434 gpertea 50 //
435 gpertea 16 if (exon_ftype_id==ftype_id && exons.Count()==1 && exons[0]->start==start && exons[0]->end==end) {
436     //the existing exon was just a dummy one created by default, discard it
437     exons.Clear();
438     covlen=0;
439     exon_ftype_id=subf_id; //allow the new subfeature to completely takeover
440     }
441     else { //multiple subfeatures, prefer those with
442     if (reader->gff_warns)
443     GMessage("GFF Warning: multiple subfeatures (%s and %s) found for %s, discarding ",
444     names->feats.getName(subf_id), names->feats.getName(exon_ftype_id),gffID);
445     if (gl->exontype!=0) { //new feature is an exon, discard previously parsed subfeatures
446     if (reader->gff_warns) GMessage("%s.\n", names->feats.getName(exon_ftype_id));
447     exon_ftype_id=subf_id;
448     exons.Clear();
449     covlen=0;
450     }
451     else { //discard new feature
452     if (reader->gff_warns) GMessage("%s.\n", names->feats.getName(subf_id));
453     return -1; //skip this 2nd subfeature type for this parent!
454     }
455     }
456     } //incoming subfeature is of different type
457     } //new subfeature type
458     } //non-mRNA parent
459 gpertea 2 int eidx=addExon(gl->fstart, gl->fend, gl->score, gl->phase,
460     gl->qstart,gl->qend, gl->is_cds, gl->exontype);
461 gpertea 16 if (eidx<0) return eidx; //this should never happen
462     if (keepAttr) {
463     if (noExonAttr) {
464     if (attrs==NULL) //place the parsed attributes directly at transcript level
465     parseAttrs(attrs, gl->info);
466     }
467     else { //need all exon-level attributes
468     parseAttrs(exons[eidx]->attrs, gl->info, true);
469     }
470 gpertea 2 }
471     return eidx;
472     }
473    
474    
475     int GffObj::addExon(uint segstart, uint segend, double sc, char fr, int qs, int qe, bool iscds, char exontype) {
476     if (exons.Count()==0) {
477     if (iscds) isCDS=true; //for now, assume CDS only if first "exon" given is a CDS
478 gpertea 16 if (exon_ftype_id<0) {
479     exon_ftype_id = isTranscript() ? gff_fid_exon : ftype_id;
480 gpertea 2 }
481     }
482 gpertea 16 //special treatment of start/stop codon features, they might be broken/split between exons
483     //and in that case some providers will still give the wrong end coordinate as start+2 (e.g. UCSC)
484     //so we should not trust the end coordinate for such features
485     if (exontype==exgffStart || exontype==exgffStop) {
486     if (strand=='-') segstart=segend;
487     else segend=segstart;
488     if (exontype==exgffStart) {
489     if (CDstart==0 || segstart<CDstart) CDstart=segstart;
490     }
491     else {
492     if (segstart>CDend) CDend=segstart;
493     }
494     }
495     else if (iscds) { //update CDS anchors:
496 gpertea 2 if (CDstart==0 || segstart<CDstart) {
497     CDstart=segstart;
498     if (exontype==exgffCDS && strand=='+') CDphase=fr;
499     }
500     if (segend>CDend) {
501     if (exontype==exgffCDS && strand=='-') CDphase=fr;
502     CDend=segend;
503     }
504     }
505 gpertea 16 else { // not a CDS/start/stop
506 gpertea 2 isCDS=false;
507     }
508     if (qs || qe) {
509     if (qs>qe) swap(qs,qe);
510     if (qs==0) qs=1;
511 gpertea 16 }
512 gpertea 2 int ovlen=0;
513 gpertea 16 if (exontype>0) { //check for overlaps between exon-type segments
514     int oi=exonOverlapIdx(segstart, segend, &ovlen);
515     if (oi>=0) { //overlap existing segment
516     if (ovlen==0) {
517     //adjacent segments will be merged
518     //e.g. CDS to (UTR|exon)
519     if ((exons[oi]->exontype>=exgffUTR && exontype==exgffCDS) ||
520     (exons[oi]->exontype==exgffCDS && exontype>=exgffUTR)) {
521     expandExon(oi, segstart, segend, exgffCDSUTR, sc, fr, qs, qe);
522     return oi;
523     }
524     //CDS adjacent to stop_codon: UCSC does (did?) this
525     if ((exons[oi]->exontype==exgffStop && exontype==exgffCDS) ||
526     (exons[oi]->exontype==exgffCDS && exontype==exgffStop)) {
527     expandExon(oi, segstart, segend, exgffCDS, sc, fr, qs, qe);
528     return oi;
529     }
530     }
531     //only allow this for CDS within exon, stop_codon within (CDS|UTR|exon),
532     // start_codon within (CDS|exon)
533     if (exons[oi]->exontype>exontype &&
534     exons[oi]->start<=segstart && exons[oi]->end>=segend &&
535     !(exons[oi]->exontype==exgffUTR && exontype==exgffCDS)) {
536     //larger segment given first, now the smaller included one is redundant
537     return oi; //only used to store attributes from current GffLine
538     }
539     if (exontype>exons[oi]->exontype &&
540     segstart<=exons[oi]->start && segend>=exons[oi]->end &&
541     !(exontype==exgffUTR && exons[oi]->exontype==exgffCDS)) {
542     //smaller segment given first, so we have to enlarge it
543     expandExon(oi, segstart, segend, exontype, sc, fr, qs, qe);
544     //this should also check for overlapping next exon (oi+1) ?
545     return oi;
546     }
547     //there is also the special case of "ribosomal slippage exception" (programmed frameshift)
548     //where two CDS segments may actually overlap for 1 or 2 bases, but there should be only one encompassing exon
549     //if (ovlen>2 || exons[oi]->exontype!=exgffCDS || exontype!=exgffCDS) {
550     // had to relax this because of some weird UCSC annotations with exons partially overlapping the CDS segments
551     /*
552     if (ovlen>2 && exons[oi]->exontype!=exgffUTR && exontype!=exgffUTR) {
553     if (gff_show_warnings)
554     GMessage("GFF Warning: discarding overlapping feature segment (%d-%d) (vs %d-%d (%s)) for GFF ID %s on %s\n",
555     segstart, segend, exons[oi]->start, exons[oi]->end, getSubfName(), gffID, getGSeqName());
556     hasErrors(true);
557     return -1; //segment NOT added
558     }
559     */
560 gpertea 2
561 gpertea 16 if ((ovlen>2 || ovlen==0) || exons[oi]->exontype!=exgffCDS || exontype!=exgffCDS) {
562     if (gff_show_warnings)
563     GMessage("GFF Warning: merging overlapping/adjacent feature segment (%d-%d) into (%d-%d) (%s) for GFF ID %s on %s\n",
564     segstart, segend, exons[oi]->start, exons[oi]->end, getSubfName(), gffID, getGSeqName());
565     expandExon(oi, segstart, segend, exontype, sc, fr, qs, qe);
566     return oi;
567     }
568     // else add the segment if the overlap is small and between two CDS segments
569     //TODO: we might want to add an attribute here with the slippage coordinate and size?
570     covlen-=ovlen;
571     }//overlap or adjacent to existing segment
572     } //check for overlap
573 gpertea 2 // --- no overlap, or accepted micro-overlap (ribosomal slippage)
574     // create & add the new segment
575     GffExon* enew=new GffExon(segstart, segend, sc, fr, qs, qe, exontype);
576     int eidx=exons.Add(enew);
577     if (eidx<0) {
578 gpertea 16 //this would actually be acceptable if the object is a "Gene" and "exons" are in fact isoforms
579     if (gff_show_warnings)
580     GMessage("GFF Warning: failed adding segment %d-%d for %s (discarded)!\n",
581 gpertea 2 segstart, segend, gffID);
582 gpertea 16 delete enew;
583     hasErrors(true);
584 gpertea 2 return -1;
585     }
586     covlen+=(int)(exons[eidx]->end-exons[eidx]->start)+1;
587     start=exons.First()->start;
588     end=exons.Last()->end;
589     if (uptr!=NULL) { //collect stats about the underlying genomic sequence
590     GSeqStat* gsd=(GSeqStat*)uptr;
591     if (start<gsd->mincoord) gsd->mincoord=start;
592     if (end>gsd->maxcoord) gsd->maxcoord=end;
593 gpertea 16 if (this->len()>gsd->maxfeat_len) {
594     gsd->maxfeat_len=this->len();
595     gsd->maxfeat=this;
596     }
597 gpertea 2 }
598     return eidx;
599     }
600    
601 gpertea 16 void GffObj::expandExon(int oi, uint segstart, uint segend, char exontype, double sc, char fr, int qs, int qe) {
602     //oi is the index of the *first* overlapping segment found that must be enlarged
603     covlen-=exons[oi]->len();
604     if (segstart<exons[oi]->start)
605     exons[oi]->start=segstart;
606     if (qs && qs<exons[oi]->qstart) exons[oi]->qstart=qs;
607     if (segend>exons[oi]->end)
608     exons[oi]->end=segend;
609     if (qe && qe>exons[oi]->qend) exons[oi]->qend=qe;
610     //warning: score cannot be properly adjusted! e.g. if it's a p-value it's just going to get worse
611     if (sc!=0) exons[oi]->score=sc;
612     covlen+=exons[oi]->len();
613     //if (exons[oi]->exontype< exontype) -- always true
614     exons[oi]->exontype = exontype;
615     if (exontype==exgffCDS) exons[oi]->phase=fr;
616     //we must check if any more exons are also overlapping this
617     int ni=oi+1; //next exon index after oi
618     while (ni<exons.Count() && segend>=exons[ni]->start) { // next segment overlaps new enlarged segment
619     //only allow this if next segment is fully included, and a subordinate
620     if (exons[ni]->exontype<exontype && exons[ni]->end<=segend) {
621     /* I guess we have to relax this due to stupid UCSC hg18 files having a start_codon sticking out
622     chr1 hg18_knownGene start_codon 69806911 69806913 0.000000 + .
623     chr1 hg18_knownGene CDS 69806911 69806912 0.000000 + 0
624     chr1 hg18_knownGene exon 69805456 69806912 0.000000 + .
625     */
626     if (exons[ni]->qstart<exons[oi]->qstart) exons[oi]->qstart=exons[ni]->qstart;
627     if (exons[ni]->qend>exons[oi]->qend) exons[oi]->qend=exons[ni]->qend;
628     exons.Delete(ni);
629     }
630     else {
631     if (gff_show_warnings) GMessage("GFF Warning: overlapping existing exon(%d-%d) while expanding to %d-%d for GFF ID %s\n",
632     exons[ni]->start, exons[ni]->end, segstart, segend, gffID);
633     //hasErrors(true);
634     break;
635     }
636     }
637     // -- make sure any other related boundaries are updated:
638     start=exons.First()->start;
639     end=exons.Last()->end;
640     if (uptr!=NULL) { //collect stats about the underlying genomic sequence
641     GSeqStat* gsd=(GSeqStat*)uptr;
642     if (start<gsd->mincoord) gsd->mincoord=start;
643     if (end>gsd->maxcoord) gsd->maxcoord=end;
644     if (this->len()>gsd->maxfeat_len) {
645     gsd->maxfeat_len=this->len();
646     gsd->maxfeat=this;
647     }
648     }
649     }
650    
651 gpertea 2 void GffObj::removeExon(int idx) {
652     /*
653     if (idx==0 && segs[0].start==gstart)
654     gstart=segs[1].start;
655     if (idx==segcount && segs[segcount].end==gend)
656     gend=segs[segcount-1].end;
657     */
658     if (idx<0 || idx>=exons.Count()) return;
659     int segstart=exons[idx]->start;
660     int segend=exons[idx]->end;
661     exons.Delete(idx);
662     covlen -= (int)(segend-segstart)+1;
663     start=exons.First()->start;
664     end=exons.Last()->end;
665     if (isCDS) { CDstart=start; CDend=end; }
666     }
667    
668 gpertea 16 void GffObj::removeExon(GffExon* p) {
669     for (int idx=0;idx<exons.Count();idx++) {
670     if (exons[idx]==p) {
671     int segstart=exons[idx]->start;
672     int segend=exons[idx]->end;
673     exons.Delete(idx);
674     covlen -= (int)(segend-segstart)+1;
675     start=exons.First()->start;
676     end=exons.Last()->end;
677     if (isCDS) { CDstart=start; CDend=end; }
678     return;
679     }
680     }
681     }
682    
683    
684    
685 gpertea 2 GffObj::GffObj(GffReader *gfrd, GffLine* gffline, bool keepAttr, bool noExonAttr):
686 gpertea 16 GSeg(0,0), exons(true,true,false), children(1,false) {
687     xstart=0;
688     xend=0;
689     xstatus=0;
690     partial=false;
691     isCDS=false;
692     uptr=NULL;
693     ulink=NULL;
694     parent=NULL;
695     udata=0;
696     flags=0;
697     CDstart=0;
698     CDend=0;
699     CDphase=0;
700     geneID=NULL;
701     gene_name=NULL;
702     attrs=NULL;
703     gffID=NULL;
704     track_id=-1;
705     gseq_id=-1;
706     ftype_id=-1;
707     exon_ftype_id=-1;
708     strand='.';
709     if (gfrd==NULL)
710 gpertea 2 GError("Cannot use this GffObj constructor with a NULL GffReader!\n");
711 gpertea 16 gffnames_ref(names);
712     if (gfrd->names==NULL) gfrd->names=names;
713     //qlen=0;qstart=0;qend=0;
714     gscore=0;
715     uscore=0;
716     covlen=0;
717     qcov=0;
718     start=gffline->fstart;
719     end=gffline->fend;
720     gseq_id=names->gseqs.addName(gffline->gseqname);
721     track_id=names->tracks.addName(gffline->track);
722     strand=gffline->strand;
723     qlen=gffline->qlen;
724     qstart=gffline->qstart;
725     qend=gffline->qend;
726     //setup flags from gffline
727     isCDS=gffline->is_cds; //for now
728     isGene(gffline->is_gene);
729     isTranscript(gffline->is_transcript || gffline->exontype!=0);
730     fromGff3(gffline->is_gff3);
731    
732     if (gffline->parents!=NULL) {
733     //GTF style -- create a GffObj directly by subfeature
734     //(also possible orphan GFF3 exon line, or an exon given before its parent (chado))
735     if (gffline->exontype!=0) { //recognized exon-like feature
736     ftype_id=gff_fid_transcript; //so this is some sort of transcript
737     exon_ftype_id=gff_fid_exon; //subfeatures MUST be exons
738     }
739     else {//unrecognized subfeatures
740     //make this GffObj of the same feature type
741     ftype_id=names->feats.addName(gffline->ftype);
742     }
743     if (gffline->ID==NULL) { //typical GTF
744     gffID=Gstrdup(gffline->parents[0]);
745     this->createdByExon(true);
746     //this is likely the first exon/segment of the feature
747     addExon(gfrd, gffline, keepAttr, noExonAttr);
748 gpertea 2 }
749 gpertea 16 else { //a parented feature with an ID -- probably an orphan GFF3 line
750     if (gffline->is_gff3 && gffline->exontype!=0) {
751     //premature exon given before its parent transcript
752     //create the transcript entry here
753     gffID=Gstrdup(gffline->parents[0]);
754     this->createdByExon(true);
755     //this is the first exon/segment of the transcript
756     addExon(gfrd, gffline, keepAttr, noExonAttr);
757     }
758     else { //unrecognized non-exon feature ? use the ID instead
759     gffID=Gstrdup(gffline->ID);
760     if (keepAttr) this->parseAttrs(attrs, gffline->info);
761     }
762 gpertea 2 }
763 gpertea 16 } //subfeature given directly
764     else { //gffline->parents==NULL
765     //create a parent feature in its own right
766 gpertea 2 gscore=gffline->score;
767     if (gffline->ID==NULL || gffline->ID[0]==0)
768 gpertea 16 GError("Error: no ID found for GFF record start\n");
769     gffID=Gstrdup(gffline->ID); //there must be an ID here
770     //if (gffline->is_transcript) ftype_id=gff_fid_mRNA;
771     //else
772     ftype_id=names->feats.addName(gffline->ftype);
773     if (gffline->is_transcript)
774     exon_ftype_id=gff_fid_exon;
775    
776     if (keepAttr) this->parseAttrs(attrs, gffline->info);
777     }//no parent
778    
779     if (gffline->gene_name!=NULL) {
780     gene_name=Gstrdup(gffline->gene_name);
781     }
782     if (gffline->gene_id!=NULL) {
783     geneID=Gstrdup(gffline->gene_id);
784     }
785    
786     GSeqStat* gsd=gfrd->gseqstats.AddIfNew(new GSeqStat(gseq_id,names->gseqs.lastNameUsed()),true);
787     uptr=gsd;
788     if (start<gsd->mincoord) gsd->mincoord=start;
789     if (end>gsd->maxcoord) gsd->maxcoord=end;
790     if (this->len()>gsd->maxfeat_len) {
791     gsd->maxfeat_len=this->len();
792     gsd->maxfeat=this;
793 gpertea 2 }
794     }
795    
796     GffLine* GffReader::nextGffLine() {
797     if (gffline!=NULL) return gffline; //caller should free gffline after processing
798     while (gffline==NULL) {
799     int llen=0;
800     buflen=GFF_LINELEN-1;
801     char* l=fgetline(linebuf, buflen, fh, &fpos, &llen);
802     if (l==NULL) {
803     return NULL; //end of file
804     }
805     int ns=0; //first nonspace position
806     while (l[ns]!=0 && isspace(l[ns])) ns++;
807     if (l[ns]=='#' || llen<10) continue;
808     gffline=new GffLine(this, l);
809     if (gffline->skip) {
810     delete gffline;
811     gffline=NULL;
812 gpertea 16 continue;
813 gpertea 2 }
814 gpertea 16 if (gffline->ID==NULL && gffline->parents==NULL) { //it must have an ID
815     //this might not be needed, already checked in the GffLine constructor
816     if (gff_warns)
817     GMessage("Warning: malformed GFF line, no parent or record Id (kipping\n");
818     delete gffline;
819     gffline=NULL;
820     //continue;
821     }
822 gpertea 2 }
823     return gffline;
824     }
825    
826     char* GffReader::gfoBuildId(const char* id, const char* ctg) {
827     //caller must free the returned pointer
828     char* buf=NULL;
829     int idlen=strlen(id);
830     GMALLOC(buf, idlen+strlen(ctg)+2);
831     strcpy(buf, id);
832     buf[idlen]='~';
833     strcpy(buf+idlen+1, ctg);
834     return buf;
835     }
836    
837     void GffReader::gfoRemove(const char* id, const char* ctg) {
838     char* buf=gfoBuildId(id,ctg);
839     phash.Remove(buf);
840     GFREE(buf);
841     }
842    
843 gpertea 16 //Warning: if gflst gets altered, idx becomes obsolete
844     GfoHolder* GffReader::gfoAdd(const char* id, const char* ctg, GffObj* gfo, int idx) {
845 gpertea 2 char* buf=gfoBuildId(id,ctg);
846 gpertea 16 GfoHolder* r=new GfoHolder(gfo,idx);
847     phash.Add(buf, r);
848 gpertea 2 GFREE(buf);
849 gpertea 16 return r;
850 gpertea 2 }
851 gpertea 16
852     GfoHolder* GffReader::gfoFind(const char* id, const char* ctg) {
853 gpertea 2 char* buf=gfoBuildId(id,ctg);
854 gpertea 16 GfoHolder* r=phash.Find(buf);
855 gpertea 2 GFREE(buf);
856     return r;
857     }
858    
859 gpertea 16 GfoHolder* GffReader::replaceGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr, int replaceidx) {
860     GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
861     GfoHolder* r=NULL;
862     if (replaceidx>=0) {
863     gflst.Put(replaceidx,newgfo);
864     r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, replaceidx);
865     }
866     else {
867     int gfoidx=gflst.Add(newgfo);
868     r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, gfoidx);
869     }
870     if (gff_warns) {
871     int* pcount=tids.Find(newgfo->gffID);
872     if (pcount!=NULL) {
873     if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
874     (*pcount)++;
875     }
876     else {
877     tids.Add(newgfo->gffID,new int(1));
878     }
879     }
880     return r;
881     }
882 gpertea 2
883 gpertea 16 GfoHolder* GffReader::updateParent(GfoHolder* newgfh, GffObj* parent) {
884     //assert(parent);
885     //assert(newgfo);
886     parent->children.Add(newgfh->gffobj);
887     if (newgfh->gffobj->parent==NULL) newgfh->gffobj->parent=parent;
888     newgfh->gffobj->setLevel(parent->getLevel()+1);
889     if (parent->isGene()) {
890     if (parent->gene_name!=NULL && newgfh->gffobj->gene_name==NULL)
891     newgfh->gffobj->gene_name=Gstrdup(parent->gene_name);
892     if (parent->geneID!=NULL && newgfh->gffobj->geneID==NULL)
893     newgfh->gffobj->geneID=Gstrdup(parent->geneID);
894     }
895    
896     return newgfh;
897 gpertea 2 }
898    
899 gpertea 16 GfoHolder* GffReader::newGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr,
900     GffObj* parent, GffExon* pexon) {
901     GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
902     GfoHolder* r=NULL;
903     int gfoidx=gflst.Add(newgfo);
904     r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, gfoidx);
905     if (parent!=NULL) {
906     updateParent(r, parent);
907     if (pexon!=NULL) parent->removeExon(pexon);
908     }
909     if (gff_warns) {
910     int* pcount=tids.Find(newgfo->gffID);
911     if (pcount!=NULL) {
912     if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
913     (*pcount)++;
914     }
915     else {
916     tids.Add(newgfo->gffID,new int(1));
917     }
918     }
919     return r;
920     }
921 gpertea 2
922 gpertea 16 GfoHolder* GffReader::updateGffRec(GfoHolder* prevgfo, GffLine* gffline,
923     bool keepAttr) {
924     if (prevgfo==NULL) return NULL;
925     prevgfo->gffobj->createdByExon(false);
926     prevgfo->gffobj->ftype_id=prevgfo->gffobj->names->feats.addName(gffline->ftype);
927     prevgfo->gffobj->start=gffline->fstart;
928     prevgfo->gffobj->end=gffline->fend;
929     prevgfo->gffobj->isGene(gffline->is_gene);
930     prevgfo->gffobj->isTranscript(gffline->is_transcript || gffline->exontype!=0);
931     prevgfo->gffobj->fromGff3(gffline->is_gff3);
932     if (keepAttr) {
933     if (prevgfo->gffobj->attrs!=NULL) prevgfo->gffobj->attrs->Clear();
934     prevgfo->gffobj->parseAttrs(prevgfo->gffobj->attrs, gffline->info);
935     }
936     return prevgfo;
937     }
938    
939    
940     bool GffReader::addExonFeature(GfoHolder* prevgfo, GffLine* gffline, GHash<CNonExon>& pex, bool noExonAttr) {
941     bool r=true;
942     if (gffline->strand!=prevgfo->gffobj->strand) {
943     GMessage("GFF Error: duplicate GFF ID '%s' (exons found on different strands of %s)\n",
944     prevgfo->gffobj->gffID, prevgfo->gffobj->getGSeqName());
945     r=false;
946     }
947     int gdist=(gffline->fstart>prevgfo->gffobj->end) ? gffline->fstart-prevgfo->gffobj->end :
948     ((gffline->fend<prevgfo->gffobj->start)? prevgfo->gffobj->start-gffline->fend :
949     0 );
950     if (gdist>(int)GFF_MAX_LOCUS) { //too far apart, most likely this is a duplicate ID
951     GMessage("Error: duplicate GFF ID '%s' (or exons too far apart)!\n",prevgfo->gffobj->gffID);
952     //validation_errors = true;
953     r=false;
954     if (!gff_warns) exit(1);
955     }
956     int eidx=prevgfo->gffobj->addExon(this, gffline, !noExonAttr, noExonAttr);
957     if (eidx>=0 && gffline->ID!=NULL && gffline->exontype==0)
958     subfPoolAdd(pex, prevgfo);
959     return r;
960     }
961    
962     CNonExon* GffReader::subfPoolCheck(GffLine* gffline, GHash<CNonExon>& pex, char*& subp_name) {
963     CNonExon* subp=NULL;
964     subp_name=NULL;
965     for (int i=0;i<gffline->num_parents;i++) {
966     if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
967     continue;
968     subp_name=gfoBuildId(gffline->parents[i], gffline->gseqname); //e.g. mRNA name
969     subp=pex.Find(subp_name);
970     if (subp!=NULL)
971     return subp;
972     GFREE(subp_name);
973     }
974     return NULL;
975     }
976    
977     void GffReader::subfPoolAdd(GHash<CNonExon>& pex, GfoHolder* newgfo) {
978     //this might become a parent feature later
979     if (newgfo->gffobj->exons.Count()>0) {
980     char* xbuf=gfoBuildId(gffline->ID, gffline->gseqname);
981     pex.Add(xbuf, new CNonExon(newgfo->idx, newgfo->gffobj,
982     newgfo->gffobj->exons[0], gffline));
983     GFREE(xbuf);
984     }
985     }
986    
987     GfoHolder* GffReader::promoteFeature(CNonExon* subp, char*& subp_name, GHash<CNonExon>& pex,
988     bool keepAttr, bool noExonAttr) {
989     GffObj* prevp=subp->parent; //grandparent of gffline (e.g. gene)
990     if (prevp!=gflst[subp->idx])
991     GError("Error promoting subfeature %s, gflst index mismatch?!\n", subp->gffline->ID);
992     subp->gffline->discardParent();
993     GfoHolder* gfoh=newGffRec(subp->gffline, keepAttr, noExonAttr, prevp, subp->exon);
994     pex.Remove(subp_name); //no longer a potential parent, moved it to phash already
995     prevp->promotedChildren(true);
996     return gfoh; //returns the holder of newly promoted feature
997     }
998    
999     //have to parse the whole file because exons can be scattered all over
1000 gpertea 2 void GffReader::readAll(bool keepAttr, bool mergeCloseExons, bool noExonAttr) {
1001 gpertea 16 bool validation_errors = false;
1002     //loc_debug=false;
1003     GHash<CNonExon> pex; //keep track of any "exon"-like features that have an ID
1004     //and thus could become promoted to parent features
1005 gpertea 2 while (nextGffLine()!=NULL) {
1006 gpertea 16 //seen this gff ID before?
1007     GfoHolder* prevseen=NULL;
1008     if (gffline->ID) //GFF3
1009     prevseen=gfoFind(gffline->ID, gffline->gseqname);
1010     if (prevseen!=NULL) {
1011     if (prevseen->gffobj->createdByExon()) {
1012     updateGffRec(prevseen, gffline, keepAttr);
1013     }
1014     else {
1015     GMessage("Error: duplicate GFF ID '%s' encountered!\n",gffline->ID);
1016     validation_errors = true;
1017     if (gff_warns) {
1018     delete gffline; gffline=NULL; continue;
1019     }
1020     else exit(1);
1021     }
1022 gpertea 2 }
1023 gpertea 16 if (gffline->parents==NULL) {//start GFF3-like record with no parent (mRNA, gene)
1024     if (!prevseen) newGffRec(gffline, keepAttr, noExonAttr);
1025 gpertea 2 }
1026 gpertea 16 else { //--- it's a parented feature (could still be a mRNA)
1027     bool found_parent=false;
1028     GfoHolder* newgfo=prevseen;
1029     for (int i=0;i<gffline->num_parents;i++) {
1030     if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
1031     continue; //skipping discarded parent feature
1032     GfoHolder* parentgfo=gfoFind(gffline->parents[i], gffline->gseqname);
1033     if (parentgfo!=NULL) { //parent GffObj parsed earlier
1034     found_parent=true;
1035     if (parentgfo->gffobj->isGene() && gffline->is_transcript
1036     && gffline->exontype==0) {
1037     //not an exon, but a transcript parented by a gene
1038     if (newgfo) {
1039     updateParent(newgfo, parentgfo->gffobj);
1040     }
1041     else {
1042     newgfo=newGffRec(gffline, keepAttr, noExonAttr, parentgfo->gffobj);
1043     }
1044     }
1045     else { //potential exon subfeature
1046     if (!addExonFeature(parentgfo, gffline, pex, noExonAttr))
1047     validation_errors=true;
1048     }
1049 gpertea 2 }
1050 gpertea 16 } //for each parsed parent Id
1051     if (!found_parent) { //new GTF-like record starting here with a subfeature directly
1052     //or it could be some chado GFF3 barf with exons declared BEFORE their parent :(
1053     //check if this feature isn't parented by a previously stored "exon" subfeature
1054     char* subp_name=NULL;
1055     CNonExon* subp=subfPoolCheck(gffline, pex, subp_name);
1056     if (subp!=NULL) { //found a subfeature that is the parent of this gffline
1057     //promote that subfeature to a full GffObj
1058     GfoHolder* gfoh=promoteFeature(subp, subp_name, pex, keepAttr, noExonAttr);
1059     //add current gffline as an exon of the newly promoted subfeature
1060     if (!addExonFeature(gfoh, gffline, pex, noExonAttr))
1061     validation_errors=true;
1062     }
1063     else { //no parent seen before, create one directly with this exon
1064     //loc_debug=true;
1065     GfoHolder* newgfo=prevseen ? prevseen : newGffRec(gffline, keepAttr, noExonAttr);
1066     if (gffline->ID!=NULL && gffline->exontype==0)
1067     subfPoolAdd(pex, newgfo);
1068     //even those with errors will be added here!
1069     }
1070     GFREE(subp_name);
1071     } //no previous parent found
1072     } //parented feature
1073     //--
1074     delete gffline;
1075     gffline=NULL;
1076     }//while gff lines
1077     gflst.finalize(this, mergeCloseExons, keepAttr, noExonAttr); //force sorting by locus if so constructed
1078 gpertea 2 // all gff records are now loaded in GList gflst
1079     // so we can free the hash
1080     phash.Clear();
1081 gpertea 16 tids.Clear();
1082     if (validation_errors) {
1083     exit(1);
1084     }
1085 gpertea 2 }
1086    
1087 gpertea 16 GffObj* GffObj::finalize(GffReader* gfr, bool mergeCloseExons, bool keepAttrs, bool noExonAttr) {
1088     //merge
1089     //always merge adjacent or overlapping segments
1090     //but if mergeCloseExons then merge even when distance is up to 5 bases
1091 gpertea 2 udata=0;
1092     uptr=NULL;
1093 gpertea 16 if (gfr->transcriptsOnly && !(isTranscript() || (isGene() && children.Count()==0))) {
1094     isDiscarded(true);
1095     }
1096     if (ftype_id==gff_fid_transcript && CDstart>0) {
1097     ftype_id=gff_fid_mRNA;
1098     //exon_ftype_id=gff_fid_exon;
1099     }
1100     //if (ftype_id==gff_fid_mRNA || exon_ftype_id==gff_fid_exon || mergeCloseExons) {
1101     if (isTranscript() || exon_ftype_id==gff_fid_exon || mergeCloseExons) {
1102 gpertea 2 int mindist=mergeCloseExons ? 5:1;
1103     for (int i=0;i<exons.Count()-1;i++) {
1104     int ni=i+1;
1105     uint mend=exons[i]->end;
1106     while (ni<exons.Count()) {
1107     int dist=(int)(exons[ni]->start-mend);
1108 gpertea 16 if (dist>mindist) break; //no merging with next segment
1109     if (gfr!=NULL && gfr->gff_warns && dist!=0 && (exons[ni]->exontype!=exgffUTR && exons[i]->exontype!=exgffUTR)) {
1110     GMessage("GFF warning: merging adjacent/overlapping segments of %s on %s (%d-%d, %d-%d)\n",
1111     gffID, getGSeqName(), exons[i]->start, exons[i]->end,exons[ni]->start, exons[ni]->end);
1112     }
1113 gpertea 2 mend=exons[ni]->end;
1114 gpertea 16 covlen-=exons[i]->len();
1115 gpertea 2 exons[i]->end=mend;
1116 gpertea 16 covlen+=exons[i]->len();
1117     covlen-=exons[ni]->len();
1118 gpertea 2 if (exons[ni]->attrs!=NULL && (exons[i]->attrs==NULL ||
1119     exons[i]->attrs->Count()<exons[ni]->attrs->Count())) {
1120     //use the other exon attributes, if more
1121     delete(exons[i]->attrs);
1122     exons[i]->attrs=exons[ni]->attrs;
1123     exons[ni]->attrs=NULL;
1124     }
1125     exons.Delete(ni);
1126     } //check for merge with next exon
1127     } //for each exon
1128     }
1129 gpertea 16 //attribute reduction for GTF records
1130     if (keepAttrs && !noExonAttr && !fromGff3()
1131     && exons.Count()>0 && exons[0]->attrs!=NULL) {
1132     bool attrs_discarded=false;
1133     for (int a=0;a<exons[0]->attrs->Count();a++) {
1134     int attr_name_id=exons[0]->attrs->Get(a)->attr_id;
1135     char* attr_name=names->attrs.getName(attr_name_id);
1136     char* attr_val =exons[0]->attrs->Get(a)->attr_val;
1137     bool sameExonAttr=true;
1138     for (int i=1;i<exons.Count();i++) {
1139     char* ov=exons[i]->getAttr(attr_name_id);
1140     if (ov==NULL || (strcmp(ov,attr_val)!=0)) {
1141     sameExonAttr=false;
1142     break;
1143     }
1144     }
1145     if (sameExonAttr) {
1146     //delete this attribute from exons level
1147     attrs_discarded=true;
1148     this->addAttr(attr_name, attr_val);
1149     for (int i=1;i<exons.Count();i++) {
1150     removeExonAttr(*(exons[i]), attr_name_id);
1151     }
1152     exons[0]->attrs->freeItem(a);
1153     }
1154     }
1155     if (attrs_discarded) exons[0]->attrs->Pack();
1156     }
1157 gpertea 2 return this;
1158     }
1159    
1160 gpertea 16 void GffObj::parseAttrs(GffAttrs*& atrlist, char* info, bool isExon) {
1161 gpertea 2 if (names==NULL)
1162     GError(ERR_NULL_GFNAMES, "parseAttrs()");
1163     if (atrlist==NULL)
1164     atrlist=new GffAttrs();
1165     char* endinfo=info+strlen(info);
1166     char* start=info;
1167     char* pch=start;
1168     while (start<endinfo) {
1169     //skip spaces
1170     while (*start==' ' && start<endinfo) start++;
1171     pch=strchr(start, ';');
1172     if (pch==NULL) pch=endinfo;
1173     else {
1174     *pch='\0';
1175     pch++;
1176     }
1177     char* ech=strchr(start,'=');
1178     if (ech!=NULL) { // attr=value format found
1179     *ech='\0';
1180 gpertea 16 //if (noExonAttr && (strcmp(start, "exon_number")==0 || strcmp(start, "exon")==0)) { start=pch; continue; }
1181     if (strcmp(start, "exon_number")==0 || strcmp(start, "exon")==0 ||
1182     strcmp(start, "exon_id")==0)
1183     { start=pch; continue; }
1184 gpertea 2 ech++;
1185     while (*ech==' ' && ech<endinfo) ech++;//skip extra spaces after the '='
1186 gpertea 16 //atrlist->Add(new GffAttr(names->attrs.addName(start),ech));
1187     //make sure we don't add the same attribute more than once
1188     if (isExon && (strcmp(start, "protein_id")==0)) {
1189     //Ensembl special case
1190     this->addAttr(start, ech);
1191     start=pch;
1192     continue;
1193     }
1194     atrlist->add_or_update(names, start, ech);
1195 gpertea 2 }
1196     /*
1197     else { //not an attr=value format
1198     atrlist->Add(new GffAttr(names->attrs.addName(start),"1"));
1199     }
1200     */
1201     start=pch;
1202     }
1203     if (atrlist->Count()==0) { delete atrlist; atrlist=NULL; }
1204     }
1205    
1206 gpertea 16 void GffObj::addAttr(const char* attrname, const char* attrvalue) {
1207 gpertea 2 if (this->attrs==NULL)
1208     this->attrs=new GffAttrs();
1209 gpertea 16 //this->attrs->Add(new GffAttr(names->attrs.addName(attrname),attrvalue));
1210     this->attrs->add_or_update(names, attrname, attrvalue);
1211 gpertea 2 }
1212    
1213 gpertea 16
1214     void GffObj::setFeatureName(const char* feature) {
1215     //change the feature name/type for a transcript
1216     int fid=names->feats.addName(feature);
1217     if (monoFeature() && exons.Count()>0)
1218     this->exon_ftype_id=fid;
1219     this->ftype_id=fid;
1220     }
1221    
1222     void GffObj::setRefName(const char* newname) {
1223     //change the feature name/type for a transcript
1224     int rid=names->gseqs.addName(newname);
1225     this->gseq_id=rid;
1226     }
1227    
1228    
1229    
1230     int GffObj::removeAttr(const char* attrname, const char* attrval) {
1231     if (this->attrs==NULL || attrname==NULL || attrname[0]==0) return 0;
1232     int aid=this->names->attrs.getId(attrname);
1233     if (aid<0) return 0;
1234     int delcount=0; //could be more than one ?
1235     for (int i=0;i<this->attrs->Count();i++) {
1236     if (aid==this->attrs->Get(i)->attr_id) {
1237     if (attrval==NULL ||
1238     strcmp(attrval, this->attrs->Get(i)->attr_val)==0) {
1239     delcount++;
1240     this->attrs->freeItem(i);
1241     }
1242     }
1243     }
1244     if (delcount>0) this->attrs->Pack();
1245     return delcount;
1246     }
1247    
1248     int GffObj::removeAttr(int aid, const char* attrval) {
1249     if (this->attrs==NULL || aid<0) return 0;
1250     int delcount=0; //could be more than one ?
1251     for (int i=0;i<this->attrs->Count();i++) {
1252     if (aid==this->attrs->Get(i)->attr_id) {
1253     if (attrval==NULL ||
1254     strcmp(attrval, this->attrs->Get(i)->attr_val)==0) {
1255     delcount++;
1256     this->attrs->freeItem(i);
1257     }
1258     }
1259     }
1260     if (delcount>0) this->attrs->Pack();
1261     return delcount;
1262     }
1263    
1264    
1265     int GffObj::removeExonAttr(GffExon& exon, const char* attrname, const char* attrval) {
1266     if (exon.attrs==NULL || attrname==NULL || attrname[0]==0) return 0;
1267     int aid=this->names->attrs.getId(attrname);
1268     if (aid<0) return 0;
1269     int delcount=0; //could be more than one
1270     for (int i=0;i<exon.attrs->Count();i++) {
1271     if (aid==exon.attrs->Get(i)->attr_id) {
1272     if (attrval==NULL ||
1273     strcmp(attrval, exon.attrs->Get(i)->attr_val)==0) {
1274     delcount++;
1275     exon.attrs->freeItem(i);
1276     }
1277     }
1278     }
1279     if (delcount>0) exon.attrs->Pack();
1280     return delcount;
1281     }
1282    
1283     int GffObj::removeExonAttr(GffExon& exon, int aid, const char* attrval) {
1284     if (exon.attrs==NULL || aid<0) return 0;
1285     int delcount=0; //could be more than one
1286     for (int i=0;i<exon.attrs->Count();i++) {
1287     if (aid==exon.attrs->Get(i)->attr_id) {
1288     if (attrval==NULL ||
1289     strcmp(attrval, exon.attrs->Get(i)->attr_val)==0) {
1290     delcount++;
1291     exon.attrs->freeItem(i);
1292     }
1293     }
1294     }
1295     if (delcount>0) exon.attrs->Pack();
1296     return delcount;
1297     }
1298    
1299    
1300 gpertea 2 void GffObj::getCDS_ends(uint& cds_start, uint& cds_end) {
1301     cds_start=0;
1302     cds_end=0;
1303     if (CDstart==0 || CDend==0) return; //no CDS info
1304     int cdsadj=0;
1305     if (CDphase=='1' || CDphase=='2') {
1306     cdsadj=CDphase-'0';
1307     }
1308     cds_start=CDstart;
1309     cds_end=CDend;
1310     if (strand=='-') cds_end-=cdsadj;
1311     else cds_start+=cdsadj;
1312     }
1313    
1314     void GffObj::mRNA_CDS_coords(uint& cds_mstart, uint& cds_mend) {
1315     //sets cds_start and cds_end to the CDS start,end coordinates on the spliced mRNA transcript
1316     cds_mstart=0;
1317     cds_mend=0;
1318     if (CDstart==0 || CDend==0) return; //no CDS info
1319     //restore normal coordinates, just in case
1320     unxcoord();
1321     int cdsadj=0;
1322     if (CDphase=='1' || CDphase=='2') {
1323     cdsadj=CDphase-'0';
1324     }
1325     /*
1326     uint seqstart=CDstart;
1327     uint seqend=CDend;
1328     */
1329     uint seqstart=exons.First()->start;
1330     uint seqend=exons.Last()->end;
1331     int s=0; //resulting nucleotide counter
1332     if (strand=='-') {
1333     for (int x=exons.Count()-1;x>=0;x--) {
1334     uint sgstart=exons[x]->start;
1335     uint sgend=exons[x]->end;
1336     if (seqend<sgstart || seqstart>sgend) continue;
1337     if (seqstart>=sgstart && seqstart<=sgend)
1338     sgstart=seqstart; //seqstart within this segment
1339     if (seqend>=sgstart && seqend<=sgend)
1340     sgend=seqend; //seqend within this segment
1341     s+=(int)(sgend-sgstart)+1;
1342     if (CDstart>=sgstart && CDstart<=sgend) {
1343     //CDstart in this segment
1344     //and we are getting the whole transcript
1345     cds_mend=s-(int)(CDstart-sgstart);
1346     }
1347     if (CDend>=sgstart && CDend<=sgend) {
1348     //CDstart in this segment
1349     //and we are getting the whole transcript
1350     cds_mstart=s-(int)(CDend-cdsadj-sgstart);
1351     }
1352     } //for each exon
1353     } // - strand
1354     else { // + strand
1355     for (int x=0;x<exons.Count();x++) {
1356     uint sgstart=exons[x]->start;
1357     uint sgend=exons[x]->end;
1358     if (seqend<sgstart || seqstart>sgend) continue;
1359     if (seqstart>=sgstart && seqstart<=sgend)
1360     sgstart=seqstart; //seqstart within this segment
1361     if (seqend>=sgstart && seqend<=sgend)
1362     sgend=seqend; //seqend within this segment
1363     s+=(int)(sgend-sgstart)+1;
1364     /* for (uint i=sgstart;i<=sgend;i++) {
1365     spliced[s]=gsubseq[i-gstart];
1366     s++;
1367     }//for each nt
1368     */
1369     if (CDstart>=sgstart && CDstart<=sgend) {
1370     //CDstart in this segment
1371     cds_mstart=s-(int)(sgend-CDstart-cdsadj);
1372     }
1373     if (CDend>=sgstart && CDend<=sgend) {
1374     //CDend in this segment
1375     cds_mend=s-(int)(sgend-CDend);
1376     }
1377     } //for each exon
1378     } // + strand
1379     //spliced[s]=0;
1380     //if (rlen!=NULL) *rlen=s;
1381     //return spliced;
1382     }
1383    
1384 gpertea 16 char* GffObj::getUnspliced(GFaSeqGet* faseq, int* rlen, GList<GSeg>* seglst)
1385     {
1386     if (faseq==NULL) { GMessage("Warning: getUnspliced(NULL,.. ) called!\n");
1387     return NULL;
1388     }
1389     //restore normal coordinates:
1390     unxcoord();
1391     if (exons.Count()==0) return NULL;
1392     int fspan=end-start+1;
1393     const char* gsubseq=faseq->subseq(start, fspan);
1394     if (gsubseq==NULL) {
1395     GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1396     }
1397     char* unspliced=NULL;
1398    
1399     int seqstart=exons.First()->start;
1400     int seqend=exons.Last()->end;
1401    
1402     int unsplicedlen = 0;
1403    
1404     unsplicedlen += seqend - seqstart + 1;
1405    
1406     GMALLOC(unspliced, unsplicedlen+1); //allocate more here
1407     //uint seqstart, seqend;
1408    
1409     int s = 0; //resulting nucleotide counter
1410     if (strand=='-')
1411     {
1412     if (seglst!=NULL)
1413     seglst->Add(new GSeg(s+1,s+1+seqend-seqstart));
1414     for (int i=seqend;i>=seqstart;i--)
1415     {
1416     unspliced[s] = ntComplement(gsubseq[i-start]);
1417     s++;
1418     }//for each nt
1419     } // - strand
1420     else
1421     { // + strand
1422     if (seglst!=NULL)
1423     seglst->Add(new GSeg(s+1,s+1+seqend-seqstart));
1424     for (int i=seqstart;i<=seqend;i++)
1425     {
1426     unspliced[s]=gsubseq[i-start];
1427     s++;
1428     }//for each nt
1429     } // + strand
1430     //assert(s <= unsplicedlen);
1431     unspliced[s]=0;
1432     if (rlen!=NULL) *rlen=s;
1433     return unspliced;
1434     }
1435    
1436 gpertea 2 char* GffObj::getSpliced(GFaSeqGet* faseq, bool CDSonly, int* rlen, uint* cds_start, uint* cds_end,
1437     GList<GSeg>* seglst) {
1438     if (CDSonly && CDstart==0) return NULL;
1439     if (faseq==NULL) { GMessage("Warning: getSpliced(NULL,.. ) called!\n");
1440     return NULL;
1441     }
1442     //restore normal coordinates:
1443     unxcoord();
1444     if (exons.Count()==0) return NULL;
1445     int fspan=end-start+1;
1446     const char* gsubseq=faseq->subseq(start, fspan);
1447     if (gsubseq==NULL) {
1448     GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1449     }
1450 gpertea 16 if (fspan<(int)(end-start+1)) { //special case: stop coordinate was extended past the gseq length, must adjust
1451     int endadj=end-start+1-fspan;
1452     uint prevend=end;
1453     end-=endadj;
1454     if (CDend>end) CDend=end;
1455     if (exons.Last()->end>end) {
1456     exons.Last()->end=end; //this could get us into trouble if exon start is also > end
1457     if (exons.Last()->start>exons.Last()->end) {
1458     GError("GffObj::getSpliced() error: improper genomic coordinate %d on %s for %s\n",
1459     prevend,getGSeqName(), getID());
1460     }
1461     covlen-=endadj;
1462     }
1463     }
1464 gpertea 2 char* spliced=NULL;
1465     GMALLOC(spliced, covlen+1); //allocate more here
1466     uint seqstart, seqend;
1467     int cdsadj=0;
1468     if (CDphase=='1' || CDphase=='2') {
1469     cdsadj=CDphase-'0';
1470     }
1471     if (CDSonly) {
1472     seqstart=CDstart;
1473     seqend=CDend;
1474     if (strand=='-') seqend-=cdsadj;
1475     else seqstart+=cdsadj;
1476     }
1477     else {
1478     seqstart=exons.First()->start;
1479     seqend=exons.Last()->end;
1480     }
1481     int s=0; //resulting nucleotide counter
1482     if (strand=='-') {
1483     for (int x=exons.Count()-1;x>=0;x--) {
1484     uint sgstart=exons[x]->start;
1485     uint sgend=exons[x]->end;
1486     if (seqend<sgstart || seqstart>sgend) continue;
1487     if (seqstart>=sgstart && seqstart<=sgend)
1488     sgstart=seqstart; //seqstart within this segment
1489     if (seqend>=sgstart && seqend<=sgend)
1490     sgend=seqend; //seqend within this segment
1491     if (seglst!=NULL)
1492     seglst->Add(new GSeg(s+1,s+1+sgend-sgstart));
1493     for (uint i=sgend;i>=sgstart;i--) {
1494     spliced[s] = ntComplement(gsubseq[i-start]);
1495     s++;
1496     }//for each nt
1497    
1498     if (!CDSonly && cds_start!=NULL && CDstart>0) {
1499     if (CDstart>=sgstart && CDstart<=sgend) {
1500     //CDstart in this segment
1501     //and we are getting the whole transcript
1502     *cds_end=s-(CDstart-sgstart);
1503     }
1504     if (CDend>=sgstart && CDend<=sgend) {
1505     //CDstart in this segment
1506     //and we are getting the whole transcript
1507     *cds_start=s-(CDend-cdsadj-sgstart);
1508     }
1509     }//update local CDS coordinates
1510     } //for each exon
1511     } // - strand
1512     else { // + strand
1513     for (int x=0;x<exons.Count();x++) {
1514     uint sgstart=exons[x]->start;
1515     uint sgend=exons[x]->end;
1516     if (seqend<sgstart || seqstart>sgend) continue;
1517     if (seqstart>=sgstart && seqstart<=sgend)
1518     sgstart=seqstart; //seqstart within this segment
1519     if (seqend>=sgstart && seqend<=sgend)
1520     sgend=seqend; //seqend within this segment
1521     if (seglst!=NULL)
1522     seglst->Add(new GSeg(s+1,s+1+sgend-sgstart));
1523     for (uint i=sgstart;i<=sgend;i++) {
1524     spliced[s]=gsubseq[i-start];
1525     s++;
1526     }//for each nt
1527     if (!CDSonly && cds_start!=NULL && CDstart>0) {
1528     if (CDstart>=sgstart && CDstart<=sgend) {
1529     //CDstart in this segment
1530     //and we are getting the whole transcript
1531     *cds_start=s-(sgend-CDstart-cdsadj);
1532     }
1533     if (CDend>=sgstart && CDend<=sgend) {
1534     //CDstart in this segment
1535     //and we are getting the whole transcript
1536     *cds_end=s-(sgend-CDend);
1537     }
1538     }//update local CDS coordinates
1539     } //for each exon
1540     } // + strand
1541     spliced[s]=0;
1542     if (rlen!=NULL) *rlen=s;
1543     return spliced;
1544     }
1545    
1546     char* GffObj::getSplicedTr(GFaSeqGet* faseq, bool CDSonly, int* rlen) {
1547     if (CDSonly && CDstart==0) return NULL;
1548     //restore normal coordinates:
1549     unxcoord();
1550     if (exons.Count()==0) return NULL;
1551     int fspan=end-start+1;
1552     const char* gsubseq=faseq->subseq(start, fspan);
1553     if (gsubseq==NULL) {
1554     GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1555     }
1556    
1557     char* translation=NULL;
1558     GMALLOC(translation, (int)(covlen/3)+1);
1559     uint seqstart, seqend;
1560     int cdsadj=0;
1561     if (CDphase=='1' || CDphase=='2') {
1562     cdsadj=CDphase-'0';
1563     }
1564     if (CDSonly) {
1565     seqstart=CDstart;
1566     seqend=CDend;
1567     if (strand=='-') seqend-=cdsadj;
1568     else seqstart+=cdsadj;
1569     }
1570     else {
1571     seqstart=exons.First()->start;
1572     seqend=exons.Last()->end;
1573     }
1574     Codon codon;
1575     int nt=0; //codon nucleotide counter (0..2)
1576     int aa=0; //aminoacid count
1577     if (strand=='-') {
1578     for (int x=exons.Count()-1;x>=0;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     }
1587     for (uint i=sgend;i>=sgstart;i--) {
1588     codon.nuc[nt]=ntComplement(gsubseq[i-start]);
1589     nt++;
1590     if (nt==3) {
1591     nt=0;
1592     translation[aa]=codon.translate();
1593     aa++;
1594     }
1595     }//for each nt
1596     } //for each exon
1597     } // - strand
1598     else { // + strand
1599     for (int x=0;x<exons.Count();x++) {
1600     uint sgstart=exons[x]->start;
1601     uint sgend=exons[x]->end;
1602     if (seqend<sgstart || seqstart>sgend) continue;
1603     if (seqstart>=sgstart && seqstart<=sgend)
1604     sgstart=seqstart; //seqstart within this segment
1605     if (seqend>=sgstart && seqend<=sgend)
1606     sgend=seqend; //seqend within this segment
1607     for (uint i=sgstart;i<=sgend;i++) {
1608     codon.nuc[nt]=gsubseq[i-start];
1609     nt++;
1610     if (nt==3) {
1611     nt=0;
1612     translation[aa]=codon.translate();
1613     aa++;
1614     }
1615     }//for each nt
1616     } //for each exon
1617     } // + strand
1618     translation[aa]=0;
1619     if (rlen!=NULL) *rlen=aa;
1620     return translation;
1621     }
1622    
1623     void GffObj::printSummary(FILE* fout) {
1624     if (fout==NULL) fout=stdout;
1625     fprintf(fout, "%s\t%c\t%d\t%d\t%4.2f\t%4.1f\n", gffID,
1626     strand, start, end, gscore, (float)qcov/10.0);
1627     }
1628    
1629 gpertea 16 void GffObj::printGxfLine(FILE* fout, const char* tlabel, const char* gseqname, bool iscds,
1630 gpertea 2 uint segstart, uint segend, int exidx, char phase, bool gff3) {
1631     static char scorestr[14];
1632     strcpy(scorestr,".");
1633     GffAttrs* xattrs=NULL;
1634     if (exidx>=0) {
1635     if (exons[exidx]->score) sprintf(scorestr,"%.2f", exons[exidx]->score);
1636     xattrs=exons[exidx]->attrs;
1637     }
1638     if (phase==0 || !iscds) phase='.';
1639     const char* ftype=iscds ? "CDS" : getSubfName();
1640     if (gff3) {
1641     fprintf(fout,
1642     "%s\t%s\t%s\t%d\t%d\t%s\t%c\t%c\tParent=%s",
1643     gseqname, tlabel, ftype, segstart, segend, scorestr, strand,
1644     phase, gffID);
1645     if (xattrs!=NULL) {
1646     for (int i=0;i<xattrs->Count();i++)
1647     fprintf(fout, ";%s=%s",names->attrs.getName(xattrs->Get(i)->attr_id),
1648     xattrs->Get(i)->attr_val);
1649     }
1650     fprintf(fout, "\n");
1651     } //GFF
1652 gpertea 16 else {//for GTF -- we print only transcripts
1653     //if (isValidTranscript())
1654     fprintf(fout, "%s\t%s\t%s\t%d\t%d\t%s\t%c\t%c\ttranscript_id \"%s\";",
1655     gseqname, tlabel, ftype, segstart, segend, scorestr, strand, phase, gffID);
1656     //char* geneid=(geneID!=NULL)? geneID : gffID;
1657     if (geneID)
1658     fprintf(fout," gene_id \"%s\";",geneID);
1659     if (gene_name!=NULL) {
1660     //fprintf(fout, " gene_name ");
1661     //if (gene_name[0]=='"') fprintf (fout, "%s;",gene_name);
1662     // else fprintf(fout, "\"%s\";",gene_name);
1663     fprintf(fout," gene_name \"%s\";",gene_name);
1664     }
1665 gpertea 2 if (xattrs!=NULL) {
1666 gpertea 16 for (int i=0;i<xattrs->Count();i++) {
1667     if (xattrs->Get(i)->attr_val==NULL) continue;
1668     const char* attrname=names->attrs.getName(xattrs->Get(i)->attr_id);
1669     fprintf(fout, " %s ",attrname);
1670     if (xattrs->Get(i)->attr_val[0]=='"')
1671     fprintf(fout, "%s;",xattrs->Get(i)->attr_val);
1672     else fprintf(fout, "\"%s\";",xattrs->Get(i)->attr_val);
1673     }
1674 gpertea 2 }
1675 gpertea 16 //for GTF, also append the GffObj attributes to each exon line
1676     if ((xattrs=this->attrs)!=NULL) {
1677     for (int i=0;i<xattrs->Count();i++) {
1678     if (xattrs->Get(i)->attr_val==NULL) continue;
1679     const char* attrname=names->attrs.getName(xattrs->Get(i)->attr_id);
1680     fprintf(fout, " %s ",attrname);
1681     if (xattrs->Get(i)->attr_val[0]=='"')
1682     fprintf(fout, "%s;",xattrs->Get(i)->attr_val);
1683     else fprintf(fout, "\"%s\";",xattrs->Get(i)->attr_val);
1684     }
1685     }
1686 gpertea 2 fprintf(fout, "\n");
1687     }//GTF
1688     }
1689    
1690 gpertea 16 void GffObj::printGxf(FILE* fout, GffPrintMode gffp,
1691     const char* tlabel, const char* gfparent) {
1692 gpertea 2 static char tmpstr[255];
1693     if (tlabel==NULL) {
1694     tlabel=track_id>=0 ? names->tracks.Get(track_id)->name :
1695     (char*)"gffobj" ;
1696     }
1697     unxcoord();
1698 gpertea 16 //if (exons.Count()==0) return;
1699     const char* gseqname=names->gseqs.Get(gseq_id)->name;
1700 gpertea 2 bool gff3 = (gffp>=pgffAny);
1701     bool showCDS = (gffp==pgtfAny || gffp==pgtfCDS || gffp==pgffCDS || gffp==pgffAny || gffp==pgffBoth);
1702     bool showExon = (gffp<=pgtfExon || gffp==pgffAny || gffp==pgffExon || gffp==pgffBoth);
1703     if (gff3) {
1704     //print GFF3 mRNA line:
1705     if (gscore>0.0) sprintf(tmpstr,"%.2f", gscore);
1706     else strcpy(tmpstr,".");
1707     uint pstart, pend;
1708     if (gffp==pgffCDS) {
1709     pstart=CDstart;
1710     pend=CDend;
1711     }
1712     else { pstart=start;pend=end; }
1713 gpertea 16 //const char* ftype=isTranscript() ? "mRNA" : getFeatureName();
1714     const char* ftype=getFeatureName();
1715 gpertea 2 fprintf(fout,
1716     "%s\t%s\t%s\t%d\t%d\t%s\t%c\t.\tID=%s",
1717     gseqname, tlabel, ftype, pstart, pend, tmpstr, strand, gffID);
1718 gpertea 16 if (CDstart>0 && !showCDS && !isCDS) fprintf(fout,";CDS=%d-%d",CDstart,CDend);
1719     if (gfparent!=NULL) {
1720     //parent override
1721     fprintf(fout, ";Parent=%s",gfparent);
1722     }
1723     else {
1724     if (parent!=NULL && !parent->isDiscarded())
1725     fprintf(fout, ";Parent=%s",parent->getID());
1726     }
1727     if (geneID!=NULL)
1728     fprintf(fout, ";geneID=%s",geneID);
1729     if (gene_name!=NULL)
1730     fprintf(fout, ";gene_name=%s",gene_name);
1731 gpertea 2 if (attrs!=NULL) {
1732     for (int i=0;i<attrs->Count();i++) {
1733 gpertea 16 const char* attrname=names->attrs.getName(attrs->Get(i)->attr_id);
1734     fprintf(fout,";%s=%s", attrname,
1735 gpertea 2 attrs->Get(i)->attr_val);
1736     }
1737     }
1738     fprintf(fout,"\n");
1739     }// gff3 mRNA line
1740     if (showExon) {
1741     //print exons
1742 gpertea 16 if (isCDS && exons.Count()>0 &&
1743     ((strand=='-' && exons.Last()->phase<'0') || (strand=='+' && exons.Last()->phase<'0')))
1744     updateExonPhase();
1745    
1746     for (int i=0;i<exons.Count();i++) {
1747     printGxfLine(fout, tlabel, gseqname, isCDS, exons[i]->start, exons[i]->end, i, exons[i]->phase, gff3);
1748     }
1749     }//printing exons
1750 gpertea 2 if (showCDS && !isCDS && CDstart>0) {
1751     GArray<GffCDSeg> cds(true,true);
1752     getCDSegs(cds);
1753     for (int i=0;i<cds.Count();i++) {
1754     printGxfLine(fout, tlabel, gseqname, true, cds[i].start, cds[i].end, -1, cds[i].phase, gff3);
1755     }
1756     } //showCDS
1757     }
1758    
1759 gpertea 16 void GffObj::updateExonPhase() {
1760     if (!isCDS) return;
1761     int cdsacc=0;
1762     if (CDphase=='1' || CDphase=='2') {
1763     cdsacc+= 3-(CDphase-'0');
1764     }
1765     if (strand=='-') { //reverse strand
1766     for (int i=exons.Count()-1;i>=0;i--) {
1767     exons[i]->phase='0'+ (3-cdsacc%3)%3;
1768     cdsacc+=exons[i]->end-exons[i]->start+1;
1769     }
1770     }
1771     else { //forward strand
1772     for (int i=0;i<exons.Count();i++) {
1773     exons[i]->phase='0'+ (3-cdsacc%3)%3;
1774     cdsacc+=exons[i]->end-exons[i]->start+1;
1775     }
1776     }
1777     }
1778 gpertea 2
1779 gpertea 16
1780 gpertea 2 void GffObj::getCDSegs(GArray<GffCDSeg>& cds) {
1781     GffCDSeg cdseg;
1782     int cdsacc=0;
1783     if (CDphase=='1' || CDphase=='2') {
1784     cdsacc+= 3-(CDphase-'0');
1785     }
1786     if (strand=='-') {
1787     for (int x=exons.Count()-1;x>=0;x--) {
1788     uint sgstart=exons[x]->start;
1789     uint sgend=exons[x]->end;
1790     if (CDend<sgstart || CDstart>sgend) continue;
1791     if (CDstart>=sgstart && CDstart<=sgend)
1792     sgstart=CDstart; //cdstart within this segment
1793     if (CDend>=sgstart && CDend<=sgend)
1794     sgend=CDend; //cdend within this segment
1795     cdseg.start=sgstart;
1796     cdseg.end=sgend;
1797     cdseg.exonidx=x;
1798     //cdseg.phase='0'+(cdsacc>0 ? (3-cdsacc%3)%3 : 0);
1799     cdseg.phase='0'+ (3-cdsacc%3)%3;
1800     cdsacc+=sgend-sgstart+1;
1801     cds.Add(cdseg);
1802     } //for each exon
1803     } // - strand
1804     else { // + strand
1805     for (int x=0;x<exons.Count();x++) {
1806     uint sgstart=exons[x]->start;
1807     uint sgend=exons[x]->end;
1808     if (CDend<sgstart || CDstart>sgend) continue;
1809     if (CDstart>=sgstart && CDstart<=sgend)
1810     sgstart=CDstart; //seqstart within this segment
1811     if (CDend>=sgstart && CDend<=sgend)
1812     sgend=CDend; //seqend within this segment
1813     cdseg.start=sgstart;
1814     cdseg.end=sgend;
1815     cdseg.exonidx=x;
1816     //cdseg.phase='0'+(cdsacc>0 ? (3-cdsacc%3)%3 : 0);
1817     cdseg.phase='0' + (3-cdsacc%3)%3 ;
1818     cdsacc+=sgend-sgstart+1;
1819     cds.Add(cdseg);
1820     } //for each exon
1821     } // + strand
1822     }