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root/gclib/gclib/gff.cpp
Revision: 16
Committed: Mon Jul 18 20:56:02 2011 UTC (8 years, 2 months ago) by gpertea
File size: 64545 byte(s)
Log Message:
sync with local source

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 16 //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 gpertea 2 //any recognized mRNA segment gets the generic "exon" type (also applies to CDS)
416 gpertea 16 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 gpertea 2 return -1;
422 gpertea 16 }
423 gpertea 2 }
424 gpertea 16 else { //non-mRNA parent feature, check this subf type
425 gpertea 2 subf_id=names->feats.addName(gl->ftype);
426 gpertea 16 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 gpertea 2 int eidx=addExon(gl->fstart, gl->fend, gl->score, gl->phase,
456     gl->qstart,gl->qend, gl->is_cds, gl->exontype);
457 gpertea 16 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 gpertea 2 }
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 gpertea 16 if (exon_ftype_id<0) {
475     exon_ftype_id = isTranscript() ? gff_fid_exon : ftype_id;
476 gpertea 2 }
477     }
478 gpertea 16 //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 gpertea 2 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 gpertea 16 else { // not a CDS/start/stop
502 gpertea 2 isCDS=false;
503     }
504     if (qs || qe) {
505     if (qs>qe) swap(qs,qe);
506     if (qs==0) qs=1;
507 gpertea 16 }
508 gpertea 2 int ovlen=0;
509 gpertea 16 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 gpertea 2
557 gpertea 16 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 gpertea 2 // --- 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 gpertea 16 //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 gpertea 2 segstart, segend, gffID);
578 gpertea 16 delete enew;
579     hasErrors(true);
580 gpertea 2 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 gpertea 16 if (this->len()>gsd->maxfeat_len) {
590     gsd->maxfeat_len=this->len();
591     gsd->maxfeat=this;
592     }
593 gpertea 2 }
594     return eidx;
595     }
596    
597 gpertea 16 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 gpertea 2 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 gpertea 16 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 gpertea 2 GffObj::GffObj(GffReader *gfrd, GffLine* gffline, bool keepAttr, bool noExonAttr):
682 gpertea 16 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 gpertea 2 GError("Cannot use this GffObj constructor with a NULL GffReader!\n");
707 gpertea 16 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 gpertea 2 }
745 gpertea 16 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 gpertea 2 }
759 gpertea 16 } //subfeature given directly
760     else { //gffline->parents==NULL
761     //create a parent feature in its own right
762 gpertea 2 gscore=gffline->score;
763     if (gffline->ID==NULL || gffline->ID[0]==0)
764 gpertea 16 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 gpertea 2 }
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 gpertea 16 continue;
809 gpertea 2 }
810 gpertea 16 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 gpertea 2 }
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 gpertea 16 //Warning: if gflst gets altered, idx becomes obsolete
840     GfoHolder* GffReader::gfoAdd(const char* id, const char* ctg, GffObj* gfo, int idx) {
841 gpertea 2 char* buf=gfoBuildId(id,ctg);
842 gpertea 16 GfoHolder* r=new GfoHolder(gfo,idx);
843     phash.Add(buf, r);
844 gpertea 2 GFREE(buf);
845 gpertea 16 return r;
846 gpertea 2 }
847 gpertea 16
848     GfoHolder* GffReader::gfoFind(const char* id, const char* ctg) {
849 gpertea 2 char* buf=gfoBuildId(id,ctg);
850 gpertea 16 GfoHolder* r=phash.Find(buf);
851 gpertea 2 GFREE(buf);
852     return r;
853     }
854    
855 gpertea 16 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 gpertea 2
879 gpertea 16 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 gpertea 2 }
894    
895 gpertea 16 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 gpertea 2
918 gpertea 16 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 gpertea 2 void GffReader::readAll(bool keepAttr, bool mergeCloseExons, bool noExonAttr) {
997 gpertea 16 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 gpertea 2 while (nextGffLine()!=NULL) {
1002 gpertea 16 //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 gpertea 2 }
1019 gpertea 16 if (gffline->parents==NULL) {//start GFF3-like record with no parent (mRNA, gene)
1020     if (!prevseen) newGffRec(gffline, keepAttr, noExonAttr);
1021 gpertea 2 }
1022 gpertea 16 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 gpertea 2 }
1046 gpertea 16 } //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 gpertea 2 // all gff records are now loaded in GList gflst
1075     // so we can free the hash
1076     phash.Clear();
1077 gpertea 16 tids.Clear();
1078     if (validation_errors) {
1079     exit(1);
1080     }
1081 gpertea 2 }
1082    
1083 gpertea 16 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 gpertea 2 udata=0;
1088     uptr=NULL;
1089 gpertea 16 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 gpertea 2 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 gpertea 16 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 gpertea 2 mend=exons[ni]->end;
1110 gpertea 16 covlen-=exons[i]->len();
1111 gpertea 2 exons[i]->end=mend;
1112 gpertea 16 covlen+=exons[i]->len();
1113     covlen-=exons[ni]->len();
1114 gpertea 2 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 gpertea 16 //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 gpertea 2 return this;
1154     }
1155    
1156 gpertea 16 void GffObj::parseAttrs(GffAttrs*& atrlist, char* info, bool isExon) {
1157 gpertea 2 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 gpertea 16 //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 gpertea 2 ech++;
1181     while (*ech==' ' && ech<endinfo) ech++;//skip extra spaces after the '='
1182 gpertea 16 //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 gpertea 2 }
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 gpertea 16 void GffObj::addAttr(const char* attrname, const char* attrvalue) {
1203 gpertea 2 if (this->attrs==NULL)
1204     this->attrs=new GffAttrs();
1205 gpertea 16 //this->attrs->Add(new GffAttr(names->attrs.addName(attrname),attrvalue));
1206     this->attrs->add_or_update(names, attrname, attrvalue);
1207 gpertea 2 }
1208    
1209 gpertea 16
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 gpertea 2 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 gpertea 16 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 gpertea 2 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 gpertea 16 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 gpertea 2 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 gpertea 16 void GffObj::printGxfLine(FILE* fout, const char* tlabel, const char* gseqname, bool iscds,
1626 gpertea 2 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 gpertea 16 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 gpertea 2 if (xattrs!=NULL) {
1662 gpertea 16 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 gpertea 2 }
1671 gpertea 16 //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 gpertea 2 fprintf(fout, "\n");
1683     }//GTF
1684     }
1685    
1686 gpertea 16 void GffObj::printGxf(FILE* fout, GffPrintMode gffp,
1687     const char* tlabel, const char* gfparent) {
1688 gpertea 2 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 gpertea 16 //if (exons.Count()==0) return;
1695     const char* gseqname=names->gseqs.Get(gseq_id)->name;
1696 gpertea 2 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 gpertea 16 //const char* ftype=isTranscript() ? "mRNA" : getFeatureName();
1710     const char* ftype=getFeatureName();
1711 gpertea 2 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 gpertea 16 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 gpertea 2 if (attrs!=NULL) {
1728     for (int i=0;i<attrs->Count();i++) {
1729 gpertea 16 const char* attrname=names->attrs.getName(attrs->Get(i)->attr_id);
1730     fprintf(fout,";%s=%s", attrname,
1731 gpertea 2 attrs->Get(i)->attr_val);
1732     }
1733     }
1734     fprintf(fout,"\n");
1735     }// gff3 mRNA line
1736     if (showExon) {
1737     //print exons
1738 gpertea 16 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 gpertea 2 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 gpertea 16 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 gpertea 2
1775 gpertea 16
1776 gpertea 2 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     }