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root/gclib/gclib/gff.cpp
Revision: 51
Committed: Thu Sep 8 01:02:11 2011 UTC (8 years ago) by gpertea
File size: 64797 byte(s)
Log Message:
fix direct CDS segment given as the only subfeature

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 gpertea 51 /*
576     if (start>0 && exontype==exgffCDS && exons.Count()==0) {
577     //adding a CDS directly as the first subfeature of a declared parent
578     segstart=start;
579     segend=end;
580     }
581     */
582 gpertea 2 GffExon* enew=new GffExon(segstart, segend, sc, fr, qs, qe, exontype);
583     int eidx=exons.Add(enew);
584     if (eidx<0) {
585 gpertea 16 //this would actually be acceptable if the object is a "Gene" and "exons" are in fact isoforms
586     if (gff_show_warnings)
587     GMessage("GFF Warning: failed adding segment %d-%d for %s (discarded)!\n",
588 gpertea 2 segstart, segend, gffID);
589 gpertea 16 delete enew;
590     hasErrors(true);
591 gpertea 2 return -1;
592     }
593     covlen+=(int)(exons[eidx]->end-exons[eidx]->start)+1;
594 gpertea 51 if (start==0) {
595     start=exons.First()->start;
596     end=exons.Last()->end;
597     }
598 gpertea 2 if (uptr!=NULL) { //collect stats about the underlying genomic sequence
599     GSeqStat* gsd=(GSeqStat*)uptr;
600     if (start<gsd->mincoord) gsd->mincoord=start;
601     if (end>gsd->maxcoord) gsd->maxcoord=end;
602 gpertea 16 if (this->len()>gsd->maxfeat_len) {
603     gsd->maxfeat_len=this->len();
604     gsd->maxfeat=this;
605     }
606 gpertea 2 }
607     return eidx;
608     }
609    
610 gpertea 16 void GffObj::expandExon(int oi, uint segstart, uint segend, char exontype, double sc, char fr, int qs, int qe) {
611     //oi is the index of the *first* overlapping segment found that must be enlarged
612     covlen-=exons[oi]->len();
613     if (segstart<exons[oi]->start)
614     exons[oi]->start=segstart;
615     if (qs && qs<exons[oi]->qstart) exons[oi]->qstart=qs;
616     if (segend>exons[oi]->end)
617     exons[oi]->end=segend;
618     if (qe && qe>exons[oi]->qend) exons[oi]->qend=qe;
619     //warning: score cannot be properly adjusted! e.g. if it's a p-value it's just going to get worse
620     if (sc!=0) exons[oi]->score=sc;
621     covlen+=exons[oi]->len();
622     //if (exons[oi]->exontype< exontype) -- always true
623     exons[oi]->exontype = exontype;
624     if (exontype==exgffCDS) exons[oi]->phase=fr;
625     //we must check if any more exons are also overlapping this
626     int ni=oi+1; //next exon index after oi
627     while (ni<exons.Count() && segend>=exons[ni]->start) { // next segment overlaps new enlarged segment
628     //only allow this if next segment is fully included, and a subordinate
629     if (exons[ni]->exontype<exontype && exons[ni]->end<=segend) {
630     /* I guess we have to relax this due to stupid UCSC hg18 files having a start_codon sticking out
631     chr1 hg18_knownGene start_codon 69806911 69806913 0.000000 + .
632     chr1 hg18_knownGene CDS 69806911 69806912 0.000000 + 0
633     chr1 hg18_knownGene exon 69805456 69806912 0.000000 + .
634     */
635     if (exons[ni]->qstart<exons[oi]->qstart) exons[oi]->qstart=exons[ni]->qstart;
636     if (exons[ni]->qend>exons[oi]->qend) exons[oi]->qend=exons[ni]->qend;
637     exons.Delete(ni);
638     }
639     else {
640     if (gff_show_warnings) GMessage("GFF Warning: overlapping existing exon(%d-%d) while expanding to %d-%d for GFF ID %s\n",
641     exons[ni]->start, exons[ni]->end, segstart, segend, gffID);
642     //hasErrors(true);
643     break;
644     }
645     }
646     // -- make sure any other related boundaries are updated:
647     start=exons.First()->start;
648     end=exons.Last()->end;
649     if (uptr!=NULL) { //collect stats about the underlying genomic sequence
650     GSeqStat* gsd=(GSeqStat*)uptr;
651     if (start<gsd->mincoord) gsd->mincoord=start;
652     if (end>gsd->maxcoord) gsd->maxcoord=end;
653     if (this->len()>gsd->maxfeat_len) {
654     gsd->maxfeat_len=this->len();
655     gsd->maxfeat=this;
656     }
657     }
658     }
659    
660 gpertea 2 void GffObj::removeExon(int idx) {
661     /*
662     if (idx==0 && segs[0].start==gstart)
663     gstart=segs[1].start;
664     if (idx==segcount && segs[segcount].end==gend)
665     gend=segs[segcount-1].end;
666     */
667     if (idx<0 || idx>=exons.Count()) return;
668     int segstart=exons[idx]->start;
669     int segend=exons[idx]->end;
670     exons.Delete(idx);
671     covlen -= (int)(segend-segstart)+1;
672     start=exons.First()->start;
673     end=exons.Last()->end;
674     if (isCDS) { CDstart=start; CDend=end; }
675     }
676    
677 gpertea 16 void GffObj::removeExon(GffExon* p) {
678     for (int idx=0;idx<exons.Count();idx++) {
679     if (exons[idx]==p) {
680     int segstart=exons[idx]->start;
681     int segend=exons[idx]->end;
682     exons.Delete(idx);
683     covlen -= (int)(segend-segstart)+1;
684     start=exons.First()->start;
685     end=exons.Last()->end;
686     if (isCDS) { CDstart=start; CDend=end; }
687     return;
688     }
689     }
690     }
691    
692    
693    
694 gpertea 2 GffObj::GffObj(GffReader *gfrd, GffLine* gffline, bool keepAttr, bool noExonAttr):
695 gpertea 16 GSeg(0,0), exons(true,true,false), children(1,false) {
696     xstart=0;
697     xend=0;
698     xstatus=0;
699     partial=false;
700     isCDS=false;
701     uptr=NULL;
702     ulink=NULL;
703     parent=NULL;
704     udata=0;
705     flags=0;
706     CDstart=0;
707     CDend=0;
708     CDphase=0;
709     geneID=NULL;
710     gene_name=NULL;
711     attrs=NULL;
712     gffID=NULL;
713     track_id=-1;
714     gseq_id=-1;
715     ftype_id=-1;
716     exon_ftype_id=-1;
717     strand='.';
718     if (gfrd==NULL)
719 gpertea 2 GError("Cannot use this GffObj constructor with a NULL GffReader!\n");
720 gpertea 16 gffnames_ref(names);
721     if (gfrd->names==NULL) gfrd->names=names;
722     //qlen=0;qstart=0;qend=0;
723     gscore=0;
724     uscore=0;
725     covlen=0;
726     qcov=0;
727     start=gffline->fstart;
728     end=gffline->fend;
729     gseq_id=names->gseqs.addName(gffline->gseqname);
730     track_id=names->tracks.addName(gffline->track);
731     strand=gffline->strand;
732     qlen=gffline->qlen;
733     qstart=gffline->qstart;
734     qend=gffline->qend;
735     //setup flags from gffline
736     isCDS=gffline->is_cds; //for now
737     isGene(gffline->is_gene);
738     isTranscript(gffline->is_transcript || gffline->exontype!=0);
739     fromGff3(gffline->is_gff3);
740    
741     if (gffline->parents!=NULL) {
742     //GTF style -- create a GffObj directly by subfeature
743     //(also possible orphan GFF3 exon line, or an exon given before its parent (chado))
744     if (gffline->exontype!=0) { //recognized exon-like feature
745     ftype_id=gff_fid_transcript; //so this is some sort of transcript
746     exon_ftype_id=gff_fid_exon; //subfeatures MUST be exons
747     }
748     else {//unrecognized subfeatures
749     //make this GffObj of the same feature type
750     ftype_id=names->feats.addName(gffline->ftype);
751     }
752     if (gffline->ID==NULL) { //typical GTF
753     gffID=Gstrdup(gffline->parents[0]);
754     this->createdByExon(true);
755     //this is likely the first exon/segment of the feature
756     addExon(gfrd, gffline, keepAttr, noExonAttr);
757 gpertea 2 }
758 gpertea 16 else { //a parented feature with an ID -- probably an orphan GFF3 line
759     if (gffline->is_gff3 && gffline->exontype!=0) {
760     //premature exon given before its parent transcript
761     //create the transcript entry here
762     gffID=Gstrdup(gffline->parents[0]);
763     this->createdByExon(true);
764     //this is the first exon/segment of the transcript
765     addExon(gfrd, gffline, keepAttr, noExonAttr);
766     }
767     else { //unrecognized non-exon feature ? use the ID instead
768     gffID=Gstrdup(gffline->ID);
769     if (keepAttr) this->parseAttrs(attrs, gffline->info);
770     }
771 gpertea 2 }
772 gpertea 16 } //subfeature given directly
773     else { //gffline->parents==NULL
774     //create a parent feature in its own right
775 gpertea 2 gscore=gffline->score;
776     if (gffline->ID==NULL || gffline->ID[0]==0)
777 gpertea 16 GError("Error: no ID found for GFF record start\n");
778     gffID=Gstrdup(gffline->ID); //there must be an ID here
779     //if (gffline->is_transcript) ftype_id=gff_fid_mRNA;
780     //else
781     ftype_id=names->feats.addName(gffline->ftype);
782     if (gffline->is_transcript)
783     exon_ftype_id=gff_fid_exon;
784    
785     if (keepAttr) this->parseAttrs(attrs, gffline->info);
786     }//no parent
787    
788     if (gffline->gene_name!=NULL) {
789     gene_name=Gstrdup(gffline->gene_name);
790     }
791     if (gffline->gene_id!=NULL) {
792     geneID=Gstrdup(gffline->gene_id);
793     }
794    
795     GSeqStat* gsd=gfrd->gseqstats.AddIfNew(new GSeqStat(gseq_id,names->gseqs.lastNameUsed()),true);
796     uptr=gsd;
797     if (start<gsd->mincoord) gsd->mincoord=start;
798     if (end>gsd->maxcoord) gsd->maxcoord=end;
799     if (this->len()>gsd->maxfeat_len) {
800     gsd->maxfeat_len=this->len();
801     gsd->maxfeat=this;
802 gpertea 2 }
803     }
804    
805     GffLine* GffReader::nextGffLine() {
806     if (gffline!=NULL) return gffline; //caller should free gffline after processing
807     while (gffline==NULL) {
808     int llen=0;
809     buflen=GFF_LINELEN-1;
810     char* l=fgetline(linebuf, buflen, fh, &fpos, &llen);
811     if (l==NULL) {
812     return NULL; //end of file
813     }
814     int ns=0; //first nonspace position
815     while (l[ns]!=0 && isspace(l[ns])) ns++;
816     if (l[ns]=='#' || llen<10) continue;
817     gffline=new GffLine(this, l);
818     if (gffline->skip) {
819     delete gffline;
820     gffline=NULL;
821 gpertea 16 continue;
822 gpertea 2 }
823 gpertea 16 if (gffline->ID==NULL && gffline->parents==NULL) { //it must have an ID
824     //this might not be needed, already checked in the GffLine constructor
825     if (gff_warns)
826     GMessage("Warning: malformed GFF line, no parent or record Id (kipping\n");
827     delete gffline;
828     gffline=NULL;
829     //continue;
830     }
831 gpertea 2 }
832     return gffline;
833     }
834    
835     char* GffReader::gfoBuildId(const char* id, const char* ctg) {
836     //caller must free the returned pointer
837     char* buf=NULL;
838     int idlen=strlen(id);
839     GMALLOC(buf, idlen+strlen(ctg)+2);
840     strcpy(buf, id);
841     buf[idlen]='~';
842     strcpy(buf+idlen+1, ctg);
843     return buf;
844     }
845    
846     void GffReader::gfoRemove(const char* id, const char* ctg) {
847     char* buf=gfoBuildId(id,ctg);
848     phash.Remove(buf);
849     GFREE(buf);
850     }
851    
852 gpertea 16 //Warning: if gflst gets altered, idx becomes obsolete
853     GfoHolder* GffReader::gfoAdd(const char* id, const char* ctg, GffObj* gfo, int idx) {
854 gpertea 2 char* buf=gfoBuildId(id,ctg);
855 gpertea 16 GfoHolder* r=new GfoHolder(gfo,idx);
856     phash.Add(buf, r);
857 gpertea 2 GFREE(buf);
858 gpertea 16 return r;
859 gpertea 2 }
860 gpertea 16
861     GfoHolder* GffReader::gfoFind(const char* id, const char* ctg) {
862 gpertea 2 char* buf=gfoBuildId(id,ctg);
863 gpertea 16 GfoHolder* r=phash.Find(buf);
864 gpertea 2 GFREE(buf);
865     return r;
866     }
867    
868 gpertea 16 GfoHolder* GffReader::replaceGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr, int replaceidx) {
869     GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
870     GfoHolder* r=NULL;
871     if (replaceidx>=0) {
872     gflst.Put(replaceidx,newgfo);
873     r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, replaceidx);
874     }
875     else {
876     int gfoidx=gflst.Add(newgfo);
877     r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, gfoidx);
878     }
879     if (gff_warns) {
880     int* pcount=tids.Find(newgfo->gffID);
881     if (pcount!=NULL) {
882     if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
883     (*pcount)++;
884     }
885     else {
886     tids.Add(newgfo->gffID,new int(1));
887     }
888     }
889     return r;
890     }
891 gpertea 2
892 gpertea 16 GfoHolder* GffReader::updateParent(GfoHolder* newgfh, GffObj* parent) {
893     //assert(parent);
894     //assert(newgfo);
895     parent->children.Add(newgfh->gffobj);
896     if (newgfh->gffobj->parent==NULL) newgfh->gffobj->parent=parent;
897     newgfh->gffobj->setLevel(parent->getLevel()+1);
898     if (parent->isGene()) {
899     if (parent->gene_name!=NULL && newgfh->gffobj->gene_name==NULL)
900     newgfh->gffobj->gene_name=Gstrdup(parent->gene_name);
901     if (parent->geneID!=NULL && newgfh->gffobj->geneID==NULL)
902     newgfh->gffobj->geneID=Gstrdup(parent->geneID);
903     }
904    
905     return newgfh;
906 gpertea 2 }
907    
908 gpertea 16 GfoHolder* GffReader::newGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr,
909     GffObj* parent, GffExon* pexon) {
910     GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
911     GfoHolder* r=NULL;
912     int gfoidx=gflst.Add(newgfo);
913     r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, gfoidx);
914     if (parent!=NULL) {
915     updateParent(r, parent);
916     if (pexon!=NULL) parent->removeExon(pexon);
917     }
918     if (gff_warns) {
919     int* pcount=tids.Find(newgfo->gffID);
920     if (pcount!=NULL) {
921     if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
922     (*pcount)++;
923     }
924     else {
925     tids.Add(newgfo->gffID,new int(1));
926     }
927     }
928     return r;
929     }
930 gpertea 2
931 gpertea 16 GfoHolder* GffReader::updateGffRec(GfoHolder* prevgfo, GffLine* gffline,
932     bool keepAttr) {
933     if (prevgfo==NULL) return NULL;
934     prevgfo->gffobj->createdByExon(false);
935     prevgfo->gffobj->ftype_id=prevgfo->gffobj->names->feats.addName(gffline->ftype);
936     prevgfo->gffobj->start=gffline->fstart;
937     prevgfo->gffobj->end=gffline->fend;
938     prevgfo->gffobj->isGene(gffline->is_gene);
939     prevgfo->gffobj->isTranscript(gffline->is_transcript || gffline->exontype!=0);
940     prevgfo->gffobj->fromGff3(gffline->is_gff3);
941     if (keepAttr) {
942     if (prevgfo->gffobj->attrs!=NULL) prevgfo->gffobj->attrs->Clear();
943     prevgfo->gffobj->parseAttrs(prevgfo->gffobj->attrs, gffline->info);
944     }
945     return prevgfo;
946     }
947    
948    
949     bool GffReader::addExonFeature(GfoHolder* prevgfo, GffLine* gffline, GHash<CNonExon>& pex, bool noExonAttr) {
950     bool r=true;
951     if (gffline->strand!=prevgfo->gffobj->strand) {
952     GMessage("GFF Error: duplicate GFF ID '%s' (exons found on different strands of %s)\n",
953     prevgfo->gffobj->gffID, prevgfo->gffobj->getGSeqName());
954     r=false;
955     }
956     int gdist=(gffline->fstart>prevgfo->gffobj->end) ? gffline->fstart-prevgfo->gffobj->end :
957     ((gffline->fend<prevgfo->gffobj->start)? prevgfo->gffobj->start-gffline->fend :
958     0 );
959     if (gdist>(int)GFF_MAX_LOCUS) { //too far apart, most likely this is a duplicate ID
960     GMessage("Error: duplicate GFF ID '%s' (or exons too far apart)!\n",prevgfo->gffobj->gffID);
961     //validation_errors = true;
962     r=false;
963     if (!gff_warns) exit(1);
964     }
965     int eidx=prevgfo->gffobj->addExon(this, gffline, !noExonAttr, noExonAttr);
966     if (eidx>=0 && gffline->ID!=NULL && gffline->exontype==0)
967     subfPoolAdd(pex, prevgfo);
968     return r;
969     }
970    
971     CNonExon* GffReader::subfPoolCheck(GffLine* gffline, GHash<CNonExon>& pex, char*& subp_name) {
972     CNonExon* subp=NULL;
973     subp_name=NULL;
974     for (int i=0;i<gffline->num_parents;i++) {
975     if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
976     continue;
977     subp_name=gfoBuildId(gffline->parents[i], gffline->gseqname); //e.g. mRNA name
978     subp=pex.Find(subp_name);
979     if (subp!=NULL)
980     return subp;
981     GFREE(subp_name);
982     }
983     return NULL;
984     }
985    
986     void GffReader::subfPoolAdd(GHash<CNonExon>& pex, GfoHolder* newgfo) {
987     //this might become a parent feature later
988     if (newgfo->gffobj->exons.Count()>0) {
989     char* xbuf=gfoBuildId(gffline->ID, gffline->gseqname);
990     pex.Add(xbuf, new CNonExon(newgfo->idx, newgfo->gffobj,
991     newgfo->gffobj->exons[0], gffline));
992     GFREE(xbuf);
993     }
994     }
995    
996     GfoHolder* GffReader::promoteFeature(CNonExon* subp, char*& subp_name, GHash<CNonExon>& pex,
997     bool keepAttr, bool noExonAttr) {
998     GffObj* prevp=subp->parent; //grandparent of gffline (e.g. gene)
999     if (prevp!=gflst[subp->idx])
1000     GError("Error promoting subfeature %s, gflst index mismatch?!\n", subp->gffline->ID);
1001     subp->gffline->discardParent();
1002     GfoHolder* gfoh=newGffRec(subp->gffline, keepAttr, noExonAttr, prevp, subp->exon);
1003     pex.Remove(subp_name); //no longer a potential parent, moved it to phash already
1004     prevp->promotedChildren(true);
1005     return gfoh; //returns the holder of newly promoted feature
1006     }
1007    
1008     //have to parse the whole file because exons can be scattered all over
1009 gpertea 2 void GffReader::readAll(bool keepAttr, bool mergeCloseExons, bool noExonAttr) {
1010 gpertea 16 bool validation_errors = false;
1011     //loc_debug=false;
1012     GHash<CNonExon> pex; //keep track of any "exon"-like features that have an ID
1013     //and thus could become promoted to parent features
1014 gpertea 2 while (nextGffLine()!=NULL) {
1015 gpertea 16 //seen this gff ID before?
1016     GfoHolder* prevseen=NULL;
1017     if (gffline->ID) //GFF3
1018     prevseen=gfoFind(gffline->ID, gffline->gseqname);
1019     if (prevseen!=NULL) {
1020     if (prevseen->gffobj->createdByExon()) {
1021     updateGffRec(prevseen, gffline, keepAttr);
1022     }
1023     else {
1024     GMessage("Error: duplicate GFF ID '%s' encountered!\n",gffline->ID);
1025     validation_errors = true;
1026     if (gff_warns) {
1027     delete gffline; gffline=NULL; continue;
1028     }
1029     else exit(1);
1030     }
1031 gpertea 2 }
1032 gpertea 16 if (gffline->parents==NULL) {//start GFF3-like record with no parent (mRNA, gene)
1033     if (!prevseen) newGffRec(gffline, keepAttr, noExonAttr);
1034 gpertea 2 }
1035 gpertea 16 else { //--- it's a parented feature (could still be a mRNA)
1036     bool found_parent=false;
1037     GfoHolder* newgfo=prevseen;
1038     for (int i=0;i<gffline->num_parents;i++) {
1039     if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
1040     continue; //skipping discarded parent feature
1041     GfoHolder* parentgfo=gfoFind(gffline->parents[i], gffline->gseqname);
1042     if (parentgfo!=NULL) { //parent GffObj parsed earlier
1043     found_parent=true;
1044     if (parentgfo->gffobj->isGene() && gffline->is_transcript
1045     && gffline->exontype==0) {
1046     //not an exon, but a transcript parented by a gene
1047     if (newgfo) {
1048     updateParent(newgfo, parentgfo->gffobj);
1049     }
1050     else {
1051     newgfo=newGffRec(gffline, keepAttr, noExonAttr, parentgfo->gffobj);
1052     }
1053     }
1054     else { //potential exon subfeature
1055     if (!addExonFeature(parentgfo, gffline, pex, noExonAttr))
1056     validation_errors=true;
1057     }
1058 gpertea 2 }
1059 gpertea 16 } //for each parsed parent Id
1060     if (!found_parent) { //new GTF-like record starting here with a subfeature directly
1061     //or it could be some chado GFF3 barf with exons declared BEFORE their parent :(
1062     //check if this feature isn't parented by a previously stored "exon" subfeature
1063     char* subp_name=NULL;
1064     CNonExon* subp=subfPoolCheck(gffline, pex, subp_name);
1065     if (subp!=NULL) { //found a subfeature that is the parent of this gffline
1066     //promote that subfeature to a full GffObj
1067     GfoHolder* gfoh=promoteFeature(subp, subp_name, pex, keepAttr, noExonAttr);
1068     //add current gffline as an exon of the newly promoted subfeature
1069     if (!addExonFeature(gfoh, gffline, pex, noExonAttr))
1070     validation_errors=true;
1071     }
1072     else { //no parent seen before, create one directly with this exon
1073     //loc_debug=true;
1074     GfoHolder* newgfo=prevseen ? prevseen : newGffRec(gffline, keepAttr, noExonAttr);
1075     if (gffline->ID!=NULL && gffline->exontype==0)
1076     subfPoolAdd(pex, newgfo);
1077     //even those with errors will be added here!
1078     }
1079     GFREE(subp_name);
1080     } //no previous parent found
1081     } //parented feature
1082     //--
1083     delete gffline;
1084     gffline=NULL;
1085     }//while gff lines
1086     gflst.finalize(this, mergeCloseExons, keepAttr, noExonAttr); //force sorting by locus if so constructed
1087 gpertea 2 // all gff records are now loaded in GList gflst
1088     // so we can free the hash
1089     phash.Clear();
1090 gpertea 16 tids.Clear();
1091     if (validation_errors) {
1092     exit(1);
1093     }
1094 gpertea 2 }
1095    
1096 gpertea 16 GffObj* GffObj::finalize(GffReader* gfr, bool mergeCloseExons, bool keepAttrs, bool noExonAttr) {
1097     //merge
1098     //always merge adjacent or overlapping segments
1099     //but if mergeCloseExons then merge even when distance is up to 5 bases
1100 gpertea 2 udata=0;
1101     uptr=NULL;
1102 gpertea 16 if (gfr->transcriptsOnly && !(isTranscript() || (isGene() && children.Count()==0))) {
1103     isDiscarded(true);
1104     }
1105     if (ftype_id==gff_fid_transcript && CDstart>0) {
1106     ftype_id=gff_fid_mRNA;
1107     //exon_ftype_id=gff_fid_exon;
1108     }
1109     //if (ftype_id==gff_fid_mRNA || exon_ftype_id==gff_fid_exon || mergeCloseExons) {
1110     if (isTranscript() || exon_ftype_id==gff_fid_exon || mergeCloseExons) {
1111 gpertea 2 int mindist=mergeCloseExons ? 5:1;
1112     for (int i=0;i<exons.Count()-1;i++) {
1113     int ni=i+1;
1114     uint mend=exons[i]->end;
1115     while (ni<exons.Count()) {
1116     int dist=(int)(exons[ni]->start-mend);
1117 gpertea 16 if (dist>mindist) break; //no merging with next segment
1118     if (gfr!=NULL && gfr->gff_warns && dist!=0 && (exons[ni]->exontype!=exgffUTR && exons[i]->exontype!=exgffUTR)) {
1119     GMessage("GFF warning: merging adjacent/overlapping segments of %s on %s (%d-%d, %d-%d)\n",
1120     gffID, getGSeqName(), exons[i]->start, exons[i]->end,exons[ni]->start, exons[ni]->end);
1121     }
1122 gpertea 2 mend=exons[ni]->end;
1123 gpertea 16 covlen-=exons[i]->len();
1124 gpertea 2 exons[i]->end=mend;
1125 gpertea 16 covlen+=exons[i]->len();
1126     covlen-=exons[ni]->len();
1127 gpertea 2 if (exons[ni]->attrs!=NULL && (exons[i]->attrs==NULL ||
1128     exons[i]->attrs->Count()<exons[ni]->attrs->Count())) {
1129     //use the other exon attributes, if more
1130     delete(exons[i]->attrs);
1131     exons[i]->attrs=exons[ni]->attrs;
1132     exons[ni]->attrs=NULL;
1133     }
1134     exons.Delete(ni);
1135     } //check for merge with next exon
1136     } //for each exon
1137     }
1138 gpertea 16 //attribute reduction for GTF records
1139     if (keepAttrs && !noExonAttr && !fromGff3()
1140     && exons.Count()>0 && exons[0]->attrs!=NULL) {
1141     bool attrs_discarded=false;
1142     for (int a=0;a<exons[0]->attrs->Count();a++) {
1143     int attr_name_id=exons[0]->attrs->Get(a)->attr_id;
1144     char* attr_name=names->attrs.getName(attr_name_id);
1145     char* attr_val =exons[0]->attrs->Get(a)->attr_val;
1146     bool sameExonAttr=true;
1147     for (int i=1;i<exons.Count();i++) {
1148     char* ov=exons[i]->getAttr(attr_name_id);
1149     if (ov==NULL || (strcmp(ov,attr_val)!=0)) {
1150     sameExonAttr=false;
1151     break;
1152     }
1153     }
1154     if (sameExonAttr) {
1155     //delete this attribute from exons level
1156     attrs_discarded=true;
1157     this->addAttr(attr_name, attr_val);
1158     for (int i=1;i<exons.Count();i++) {
1159     removeExonAttr(*(exons[i]), attr_name_id);
1160     }
1161     exons[0]->attrs->freeItem(a);
1162     }
1163     }
1164     if (attrs_discarded) exons[0]->attrs->Pack();
1165     }
1166 gpertea 2 return this;
1167     }
1168    
1169 gpertea 16 void GffObj::parseAttrs(GffAttrs*& atrlist, char* info, bool isExon) {
1170 gpertea 2 if (names==NULL)
1171     GError(ERR_NULL_GFNAMES, "parseAttrs()");
1172     if (atrlist==NULL)
1173     atrlist=new GffAttrs();
1174     char* endinfo=info+strlen(info);
1175     char* start=info;
1176     char* pch=start;
1177     while (start<endinfo) {
1178     //skip spaces
1179     while (*start==' ' && start<endinfo) start++;
1180     pch=strchr(start, ';');
1181     if (pch==NULL) pch=endinfo;
1182     else {
1183     *pch='\0';
1184     pch++;
1185     }
1186     char* ech=strchr(start,'=');
1187     if (ech!=NULL) { // attr=value format found
1188     *ech='\0';
1189 gpertea 16 //if (noExonAttr && (strcmp(start, "exon_number")==0 || strcmp(start, "exon")==0)) { start=pch; continue; }
1190     if (strcmp(start, "exon_number")==0 || strcmp(start, "exon")==0 ||
1191     strcmp(start, "exon_id")==0)
1192     { start=pch; continue; }
1193 gpertea 2 ech++;
1194     while (*ech==' ' && ech<endinfo) ech++;//skip extra spaces after the '='
1195 gpertea 16 //atrlist->Add(new GffAttr(names->attrs.addName(start),ech));
1196     //make sure we don't add the same attribute more than once
1197     if (isExon && (strcmp(start, "protein_id")==0)) {
1198     //Ensembl special case
1199     this->addAttr(start, ech);
1200     start=pch;
1201     continue;
1202     }
1203     atrlist->add_or_update(names, start, ech);
1204 gpertea 2 }
1205     /*
1206     else { //not an attr=value format
1207     atrlist->Add(new GffAttr(names->attrs.addName(start),"1"));
1208     }
1209     */
1210     start=pch;
1211     }
1212     if (atrlist->Count()==0) { delete atrlist; atrlist=NULL; }
1213     }
1214    
1215 gpertea 16 void GffObj::addAttr(const char* attrname, const char* attrvalue) {
1216 gpertea 2 if (this->attrs==NULL)
1217     this->attrs=new GffAttrs();
1218 gpertea 16 //this->attrs->Add(new GffAttr(names->attrs.addName(attrname),attrvalue));
1219     this->attrs->add_or_update(names, attrname, attrvalue);
1220 gpertea 2 }
1221    
1222 gpertea 16
1223     void GffObj::setFeatureName(const char* feature) {
1224     //change the feature name/type for a transcript
1225     int fid=names->feats.addName(feature);
1226     if (monoFeature() && exons.Count()>0)
1227     this->exon_ftype_id=fid;
1228     this->ftype_id=fid;
1229     }
1230    
1231     void GffObj::setRefName(const char* newname) {
1232     //change the feature name/type for a transcript
1233     int rid=names->gseqs.addName(newname);
1234     this->gseq_id=rid;
1235     }
1236    
1237    
1238    
1239     int GffObj::removeAttr(const char* attrname, const char* attrval) {
1240     if (this->attrs==NULL || attrname==NULL || attrname[0]==0) return 0;
1241     int aid=this->names->attrs.getId(attrname);
1242     if (aid<0) return 0;
1243     int delcount=0; //could be more than one ?
1244     for (int i=0;i<this->attrs->Count();i++) {
1245     if (aid==this->attrs->Get(i)->attr_id) {
1246     if (attrval==NULL ||
1247     strcmp(attrval, this->attrs->Get(i)->attr_val)==0) {
1248     delcount++;
1249     this->attrs->freeItem(i);
1250     }
1251     }
1252     }
1253     if (delcount>0) this->attrs->Pack();
1254     return delcount;
1255     }
1256    
1257     int GffObj::removeAttr(int aid, const char* attrval) {
1258     if (this->attrs==NULL || aid<0) return 0;
1259     int delcount=0; //could be more than one ?
1260     for (int i=0;i<this->attrs->Count();i++) {
1261     if (aid==this->attrs->Get(i)->attr_id) {
1262     if (attrval==NULL ||
1263     strcmp(attrval, this->attrs->Get(i)->attr_val)==0) {
1264     delcount++;
1265     this->attrs->freeItem(i);
1266     }
1267     }
1268     }
1269     if (delcount>0) this->attrs->Pack();
1270     return delcount;
1271     }
1272    
1273    
1274     int GffObj::removeExonAttr(GffExon& exon, const char* attrname, const char* attrval) {
1275     if (exon.attrs==NULL || attrname==NULL || attrname[0]==0) return 0;
1276     int aid=this->names->attrs.getId(attrname);
1277     if (aid<0) return 0;
1278     int delcount=0; //could be more than one
1279     for (int i=0;i<exon.attrs->Count();i++) {
1280     if (aid==exon.attrs->Get(i)->attr_id) {
1281     if (attrval==NULL ||
1282     strcmp(attrval, exon.attrs->Get(i)->attr_val)==0) {
1283     delcount++;
1284     exon.attrs->freeItem(i);
1285     }
1286     }
1287     }
1288     if (delcount>0) exon.attrs->Pack();
1289     return delcount;
1290     }
1291    
1292     int GffObj::removeExonAttr(GffExon& exon, int aid, const char* attrval) {
1293     if (exon.attrs==NULL || aid<0) return 0;
1294     int delcount=0; //could be more than one
1295     for (int i=0;i<exon.attrs->Count();i++) {
1296     if (aid==exon.attrs->Get(i)->attr_id) {
1297     if (attrval==NULL ||
1298     strcmp(attrval, exon.attrs->Get(i)->attr_val)==0) {
1299     delcount++;
1300     exon.attrs->freeItem(i);
1301     }
1302     }
1303     }
1304     if (delcount>0) exon.attrs->Pack();
1305     return delcount;
1306     }
1307    
1308    
1309 gpertea 2 void GffObj::getCDS_ends(uint& cds_start, uint& cds_end) {
1310     cds_start=0;
1311     cds_end=0;
1312     if (CDstart==0 || CDend==0) return; //no CDS info
1313     int cdsadj=0;
1314     if (CDphase=='1' || CDphase=='2') {
1315     cdsadj=CDphase-'0';
1316     }
1317     cds_start=CDstart;
1318     cds_end=CDend;
1319     if (strand=='-') cds_end-=cdsadj;
1320     else cds_start+=cdsadj;
1321     }
1322    
1323     void GffObj::mRNA_CDS_coords(uint& cds_mstart, uint& cds_mend) {
1324     //sets cds_start and cds_end to the CDS start,end coordinates on the spliced mRNA transcript
1325     cds_mstart=0;
1326     cds_mend=0;
1327     if (CDstart==0 || CDend==0) return; //no CDS info
1328     //restore normal coordinates, just in case
1329     unxcoord();
1330     int cdsadj=0;
1331     if (CDphase=='1' || CDphase=='2') {
1332     cdsadj=CDphase-'0';
1333     }
1334     /*
1335     uint seqstart=CDstart;
1336     uint seqend=CDend;
1337     */
1338     uint seqstart=exons.First()->start;
1339     uint seqend=exons.Last()->end;
1340     int s=0; //resulting nucleotide counter
1341     if (strand=='-') {
1342     for (int x=exons.Count()-1;x>=0;x--) {
1343     uint sgstart=exons[x]->start;
1344     uint sgend=exons[x]->end;
1345     if (seqend<sgstart || seqstart>sgend) continue;
1346     if (seqstart>=sgstart && seqstart<=sgend)
1347     sgstart=seqstart; //seqstart within this segment
1348     if (seqend>=sgstart && seqend<=sgend)
1349     sgend=seqend; //seqend within this segment
1350     s+=(int)(sgend-sgstart)+1;
1351     if (CDstart>=sgstart && CDstart<=sgend) {
1352     //CDstart in this segment
1353     //and we are getting the whole transcript
1354     cds_mend=s-(int)(CDstart-sgstart);
1355     }
1356     if (CDend>=sgstart && CDend<=sgend) {
1357     //CDstart in this segment
1358     //and we are getting the whole transcript
1359     cds_mstart=s-(int)(CDend-cdsadj-sgstart);
1360     }
1361     } //for each exon
1362     } // - strand
1363     else { // + strand
1364     for (int x=0;x<exons.Count();x++) {
1365     uint sgstart=exons[x]->start;
1366     uint sgend=exons[x]->end;
1367     if (seqend<sgstart || seqstart>sgend) continue;
1368     if (seqstart>=sgstart && seqstart<=sgend)
1369     sgstart=seqstart; //seqstart within this segment
1370     if (seqend>=sgstart && seqend<=sgend)
1371     sgend=seqend; //seqend within this segment
1372     s+=(int)(sgend-sgstart)+1;
1373     /* for (uint i=sgstart;i<=sgend;i++) {
1374     spliced[s]=gsubseq[i-gstart];
1375     s++;
1376     }//for each nt
1377     */
1378     if (CDstart>=sgstart && CDstart<=sgend) {
1379     //CDstart in this segment
1380     cds_mstart=s-(int)(sgend-CDstart-cdsadj);
1381     }
1382     if (CDend>=sgstart && CDend<=sgend) {
1383     //CDend in this segment
1384     cds_mend=s-(int)(sgend-CDend);
1385     }
1386     } //for each exon
1387     } // + strand
1388     //spliced[s]=0;
1389     //if (rlen!=NULL) *rlen=s;
1390     //return spliced;
1391     }
1392    
1393 gpertea 16 char* GffObj::getUnspliced(GFaSeqGet* faseq, int* rlen, GList<GSeg>* seglst)
1394     {
1395     if (faseq==NULL) { GMessage("Warning: getUnspliced(NULL,.. ) called!\n");
1396     return NULL;
1397     }
1398     //restore normal coordinates:
1399     unxcoord();
1400     if (exons.Count()==0) return NULL;
1401     int fspan=end-start+1;
1402     const char* gsubseq=faseq->subseq(start, fspan);
1403     if (gsubseq==NULL) {
1404     GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1405     }
1406     char* unspliced=NULL;
1407    
1408     int seqstart=exons.First()->start;
1409     int seqend=exons.Last()->end;
1410    
1411     int unsplicedlen = 0;
1412    
1413     unsplicedlen += seqend - seqstart + 1;
1414    
1415     GMALLOC(unspliced, unsplicedlen+1); //allocate more here
1416     //uint seqstart, seqend;
1417    
1418     int s = 0; //resulting nucleotide counter
1419     if (strand=='-')
1420     {
1421     if (seglst!=NULL)
1422     seglst->Add(new GSeg(s+1,s+1+seqend-seqstart));
1423     for (int i=seqend;i>=seqstart;i--)
1424     {
1425     unspliced[s] = ntComplement(gsubseq[i-start]);
1426     s++;
1427     }//for each nt
1428     } // - strand
1429     else
1430     { // + strand
1431     if (seglst!=NULL)
1432     seglst->Add(new GSeg(s+1,s+1+seqend-seqstart));
1433     for (int i=seqstart;i<=seqend;i++)
1434     {
1435     unspliced[s]=gsubseq[i-start];
1436     s++;
1437     }//for each nt
1438     } // + strand
1439     //assert(s <= unsplicedlen);
1440     unspliced[s]=0;
1441     if (rlen!=NULL) *rlen=s;
1442     return unspliced;
1443     }
1444    
1445 gpertea 2 char* GffObj::getSpliced(GFaSeqGet* faseq, bool CDSonly, int* rlen, uint* cds_start, uint* cds_end,
1446     GList<GSeg>* seglst) {
1447     if (CDSonly && CDstart==0) return NULL;
1448     if (faseq==NULL) { GMessage("Warning: getSpliced(NULL,.. ) called!\n");
1449     return NULL;
1450     }
1451     //restore normal coordinates:
1452     unxcoord();
1453     if (exons.Count()==0) return NULL;
1454     int fspan=end-start+1;
1455     const char* gsubseq=faseq->subseq(start, fspan);
1456     if (gsubseq==NULL) {
1457     GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1458     }
1459 gpertea 16 if (fspan<(int)(end-start+1)) { //special case: stop coordinate was extended past the gseq length, must adjust
1460     int endadj=end-start+1-fspan;
1461     uint prevend=end;
1462     end-=endadj;
1463     if (CDend>end) CDend=end;
1464     if (exons.Last()->end>end) {
1465     exons.Last()->end=end; //this could get us into trouble if exon start is also > end
1466     if (exons.Last()->start>exons.Last()->end) {
1467     GError("GffObj::getSpliced() error: improper genomic coordinate %d on %s for %s\n",
1468     prevend,getGSeqName(), getID());
1469     }
1470     covlen-=endadj;
1471     }
1472     }
1473 gpertea 2 char* spliced=NULL;
1474     GMALLOC(spliced, covlen+1); //allocate more here
1475     uint seqstart, seqend;
1476     int cdsadj=0;
1477     if (CDphase=='1' || CDphase=='2') {
1478     cdsadj=CDphase-'0';
1479     }
1480     if (CDSonly) {
1481     seqstart=CDstart;
1482     seqend=CDend;
1483     if (strand=='-') seqend-=cdsadj;
1484     else seqstart+=cdsadj;
1485     }
1486     else {
1487     seqstart=exons.First()->start;
1488     seqend=exons.Last()->end;
1489     }
1490     int s=0; //resulting nucleotide counter
1491     if (strand=='-') {
1492     for (int x=exons.Count()-1;x>=0;x--) {
1493     uint sgstart=exons[x]->start;
1494     uint sgend=exons[x]->end;
1495     if (seqend<sgstart || seqstart>sgend) continue;
1496     if (seqstart>=sgstart && seqstart<=sgend)
1497     sgstart=seqstart; //seqstart within this segment
1498     if (seqend>=sgstart && seqend<=sgend)
1499     sgend=seqend; //seqend within this segment
1500     if (seglst!=NULL)
1501     seglst->Add(new GSeg(s+1,s+1+sgend-sgstart));
1502     for (uint i=sgend;i>=sgstart;i--) {
1503     spliced[s] = ntComplement(gsubseq[i-start]);
1504     s++;
1505     }//for each nt
1506    
1507     if (!CDSonly && cds_start!=NULL && CDstart>0) {
1508     if (CDstart>=sgstart && CDstart<=sgend) {
1509     //CDstart in this segment
1510     //and we are getting the whole transcript
1511     *cds_end=s-(CDstart-sgstart);
1512     }
1513     if (CDend>=sgstart && CDend<=sgend) {
1514     //CDstart in this segment
1515     //and we are getting the whole transcript
1516     *cds_start=s-(CDend-cdsadj-sgstart);
1517     }
1518     }//update local CDS coordinates
1519     } //for each exon
1520     } // - strand
1521     else { // + strand
1522     for (int x=0;x<exons.Count();x++) {
1523     uint sgstart=exons[x]->start;
1524     uint sgend=exons[x]->end;
1525     if (seqend<sgstart || seqstart>sgend) continue;
1526     if (seqstart>=sgstart && seqstart<=sgend)
1527     sgstart=seqstart; //seqstart within this segment
1528     if (seqend>=sgstart && seqend<=sgend)
1529     sgend=seqend; //seqend within this segment
1530     if (seglst!=NULL)
1531     seglst->Add(new GSeg(s+1,s+1+sgend-sgstart));
1532     for (uint i=sgstart;i<=sgend;i++) {
1533     spliced[s]=gsubseq[i-start];
1534     s++;
1535     }//for each nt
1536     if (!CDSonly && cds_start!=NULL && CDstart>0) {
1537     if (CDstart>=sgstart && CDstart<=sgend) {
1538     //CDstart in this segment
1539     //and we are getting the whole transcript
1540     *cds_start=s-(sgend-CDstart-cdsadj);
1541     }
1542     if (CDend>=sgstart && CDend<=sgend) {
1543     //CDstart in this segment
1544     //and we are getting the whole transcript
1545     *cds_end=s-(sgend-CDend);
1546     }
1547     }//update local CDS coordinates
1548     } //for each exon
1549     } // + strand
1550     spliced[s]=0;
1551     if (rlen!=NULL) *rlen=s;
1552     return spliced;
1553     }
1554    
1555     char* GffObj::getSplicedTr(GFaSeqGet* faseq, bool CDSonly, int* rlen) {
1556     if (CDSonly && CDstart==0) return NULL;
1557     //restore normal coordinates:
1558     unxcoord();
1559     if (exons.Count()==0) return NULL;
1560     int fspan=end-start+1;
1561     const char* gsubseq=faseq->subseq(start, fspan);
1562     if (gsubseq==NULL) {
1563     GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1564     }
1565    
1566     char* translation=NULL;
1567     GMALLOC(translation, (int)(covlen/3)+1);
1568     uint seqstart, seqend;
1569     int cdsadj=0;
1570     if (CDphase=='1' || CDphase=='2') {
1571     cdsadj=CDphase-'0';
1572     }
1573     if (CDSonly) {
1574     seqstart=CDstart;
1575     seqend=CDend;
1576     if (strand=='-') seqend-=cdsadj;
1577     else seqstart+=cdsadj;
1578     }
1579     else {
1580     seqstart=exons.First()->start;
1581     seqend=exons.Last()->end;
1582     }
1583     Codon codon;
1584     int nt=0; //codon nucleotide counter (0..2)
1585     int aa=0; //aminoacid count
1586     if (strand=='-') {
1587     for (int x=exons.Count()-1;x>=0;x--) {
1588     uint sgstart=exons[x]->start;
1589     uint sgend=exons[x]->end;
1590     if (seqend<sgstart || seqstart>sgend) continue;
1591     if (seqstart>=sgstart && seqstart<=sgend)
1592     sgstart=seqstart; //seqstart within this segment
1593     if (seqend>=sgstart && seqend<=sgend) {
1594     sgend=seqend; //seqend within this segment
1595     }
1596     for (uint i=sgend;i>=sgstart;i--) {
1597     codon.nuc[nt]=ntComplement(gsubseq[i-start]);
1598     nt++;
1599     if (nt==3) {
1600     nt=0;
1601     translation[aa]=codon.translate();
1602     aa++;
1603     }
1604     }//for each nt
1605     } //for each exon
1606     } // - strand
1607     else { // + strand
1608     for (int x=0;x<exons.Count();x++) {
1609     uint sgstart=exons[x]->start;
1610     uint sgend=exons[x]->end;
1611     if (seqend<sgstart || seqstart>sgend) continue;
1612     if (seqstart>=sgstart && seqstart<=sgend)
1613     sgstart=seqstart; //seqstart within this segment
1614     if (seqend>=sgstart && seqend<=sgend)
1615     sgend=seqend; //seqend within this segment
1616     for (uint i=sgstart;i<=sgend;i++) {
1617     codon.nuc[nt]=gsubseq[i-start];
1618     nt++;
1619     if (nt==3) {
1620     nt=0;
1621     translation[aa]=codon.translate();
1622     aa++;
1623     }
1624     }//for each nt
1625     } //for each exon
1626     } // + strand
1627     translation[aa]=0;
1628     if (rlen!=NULL) *rlen=aa;
1629     return translation;
1630     }
1631    
1632     void GffObj::printSummary(FILE* fout) {
1633     if (fout==NULL) fout=stdout;
1634     fprintf(fout, "%s\t%c\t%d\t%d\t%4.2f\t%4.1f\n", gffID,
1635     strand, start, end, gscore, (float)qcov/10.0);
1636     }
1637    
1638 gpertea 16 void GffObj::printGxfLine(FILE* fout, const char* tlabel, const char* gseqname, bool iscds,
1639 gpertea 2 uint segstart, uint segend, int exidx, char phase, bool gff3) {
1640     static char scorestr[14];
1641     strcpy(scorestr,".");
1642     GffAttrs* xattrs=NULL;
1643     if (exidx>=0) {
1644     if (exons[exidx]->score) sprintf(scorestr,"%.2f", exons[exidx]->score);
1645     xattrs=exons[exidx]->attrs;
1646     }
1647     if (phase==0 || !iscds) phase='.';
1648     const char* ftype=iscds ? "CDS" : getSubfName();
1649     if (gff3) {
1650     fprintf(fout,
1651     "%s\t%s\t%s\t%d\t%d\t%s\t%c\t%c\tParent=%s",
1652     gseqname, tlabel, ftype, segstart, segend, scorestr, strand,
1653     phase, gffID);
1654     if (xattrs!=NULL) {
1655     for (int i=0;i<xattrs->Count();i++)
1656     fprintf(fout, ";%s=%s",names->attrs.getName(xattrs->Get(i)->attr_id),
1657     xattrs->Get(i)->attr_val);
1658     }
1659     fprintf(fout, "\n");
1660     } //GFF
1661 gpertea 16 else {//for GTF -- we print only transcripts
1662     //if (isValidTranscript())
1663     fprintf(fout, "%s\t%s\t%s\t%d\t%d\t%s\t%c\t%c\ttranscript_id \"%s\";",
1664     gseqname, tlabel, ftype, segstart, segend, scorestr, strand, phase, gffID);
1665     //char* geneid=(geneID!=NULL)? geneID : gffID;
1666     if (geneID)
1667     fprintf(fout," gene_id \"%s\";",geneID);
1668     if (gene_name!=NULL) {
1669     //fprintf(fout, " gene_name ");
1670     //if (gene_name[0]=='"') fprintf (fout, "%s;",gene_name);
1671     // else fprintf(fout, "\"%s\";",gene_name);
1672     fprintf(fout," gene_name \"%s\";",gene_name);
1673     }
1674 gpertea 2 if (xattrs!=NULL) {
1675 gpertea 16 for (int i=0;i<xattrs->Count();i++) {
1676     if (xattrs->Get(i)->attr_val==NULL) continue;
1677     const char* attrname=names->attrs.getName(xattrs->Get(i)->attr_id);
1678     fprintf(fout, " %s ",attrname);
1679     if (xattrs->Get(i)->attr_val[0]=='"')
1680     fprintf(fout, "%s;",xattrs->Get(i)->attr_val);
1681     else fprintf(fout, "\"%s\";",xattrs->Get(i)->attr_val);
1682     }
1683 gpertea 2 }
1684 gpertea 16 //for GTF, also append the GffObj attributes to each exon line
1685     if ((xattrs=this->attrs)!=NULL) {
1686     for (int i=0;i<xattrs->Count();i++) {
1687     if (xattrs->Get(i)->attr_val==NULL) continue;
1688     const char* attrname=names->attrs.getName(xattrs->Get(i)->attr_id);
1689     fprintf(fout, " %s ",attrname);
1690     if (xattrs->Get(i)->attr_val[0]=='"')
1691     fprintf(fout, "%s;",xattrs->Get(i)->attr_val);
1692     else fprintf(fout, "\"%s\";",xattrs->Get(i)->attr_val);
1693     }
1694     }
1695 gpertea 2 fprintf(fout, "\n");
1696     }//GTF
1697     }
1698    
1699 gpertea 16 void GffObj::printGxf(FILE* fout, GffPrintMode gffp,
1700     const char* tlabel, const char* gfparent) {
1701 gpertea 2 static char tmpstr[255];
1702     if (tlabel==NULL) {
1703     tlabel=track_id>=0 ? names->tracks.Get(track_id)->name :
1704     (char*)"gffobj" ;
1705     }
1706     unxcoord();
1707 gpertea 16 //if (exons.Count()==0) return;
1708     const char* gseqname=names->gseqs.Get(gseq_id)->name;
1709 gpertea 2 bool gff3 = (gffp>=pgffAny);
1710     bool showCDS = (gffp==pgtfAny || gffp==pgtfCDS || gffp==pgffCDS || gffp==pgffAny || gffp==pgffBoth);
1711     bool showExon = (gffp<=pgtfExon || gffp==pgffAny || gffp==pgffExon || gffp==pgffBoth);
1712     if (gff3) {
1713     //print GFF3 mRNA line:
1714     if (gscore>0.0) sprintf(tmpstr,"%.2f", gscore);
1715     else strcpy(tmpstr,".");
1716     uint pstart, pend;
1717     if (gffp==pgffCDS) {
1718     pstart=CDstart;
1719     pend=CDend;
1720     }
1721     else { pstart=start;pend=end; }
1722 gpertea 16 //const char* ftype=isTranscript() ? "mRNA" : getFeatureName();
1723     const char* ftype=getFeatureName();
1724 gpertea 2 fprintf(fout,
1725     "%s\t%s\t%s\t%d\t%d\t%s\t%c\t.\tID=%s",
1726     gseqname, tlabel, ftype, pstart, pend, tmpstr, strand, gffID);
1727 gpertea 16 if (CDstart>0 && !showCDS && !isCDS) fprintf(fout,";CDS=%d-%d",CDstart,CDend);
1728     if (gfparent!=NULL) {
1729     //parent override
1730     fprintf(fout, ";Parent=%s",gfparent);
1731     }
1732     else {
1733     if (parent!=NULL && !parent->isDiscarded())
1734     fprintf(fout, ";Parent=%s",parent->getID());
1735     }
1736     if (geneID!=NULL)
1737     fprintf(fout, ";geneID=%s",geneID);
1738     if (gene_name!=NULL)
1739     fprintf(fout, ";gene_name=%s",gene_name);
1740 gpertea 2 if (attrs!=NULL) {
1741     for (int i=0;i<attrs->Count();i++) {
1742 gpertea 16 const char* attrname=names->attrs.getName(attrs->Get(i)->attr_id);
1743     fprintf(fout,";%s=%s", attrname,
1744 gpertea 2 attrs->Get(i)->attr_val);
1745     }
1746     }
1747     fprintf(fout,"\n");
1748     }// gff3 mRNA line
1749     if (showExon) {
1750     //print exons
1751 gpertea 16 if (isCDS && exons.Count()>0 &&
1752     ((strand=='-' && exons.Last()->phase<'0') || (strand=='+' && exons.Last()->phase<'0')))
1753     updateExonPhase();
1754    
1755     for (int i=0;i<exons.Count();i++) {
1756     printGxfLine(fout, tlabel, gseqname, isCDS, exons[i]->start, exons[i]->end, i, exons[i]->phase, gff3);
1757     }
1758     }//printing exons
1759 gpertea 2 if (showCDS && !isCDS && CDstart>0) {
1760     GArray<GffCDSeg> cds(true,true);
1761     getCDSegs(cds);
1762     for (int i=0;i<cds.Count();i++) {
1763     printGxfLine(fout, tlabel, gseqname, true, cds[i].start, cds[i].end, -1, cds[i].phase, gff3);
1764     }
1765     } //showCDS
1766     }
1767    
1768 gpertea 16 void GffObj::updateExonPhase() {
1769     if (!isCDS) return;
1770     int cdsacc=0;
1771     if (CDphase=='1' || CDphase=='2') {
1772     cdsacc+= 3-(CDphase-'0');
1773     }
1774     if (strand=='-') { //reverse strand
1775     for (int i=exons.Count()-1;i>=0;i--) {
1776     exons[i]->phase='0'+ (3-cdsacc%3)%3;
1777     cdsacc+=exons[i]->end-exons[i]->start+1;
1778     }
1779     }
1780     else { //forward strand
1781     for (int i=0;i<exons.Count();i++) {
1782     exons[i]->phase='0'+ (3-cdsacc%3)%3;
1783     cdsacc+=exons[i]->end-exons[i]->start+1;
1784     }
1785     }
1786     }
1787 gpertea 2
1788 gpertea 16
1789 gpertea 2 void GffObj::getCDSegs(GArray<GffCDSeg>& cds) {
1790     GffCDSeg cdseg;
1791     int cdsacc=0;
1792     if (CDphase=='1' || CDphase=='2') {
1793     cdsacc+= 3-(CDphase-'0');
1794     }
1795     if (strand=='-') {
1796     for (int x=exons.Count()-1;x>=0;x--) {
1797     uint sgstart=exons[x]->start;
1798     uint sgend=exons[x]->end;
1799     if (CDend<sgstart || CDstart>sgend) continue;
1800     if (CDstart>=sgstart && CDstart<=sgend)
1801     sgstart=CDstart; //cdstart within this segment
1802     if (CDend>=sgstart && CDend<=sgend)
1803     sgend=CDend; //cdend within this segment
1804     cdseg.start=sgstart;
1805     cdseg.end=sgend;
1806     cdseg.exonidx=x;
1807     //cdseg.phase='0'+(cdsacc>0 ? (3-cdsacc%3)%3 : 0);
1808     cdseg.phase='0'+ (3-cdsacc%3)%3;
1809     cdsacc+=sgend-sgstart+1;
1810     cds.Add(cdseg);
1811     } //for each exon
1812     } // - strand
1813     else { // + strand
1814     for (int x=0;x<exons.Count();x++) {
1815     uint sgstart=exons[x]->start;
1816     uint sgend=exons[x]->end;
1817     if (CDend<sgstart || CDstart>sgend) continue;
1818     if (CDstart>=sgstart && CDstart<=sgend)
1819     sgstart=CDstart; //seqstart within this segment
1820     if (CDend>=sgstart && CDend<=sgend)
1821     sgend=CDend; //seqend within this segment
1822     cdseg.start=sgstart;
1823     cdseg.end=sgend;
1824     cdseg.exonidx=x;
1825     //cdseg.phase='0'+(cdsacc>0 ? (3-cdsacc%3)%3 : 0);
1826     cdseg.phase='0' + (3-cdsacc%3)%3 ;
1827     cdsacc+=sgend-sgstart+1;
1828     cds.Add(cdseg);
1829     } //for each exon
1830     } // + strand
1831     }