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root/gclib/gclib/gff.cpp
Revision: 151
Committed: Fri Jan 13 22:56:48 2012 UTC (7 years, 10 months ago) by gpertea
File size: 67237 byte(s)
Log Message:
wip: trans-spliced and fusion transcripts

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 gpertea 115 const uint GFF_MAX_INTRON= 6000000; //Ensembl shows a >5MB human intron
11 gpertea 16 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 150 char* GffLine::extractAttr(const char* attr, bool caseStrict, bool enforce_GTF2) {
56 gpertea 16 //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 gpertea 150 int attrlen=strlen(attr);
60     char cend=attr[attrlen-1];
61     //char* pos = (caseStrict) ? strstr(info, attr) : strifind(info, attr);
62     //must make sure attr is not found in quoted text
63     char* pos=info;
64     char prevch=0;
65     bool in_str=false;
66     bool notfound=true;
67     int (*strcmpfn)(const char*, const char*, int) = caseStrict ? Gstrcmp : Gstricmp;
68     while (notfound && *pos) {
69     char ch=*pos;
70     if (ch=='"') {
71     in_str=!in_str;
72     pos++;
73     prevch=ch;
74     continue;
75     }
76     if (!in_str && (prevch==0 || prevch==' ' || prevch == ';')
77     && strcmpfn(attr, pos, attrlen)==0) {
78     //attr match found
79     //check for word boundary on right
80     char* epos=pos+attrlen;
81     if (cend=='=' || cend==' ' || *epos==0 || *epos==' ') {
82     notfound=false;
83     break;
84     }
85     //not a perfect match, move on
86     pos=epos;
87     prevch=*(pos-1);
88     continue;
89     }
90     //not a match or in_str
91     prevch=ch;
92     pos++;
93     }
94     if (notfound) return NULL;
95     char* vp=pos+attrlen;
96 gpertea 16 while (*vp==' ') vp++;
97     if (*vp==';' || *vp==0)
98 gpertea 150 GError("Error parsing value of GFF attribute \"%s\", line:\n%s\n", attr, dupline);
99 gpertea 16 bool dq_enclosed=false; //value string enclosed by double quotes
100     if (*vp=='"') {
101     dq_enclosed=true;
102     vp++;
103     }
104     if (enforce_GTF2 && !dq_enclosed)
105 gpertea 150 GError(GTF2_ERR,attr, dupline);
106 gpertea 16 char* vend=vp;
107     if (dq_enclosed) {
108     while (*vend!='"' && *vend!=';' && *vend!=0) vend++;
109     }
110     else {
111     while (*vend!=';' && *vend!=0) vend++;
112     }
113     if (enforce_GTF2 && *vend!='"')
114 gpertea 150 GError(GTF2_ERR, attr, dupline);
115 gpertea 16 char *r=Gstrdup(vp, vend-1);
116     //-- now remove this attribute from the info string
117     while (*vend!=0 && (*vend=='"' || *vend==';' || *vend==' ')) vend++;
118     if (*vend==0) vend--;
119     for (char *src=vend, *dest=pos;;src++,dest++) {
120     *dest=*src;
121     if (*src==0) break;
122     }
123     return r;
124     }
125 gpertea 2
126 gpertea 16 static char fnamelc[128];
127    
128 gpertea 2 GffLine::GffLine(GffReader* reader, const char* l) {
129 gpertea 16 llen=strlen(l);
130     GMALLOC(line,llen+1);
131     memcpy(line, l, llen+1);
132     GMALLOC(dupline, llen+1);
133     memcpy(dupline, l, llen+1);
134 gpertea 2 skip=true;
135     gseqname=NULL;
136     track=NULL;
137     ftype=NULL;
138     info=NULL;
139 gpertea 16 _parents=NULL;
140     _parents_len=0;
141     num_parents=0;
142     parents=NULL;
143     is_gff3=false;
144 gpertea 2 is_cds=false;
145 gpertea 16 is_transcript=false;
146 gpertea 2 is_exon=false;
147 gpertea 16 is_gene=false;
148 gpertea 2 exontype=0;
149 gpertea 16 gene_id=NULL;
150     gene_name=NULL;
151 gpertea 2 qstart=0;
152     qend=0;
153     qlen=0;
154     ID=NULL;
155     char* t[9];
156     int i=0;
157     int tidx=1;
158     t[0]=line;
159    
160     while (line[i]!=0) {
161     if (line[i]=='\t') {
162     line[i]=0;
163     t[tidx]=line+i+1;
164     tidx++;
165     if (tidx>8) break;
166     }
167     i++;
168     }
169    
170     if (tidx<8) { // ignore non-GFF lines
171     // GMessage("Warning: error parsing GFF/GTF line:\n%s\n", l);
172     return;
173     }
174     gseqname=t[0];
175     track=t[1];
176     ftype=t[2];
177     info=t[8];
178     char* p=t[3];
179 gpertea 66 if (!parseUInt(p,fstart)) {
180     //FIXME: chromosome_band entries in Flybase
181     GMessage("Warning: invalid start coordinate at line:\n%s\n",l);
182     return;
183     }
184 gpertea 2 p=t[4];
185 gpertea 66 if (!parseUInt(p,fend)) {
186     GMessage("Warning: invalid end coordinate at line:\n%s\n",l);
187     return;
188     }
189 gpertea 144 if (fend<fstart) Gswap(fend,fstart); //make sure fstart>=fend, always
190 gpertea 2 p=t[5];
191     if (p[0]=='.' && p[1]==0) {
192     score=0;
193     }
194     else {
195     if (!parseDouble(p,score))
196     GError("Error parsing feature score from GFF line:\n%s\n",l);
197     }
198     strand=*t[6];
199     if (strand!='+' && strand!='-' && strand!='.')
200     GError("Error parsing strand (%c) from GFF line:\n%s\n",strand,l);
201 gpertea 16 phase=*t[7]; // must be '.', '0', '1' or '2'
202 gpertea 2 ID=NULL;
203     // exon/CDS/mrna filter
204 gpertea 16 strncpy(fnamelc, ftype, 127);
205     fnamelc[127]=0;
206 gpertea 2 strlower(fnamelc); //convert to lower case
207 gpertea 16 bool is_t_data=false;
208 gpertea 2 if (strstr(fnamelc, "utr")!=NULL) {
209     exontype=exgffUTR;
210     is_exon=true;
211 gpertea 16 is_t_data=true;
212 gpertea 2 }
213 gpertea 66 else if (endsWith(fnamelc, "exon")) {
214 gpertea 2 exontype=exgffExon;
215     is_exon=true;
216 gpertea 16 is_t_data=true;
217 gpertea 2 }
218 gpertea 16 else if (strstr(fnamelc, "stop") &&
219     (strstr(fnamelc, "codon") || strstr(fnamelc, "cds"))){
220 gpertea 2 exontype=exgffStop;
221 gpertea 16 is_cds=true; //though some place it outside the last CDS segment
222     is_t_data=true;
223     }
224     else if (strstr(fnamelc, "start") &&
225     ((strstr(fnamelc, "codon")!=NULL) || strstr(fnamelc, "cds")!=NULL)){
226     exontype=exgffStart;
227 gpertea 2 is_cds=true;
228 gpertea 16 is_t_data=true;
229 gpertea 2 }
230     else if (strcmp(fnamelc, "cds")==0) {
231     exontype=exgffCDS;
232     is_cds=true;
233 gpertea 16 is_t_data=true;
234 gpertea 2 }
235 gpertea 16 else if (endsWith(fnamelc, "gene") || startsWith(fnamelc, "gene")) {
236     is_gene=true;
237     is_t_data=true; //because its name will be attached to parented transcripts
238 gpertea 2 }
239 gpertea 16 else if (endsWith(fnamelc,"rna") || endsWith(fnamelc,"transcript")) {
240     is_transcript=true;
241     is_t_data=true;
242     }
243 gpertea 2
244 gpertea 16 if (reader->transcriptsOnly && !is_t_data) {
245     char* id=extractAttr("ID=");
246     if (id==NULL) id=extractAttr("transcript_id");
247     //GMessage("Discarding non-transcript line:\n%s\n",l);
248     if (id!=NULL) {
249     reader->discarded_ids.Add(id, new int(1));
250     GFREE(id);
251     }
252     return; //skip this line, unwanted feature name
253 gpertea 2 }
254 gpertea 150 ID=extractAttr("ID=",true);
255     char* Parent=extractAttr("Parent=",true);
256 gpertea 16 is_gff3=(ID!=NULL || Parent!=NULL);
257     if (is_gff3) {
258     //parse as GFF3
259     if (ID!=NULL) {
260     //has ID attr so it's likely to be a parent feature
261     //look for explicit gene name
262 gpertea 150 gene_name=extractAttr("gene_name=");
263 gpertea 16 if (gene_name==NULL) {
264 gpertea 150 gene_name=extractAttr("geneName=");
265 gpertea 16 if (gene_name==NULL) {
266 gpertea 150 gene_name=extractAttr("gene_sym=");
267 gpertea 16 if (gene_name==NULL) {
268 gpertea 150 gene_name=extractAttr("gene=");
269 gpertea 16 }
270     }
271     }
272 gpertea 150 gene_id=extractAttr("geneID=");
273 gpertea 16 if (gene_id==NULL) {
274 gpertea 150 gene_id=extractAttr("gene_id=");
275 gpertea 16 }
276     if (is_gene) {
277     //special case: keep the Name and ID attributes of the gene feature
278     if (gene_name==NULL)
279     gene_name=extractAttr("Name=");
280     if (gene_id==NULL) //the ID is also gene_id in this case
281     gene_id=Gstrdup(ID);
282     //skip=false;
283     //return;
284     GFREE(Parent); //TMI, we really don't care about gene Parents?
285     } //gene feature
286     }// has GFF3 ID
287     if (Parent!=NULL) {
288     //keep Parent attr
289     //parse multiple parents
290     num_parents=1;
291     p=Parent;
292     int last_delim_pos=-1;
293     while (*p!=';' && *p!=0) {
294     if (*p==',' && *(p+1)!=0 && *(p+1)!=';') {
295     num_parents++;
296     last_delim_pos=(p-Parent);
297     }
298     p++;
299     }
300     _parents_len=p-Parent+1;
301     _parents=Parent;
302     GMALLOC(parents, num_parents*sizeof(char*));
303     parents[0]=_parents;
304     int i=1;
305     if (last_delim_pos>0) {
306     for (p=_parents+1;p<=_parents+last_delim_pos;p++) {
307     if (*p==',') {
308     char* ep=p-1;
309     while (*ep==' ' && ep>_parents) ep--;
310     *(ep+1)=0; //end the string there
311     parents[i]=p+1;
312     i++;
313     }
314     }
315     }
316     } //has Parent field
317     } //GFF3
318     else { // GTF-like expected
319 gpertea 150 Parent=extractAttr("transcript_id",true);
320 gpertea 16 if (Parent!=NULL) { //GTF2 format detected
321     if (is_transcript) {
322     // atypical GTF with a parent transcript line declared
323     ID=Parent;
324     Parent=NULL;
325     }
326     gene_id=extractAttr("gene_id"); // for GTF this is the only attribute accepted as geneID
327 gpertea 150 if (gene_id==NULL)
328     gene_id=extractAttr("geneid");
329 gpertea 16 gene_name=extractAttr("gene_name");
330     if (gene_name==NULL) {
331 gpertea 150
332 gpertea 16 gene_name=extractAttr("gene_sym");
333 gpertea 150 if (gene_name==NULL) {
334 gpertea 16 gene_name=extractAttr("gene");
335 gpertea 150 if (gene_name==NULL)
336     gene_name=extractAttr("genesymbol");
337     }
338 gpertea 16 }
339 gpertea 2 //prepare for parseAttr by adding '=' character instead of spaces for all attributes
340     //after the attribute name
341     p=info;
342     bool noed=true; //not edited after the last delim
343     bool nsp=false; //non-space found after last delim
344     while (*p!=0) {
345 gpertea 16 if (*p==' ') {
346     if (nsp && noed) {
347     *p='=';
348     noed=false;
349     p++;
350     continue;
351     }
352     }
353     else nsp=true; //non-space
354     if (*p==';') { noed=true; nsp=false; }
355     p++;
356     }
357     } //GTF2 detected (no parent line)
358     else {// Parent is NULL, check for jigsaw format or other pre-GTF2 format
359     //char* fexon=strstr(fnamelc, "exon");
360     //if (fexon!=NULL) {
361     if (exontype==exgffExon) {
362 gpertea 2 if (startsWith(track,"jigsaw")) {
363 gpertea 16 is_cds=true;
364     strcpy(track,"jigsaw");
365     p=strchr(info,';');
366     if (p==NULL) { Parent=Gstrdup(info); info=NULL; }
367     else { Parent=Gstrdup(info,p-1);
368     info=p+1;
369     }
370     }
371     } //exon feature?
372     if (Parent==NULL && exontype>=exgffCDS &&
373     (i=strcspn(info,"; \t\n\r"))<=(int)(strlen(info)+1)) {
374     //one word ID ? really desperate attempt to parse it here
375 gpertea 2 Parent=Gstrdup(info,info+i-1);
376 gpertea 16 info=NULL; //discard anything else on the line
377     }
378     }
379     if (Parent!=NULL) { //GTF transcript_id for exon/CDS feature
380     _parents=Parent;
381     GMALLOC(parents,sizeof(char*));
382     num_parents=1;
383     parents[0]=_parents;
384     }
385     } //GTF-like
386 gpertea 2
387 gpertea 16 //parse other potentially useful features
388     if (is_gff3) {
389     if ((p=strstr(info,"Target="))!=NULL) { //has Target attr
390     p+=7;
391     while (*p!=';' && *p!=0 && *p!=' ') p++;
392     if (*p!=' ') {
393     GError("Error parsing target coordinates from GFF line:\n%s\n",l);
394     }
395     if (!parseUInt(p,qstart))
396     GError("Error parsing target start coordinate from GFF line:\n%s\n",l);
397     if (*p!=' ') {
398     GError("Error parsing next target coordinate from GFF line:\n%s\n",l);
399     }
400     p++;
401     if (!parseUInt(p,qend))
402     GError("Error parsing target end coordinate from GFF line:\n%s\n",l);
403 gpertea 2 }
404 gpertea 16 if ((p=strifind(info,"Qreg="))!=NULL) { //has Qreg attr
405     p+=5;
406     if (!parseUInt(p,qstart))
407     GError("Error parsing target start coordinate from GFF line:\n%s\n",l);
408     if (*p!='-') {
409     GError("Error parsing next target coordinate from GFF line:\n%s\n",l);
410     }
411     p++;
412     if (!parseUInt(p,qend))
413     GError("Error parsing target end coordinate from GFF line:\n%s\n",l);
414     if (*p=='|' || *p==':') {
415     p++;
416     if (!parseUInt(p,qlen))
417     GError("Error parsing target length from GFF Qreg|: \n%s\n",l);
418     }
419     }//has Qreg attr
420     if (qlen==0 && (p=strifind(info,"Qlen="))!=NULL) {
421     p+=5;
422     if (!parseUInt(p,qlen))
423     GError("Error parsing target length from GFF Qlen:\n%s\n",l);
424 gpertea 2 }
425 gpertea 16 }//parsing some useful attributes in GFF3 records
426     if (ID==NULL && parents==NULL) {
427     if (reader->gff_warns)
428     GMessage("Warning: could not parse ID or Parent from GFF line:\n%s\n",dupline);
429     return; //skip
430 gpertea 2 }
431     skip=false;
432     }
433    
434 gpertea 55
435     void GffObj::addCDS(uint cd_start, uint cd_end, char phase) {
436     if (cd_start>=this->start) {
437     this->CDstart=cd_start;
438     if (strand=='+') this->CDphase=phase;
439     }
440     else this->CDstart=this->start;
441     if (cd_end<=this->end) {
442     this->CDend=cd_end;
443     if (strand=='-') this->CDphase=phase;
444     }
445     else this->CDend=this->end;
446     isTranscript(true);
447     exon_ftype_id=gff_fid_exon;
448     if (monoFeature()) {
449     if (exons.Count()==0) addExon(this->start, this->end,0,'.',0,0,false,exgffExon);
450     else exons[0]->exontype=exgffExon;
451     }
452     }
453    
454 gpertea 16 int GffObj::addExon(GffReader* reader, GffLine* gl, bool keepAttr, bool noExonAttr) {
455 gpertea 2 //this will make sure we have the right subftype_id!
456 gpertea 55 //int subf_id=-1;
457     if (!isTranscript() && gl->is_cds) {
458 gpertea 50 isTranscript(true);
459     exon_ftype_id=gff_fid_exon;
460     if (exons.Count()==1) exons[0]->exontype=exgffExon;
461     }
462 gpertea 16 if (isTranscript()) {
463     if (exon_ftype_id<0) {//exon_ftype_id=gff_fid_exon;
464     if (gl->exontype>0) exon_ftype_id=gff_fid_exon;
465     else exon_ftype_id=names->feats.addName(gl->ftype);
466     }
467 gpertea 2 //any recognized mRNA segment gets the generic "exon" type (also applies to CDS)
468 gpertea 16 if (gl->exontype==0 && !gl->is_transcript) {
469     //extraneous mRNA feature, discard
470     if (reader->gff_warns)
471     GMessage("Warning: discarding unrecognized transcript subfeature %s of %s\n",
472     gl->ftype, gffID);
473 gpertea 2 return -1;
474 gpertea 16 }
475 gpertea 2 }
476 gpertea 16 else { //non-mRNA parent feature, check this subf type
477 gpertea 55 int subf_id=names->feats.addName(gl->ftype);
478 gpertea 16 if (exon_ftype_id<0 || exons.Count()==0) //never assigned a subfeature type before (e.g. first exon being added)
479     exon_ftype_id=subf_id;
480     else {
481     if (exon_ftype_id!=subf_id) {
482 gpertea 50 //
483 gpertea 16 if (exon_ftype_id==ftype_id && exons.Count()==1 && exons[0]->start==start && exons[0]->end==end) {
484     //the existing exon was just a dummy one created by default, discard it
485     exons.Clear();
486     covlen=0;
487     exon_ftype_id=subf_id; //allow the new subfeature to completely takeover
488     }
489     else { //multiple subfeatures, prefer those with
490     if (reader->gff_warns)
491     GMessage("GFF Warning: multiple subfeatures (%s and %s) found for %s, discarding ",
492     names->feats.getName(subf_id), names->feats.getName(exon_ftype_id),gffID);
493     if (gl->exontype!=0) { //new feature is an exon, discard previously parsed subfeatures
494     if (reader->gff_warns) GMessage("%s.\n", names->feats.getName(exon_ftype_id));
495     exon_ftype_id=subf_id;
496     exons.Clear();
497     covlen=0;
498     }
499     else { //discard new feature
500     if (reader->gff_warns) GMessage("%s.\n", names->feats.getName(subf_id));
501     return -1; //skip this 2nd subfeature type for this parent!
502     }
503     }
504     } //incoming subfeature is of different type
505     } //new subfeature type
506     } //non-mRNA parent
507 gpertea 2 int eidx=addExon(gl->fstart, gl->fend, gl->score, gl->phase,
508     gl->qstart,gl->qend, gl->is_cds, gl->exontype);
509 gpertea 16 if (eidx<0) return eidx; //this should never happen
510     if (keepAttr) {
511     if (noExonAttr) {
512     if (attrs==NULL) //place the parsed attributes directly at transcript level
513     parseAttrs(attrs, gl->info);
514     }
515     else { //need all exon-level attributes
516     parseAttrs(exons[eidx]->attrs, gl->info, true);
517     }
518 gpertea 2 }
519     return eidx;
520     }
521    
522    
523     int GffObj::addExon(uint segstart, uint segend, double sc, char fr, int qs, int qe, bool iscds, char exontype) {
524     if (exons.Count()==0) {
525     if (iscds) isCDS=true; //for now, assume CDS only if first "exon" given is a CDS
526 gpertea 16 if (exon_ftype_id<0) {
527     exon_ftype_id = isTranscript() ? gff_fid_exon : ftype_id;
528 gpertea 2 }
529     }
530 gpertea 16 //special treatment of start/stop codon features, they might be broken/split between exons
531     //and in that case some providers will still give the wrong end coordinate as start+2 (e.g. UCSC)
532     //so we should not trust the end coordinate for such features
533     if (exontype==exgffStart || exontype==exgffStop) {
534     if (strand=='-') segstart=segend;
535     else segend=segstart;
536     if (exontype==exgffStart) {
537     if (CDstart==0 || segstart<CDstart) CDstart=segstart;
538     }
539     else {
540     if (segstart>CDend) CDend=segstart;
541     }
542     }
543     else if (iscds) { //update CDS anchors:
544 gpertea 2 if (CDstart==0 || segstart<CDstart) {
545     CDstart=segstart;
546     if (exontype==exgffCDS && strand=='+') CDphase=fr;
547     }
548     if (segend>CDend) {
549     if (exontype==exgffCDS && strand=='-') CDphase=fr;
550     CDend=segend;
551     }
552     }
553 gpertea 16 else { // not a CDS/start/stop
554 gpertea 2 isCDS=false;
555     }
556     if (qs || qe) {
557 gpertea 144 if (qs>qe) Gswap(qs,qe);
558 gpertea 2 if (qs==0) qs=1;
559 gpertea 16 }
560 gpertea 2 int ovlen=0;
561 gpertea 16 if (exontype>0) { //check for overlaps between exon-type segments
562     int oi=exonOverlapIdx(segstart, segend, &ovlen);
563     if (oi>=0) { //overlap existing segment
564     if (ovlen==0) {
565     //adjacent segments will be merged
566     //e.g. CDS to (UTR|exon)
567     if ((exons[oi]->exontype>=exgffUTR && exontype==exgffCDS) ||
568     (exons[oi]->exontype==exgffCDS && exontype>=exgffUTR)) {
569     expandExon(oi, segstart, segend, exgffCDSUTR, sc, fr, qs, qe);
570     return oi;
571     }
572     //CDS adjacent to stop_codon: UCSC does (did?) this
573     if ((exons[oi]->exontype==exgffStop && exontype==exgffCDS) ||
574     (exons[oi]->exontype==exgffCDS && exontype==exgffStop)) {
575     expandExon(oi, segstart, segend, exgffCDS, sc, fr, qs, qe);
576     return oi;
577     }
578     }
579     //only allow this for CDS within exon, stop_codon within (CDS|UTR|exon),
580     // start_codon within (CDS|exon)
581     if (exons[oi]->exontype>exontype &&
582     exons[oi]->start<=segstart && exons[oi]->end>=segend &&
583     !(exons[oi]->exontype==exgffUTR && exontype==exgffCDS)) {
584     //larger segment given first, now the smaller included one is redundant
585     return oi; //only used to store attributes from current GffLine
586     }
587     if (exontype>exons[oi]->exontype &&
588     segstart<=exons[oi]->start && segend>=exons[oi]->end &&
589     !(exontype==exgffUTR && exons[oi]->exontype==exgffCDS)) {
590     //smaller segment given first, so we have to enlarge it
591     expandExon(oi, segstart, segend, exontype, sc, fr, qs, qe);
592     //this should also check for overlapping next exon (oi+1) ?
593     return oi;
594     }
595     //there is also the special case of "ribosomal slippage exception" (programmed frameshift)
596     //where two CDS segments may actually overlap for 1 or 2 bases, but there should be only one encompassing exon
597     //if (ovlen>2 || exons[oi]->exontype!=exgffCDS || exontype!=exgffCDS) {
598     // had to relax this because of some weird UCSC annotations with exons partially overlapping the CDS segments
599     /*
600     if (ovlen>2 && exons[oi]->exontype!=exgffUTR && exontype!=exgffUTR) {
601     if (gff_show_warnings)
602     GMessage("GFF Warning: discarding overlapping feature segment (%d-%d) (vs %d-%d (%s)) for GFF ID %s on %s\n",
603     segstart, segend, exons[oi]->start, exons[oi]->end, getSubfName(), gffID, getGSeqName());
604     hasErrors(true);
605     return -1; //segment NOT added
606     }
607     */
608 gpertea 2
609 gpertea 16 if ((ovlen>2 || ovlen==0) || exons[oi]->exontype!=exgffCDS || exontype!=exgffCDS) {
610     if (gff_show_warnings)
611     GMessage("GFF Warning: merging overlapping/adjacent feature segment (%d-%d) into (%d-%d) (%s) for GFF ID %s on %s\n",
612     segstart, segend, exons[oi]->start, exons[oi]->end, getSubfName(), gffID, getGSeqName());
613     expandExon(oi, segstart, segend, exontype, sc, fr, qs, qe);
614     return oi;
615     }
616     // else add the segment if the overlap is small and between two CDS segments
617     //TODO: we might want to add an attribute here with the slippage coordinate and size?
618     covlen-=ovlen;
619     }//overlap or adjacent to existing segment
620     } //check for overlap
621 gpertea 2 // --- no overlap, or accepted micro-overlap (ribosomal slippage)
622     // create & add the new segment
623 gpertea 51 /*
624     if (start>0 && exontype==exgffCDS && exons.Count()==0) {
625     //adding a CDS directly as the first subfeature of a declared parent
626     segstart=start;
627     segend=end;
628     }
629     */
630 gpertea 2 GffExon* enew=new GffExon(segstart, segend, sc, fr, qs, qe, exontype);
631     int eidx=exons.Add(enew);
632     if (eidx<0) {
633 gpertea 16 //this would actually be acceptable if the object is a "Gene" and "exons" are in fact isoforms
634     if (gff_show_warnings)
635     GMessage("GFF Warning: failed adding segment %d-%d for %s (discarded)!\n",
636 gpertea 2 segstart, segend, gffID);
637 gpertea 16 delete enew;
638     hasErrors(true);
639 gpertea 2 return -1;
640     }
641     covlen+=(int)(exons[eidx]->end-exons[eidx]->start)+1;
642 gpertea 55 //adjust parent feature coordinates to contain this exon
643     if (start==0 || start>exons.First()->start) {
644 gpertea 51 start=exons.First()->start;
645     }
646 gpertea 55 if (end<exons.Last()->end) end=exons.Last()->end;
647    
648 gpertea 2 if (uptr!=NULL) { //collect stats about the underlying genomic sequence
649     GSeqStat* gsd=(GSeqStat*)uptr;
650     if (start<gsd->mincoord) gsd->mincoord=start;
651     if (end>gsd->maxcoord) gsd->maxcoord=end;
652 gpertea 16 if (this->len()>gsd->maxfeat_len) {
653     gsd->maxfeat_len=this->len();
654     gsd->maxfeat=this;
655     }
656 gpertea 2 }
657     return eidx;
658     }
659    
660 gpertea 16 void GffObj::expandExon(int oi, uint segstart, uint segend, char exontype, double sc, char fr, int qs, int qe) {
661     //oi is the index of the *first* overlapping segment found that must be enlarged
662     covlen-=exons[oi]->len();
663     if (segstart<exons[oi]->start)
664     exons[oi]->start=segstart;
665     if (qs && qs<exons[oi]->qstart) exons[oi]->qstart=qs;
666     if (segend>exons[oi]->end)
667     exons[oi]->end=segend;
668     if (qe && qe>exons[oi]->qend) exons[oi]->qend=qe;
669     //warning: score cannot be properly adjusted! e.g. if it's a p-value it's just going to get worse
670     if (sc!=0) exons[oi]->score=sc;
671     covlen+=exons[oi]->len();
672     //if (exons[oi]->exontype< exontype) -- always true
673     exons[oi]->exontype = exontype;
674     if (exontype==exgffCDS) exons[oi]->phase=fr;
675     //we must check if any more exons are also overlapping this
676     int ni=oi+1; //next exon index after oi
677     while (ni<exons.Count() && segend>=exons[ni]->start) { // next segment overlaps new enlarged segment
678     //only allow this if next segment is fully included, and a subordinate
679     if (exons[ni]->exontype<exontype && exons[ni]->end<=segend) {
680     /* I guess we have to relax this due to stupid UCSC hg18 files having a start_codon sticking out
681     chr1 hg18_knownGene start_codon 69806911 69806913 0.000000 + .
682     chr1 hg18_knownGene CDS 69806911 69806912 0.000000 + 0
683     chr1 hg18_knownGene exon 69805456 69806912 0.000000 + .
684     */
685     if (exons[ni]->qstart<exons[oi]->qstart) exons[oi]->qstart=exons[ni]->qstart;
686     if (exons[ni]->qend>exons[oi]->qend) exons[oi]->qend=exons[ni]->qend;
687     exons.Delete(ni);
688     }
689     else {
690     if (gff_show_warnings) GMessage("GFF Warning: overlapping existing exon(%d-%d) while expanding to %d-%d for GFF ID %s\n",
691     exons[ni]->start, exons[ni]->end, segstart, segend, gffID);
692     //hasErrors(true);
693     break;
694     }
695     }
696     // -- make sure any other related boundaries are updated:
697     start=exons.First()->start;
698     end=exons.Last()->end;
699     if (uptr!=NULL) { //collect stats about the underlying genomic sequence
700     GSeqStat* gsd=(GSeqStat*)uptr;
701     if (start<gsd->mincoord) gsd->mincoord=start;
702     if (end>gsd->maxcoord) gsd->maxcoord=end;
703     if (this->len()>gsd->maxfeat_len) {
704     gsd->maxfeat_len=this->len();
705     gsd->maxfeat=this;
706     }
707     }
708     }
709    
710 gpertea 2 void GffObj::removeExon(int idx) {
711     /*
712     if (idx==0 && segs[0].start==gstart)
713     gstart=segs[1].start;
714     if (idx==segcount && segs[segcount].end==gend)
715     gend=segs[segcount-1].end;
716     */
717     if (idx<0 || idx>=exons.Count()) return;
718     int segstart=exons[idx]->start;
719     int segend=exons[idx]->end;
720     exons.Delete(idx);
721     covlen -= (int)(segend-segstart)+1;
722     start=exons.First()->start;
723     end=exons.Last()->end;
724     if (isCDS) { CDstart=start; CDend=end; }
725     }
726    
727 gpertea 16 void GffObj::removeExon(GffExon* p) {
728     for (int idx=0;idx<exons.Count();idx++) {
729     if (exons[idx]==p) {
730     int segstart=exons[idx]->start;
731     int segend=exons[idx]->end;
732     exons.Delete(idx);
733     covlen -= (int)(segend-segstart)+1;
734     start=exons.First()->start;
735     end=exons.Last()->end;
736     if (isCDS) { CDstart=start; CDend=end; }
737     return;
738     }
739     }
740     }
741    
742    
743    
744 gpertea 2 GffObj::GffObj(GffReader *gfrd, GffLine* gffline, bool keepAttr, bool noExonAttr):
745 gpertea 16 GSeg(0,0), exons(true,true,false), children(1,false) {
746     xstart=0;
747     xend=0;
748     xstatus=0;
749     partial=false;
750     isCDS=false;
751     uptr=NULL;
752     ulink=NULL;
753     parent=NULL;
754     udata=0;
755     flags=0;
756     CDstart=0;
757     CDend=0;
758     CDphase=0;
759     geneID=NULL;
760     gene_name=NULL;
761     attrs=NULL;
762     gffID=NULL;
763     track_id=-1;
764     gseq_id=-1;
765     ftype_id=-1;
766     exon_ftype_id=-1;
767     strand='.';
768     if (gfrd==NULL)
769 gpertea 2 GError("Cannot use this GffObj constructor with a NULL GffReader!\n");
770 gpertea 16 gffnames_ref(names);
771     if (gfrd->names==NULL) gfrd->names=names;
772     //qlen=0;qstart=0;qend=0;
773     gscore=0;
774     uscore=0;
775     covlen=0;
776     qcov=0;
777     start=gffline->fstart;
778     end=gffline->fend;
779     gseq_id=names->gseqs.addName(gffline->gseqname);
780     track_id=names->tracks.addName(gffline->track);
781     strand=gffline->strand;
782     qlen=gffline->qlen;
783     qstart=gffline->qstart;
784     qend=gffline->qend;
785     //setup flags from gffline
786     isCDS=gffline->is_cds; //for now
787     isGene(gffline->is_gene);
788     isTranscript(gffline->is_transcript || gffline->exontype!=0);
789     fromGff3(gffline->is_gff3);
790    
791     if (gffline->parents!=NULL) {
792     //GTF style -- create a GffObj directly by subfeature
793     //(also possible orphan GFF3 exon line, or an exon given before its parent (chado))
794     if (gffline->exontype!=0) { //recognized exon-like feature
795     ftype_id=gff_fid_transcript; //so this is some sort of transcript
796     exon_ftype_id=gff_fid_exon; //subfeatures MUST be exons
797     }
798     else {//unrecognized subfeatures
799     //make this GffObj of the same feature type
800     ftype_id=names->feats.addName(gffline->ftype);
801     }
802     if (gffline->ID==NULL) { //typical GTF
803     gffID=Gstrdup(gffline->parents[0]);
804     this->createdByExon(true);
805     //this is likely the first exon/segment of the feature
806     addExon(gfrd, gffline, keepAttr, noExonAttr);
807 gpertea 2 }
808 gpertea 16 else { //a parented feature with an ID -- probably an orphan GFF3 line
809     if (gffline->is_gff3 && gffline->exontype!=0) {
810     //premature exon given before its parent transcript
811     //create the transcript entry here
812     gffID=Gstrdup(gffline->parents[0]);
813     this->createdByExon(true);
814     //this is the first exon/segment of the transcript
815     addExon(gfrd, gffline, keepAttr, noExonAttr);
816     }
817     else { //unrecognized non-exon feature ? use the ID instead
818     gffID=Gstrdup(gffline->ID);
819     if (keepAttr) this->parseAttrs(attrs, gffline->info);
820     }
821 gpertea 2 }
822 gpertea 16 } //subfeature given directly
823     else { //gffline->parents==NULL
824     //create a parent feature in its own right
825 gpertea 2 gscore=gffline->score;
826     if (gffline->ID==NULL || gffline->ID[0]==0)
827 gpertea 16 GError("Error: no ID found for GFF record start\n");
828     gffID=Gstrdup(gffline->ID); //there must be an ID here
829     //if (gffline->is_transcript) ftype_id=gff_fid_mRNA;
830     //else
831     ftype_id=names->feats.addName(gffline->ftype);
832     if (gffline->is_transcript)
833     exon_ftype_id=gff_fid_exon;
834    
835     if (keepAttr) this->parseAttrs(attrs, gffline->info);
836     }//no parent
837    
838     if (gffline->gene_name!=NULL) {
839     gene_name=Gstrdup(gffline->gene_name);
840     }
841     if (gffline->gene_id!=NULL) {
842     geneID=Gstrdup(gffline->gene_id);
843     }
844    
845     GSeqStat* gsd=gfrd->gseqstats.AddIfNew(new GSeqStat(gseq_id,names->gseqs.lastNameUsed()),true);
846     uptr=gsd;
847     if (start<gsd->mincoord) gsd->mincoord=start;
848     if (end>gsd->maxcoord) gsd->maxcoord=end;
849     if (this->len()>gsd->maxfeat_len) {
850     gsd->maxfeat_len=this->len();
851     gsd->maxfeat=this;
852 gpertea 2 }
853     }
854    
855     GffLine* GffReader::nextGffLine() {
856     if (gffline!=NULL) return gffline; //caller should free gffline after processing
857     while (gffline==NULL) {
858     int llen=0;
859     buflen=GFF_LINELEN-1;
860     char* l=fgetline(linebuf, buflen, fh, &fpos, &llen);
861     if (l==NULL) {
862     return NULL; //end of file
863     }
864     int ns=0; //first nonspace position
865     while (l[ns]!=0 && isspace(l[ns])) ns++;
866     if (l[ns]=='#' || llen<10) continue;
867     gffline=new GffLine(this, l);
868     if (gffline->skip) {
869     delete gffline;
870     gffline=NULL;
871 gpertea 16 continue;
872 gpertea 2 }
873 gpertea 16 if (gffline->ID==NULL && gffline->parents==NULL) { //it must have an ID
874     //this might not be needed, already checked in the GffLine constructor
875     if (gff_warns)
876     GMessage("Warning: malformed GFF line, no parent or record Id (kipping\n");
877     delete gffline;
878     gffline=NULL;
879     //continue;
880     }
881 gpertea 2 }
882     return gffline;
883     }
884    
885 gpertea 151
886 gpertea 2 char* GffReader::gfoBuildId(const char* id, const char* ctg) {
887     //caller must free the returned pointer
888     char* buf=NULL;
889     int idlen=strlen(id);
890     GMALLOC(buf, idlen+strlen(ctg)+2);
891     strcpy(buf, id);
892     buf[idlen]='~';
893     strcpy(buf+idlen+1, ctg);
894     return buf;
895     }
896 gpertea 151 /*
897 gpertea 2 void GffReader::gfoRemove(const char* id, const char* ctg) {
898     char* buf=gfoBuildId(id,ctg);
899     phash.Remove(buf);
900     GFREE(buf);
901     }
902 gpertea 151 */
903 gpertea 16 //Warning: if gflst gets altered, idx becomes obsolete
904 gpertea 151 GfoHolder* GffReader::gfoAdd(GffObj* gfo, int idx) {
905     GVec<GfoHolder>* glst=new GVec<GfoHolder>(1);
906     GfoHolder gh(gfo,idx);
907     int i=glst->Add(gh);
908     phash.Add(gfo->gffID, glst);
909     return &(glst->Get(i));
910 gpertea 2 }
911 gpertea 16
912 gpertea 151 GfoHolder* GffReader::gfoAdd(GVec<GfoHolder>& glst, GffObj* gfo, int idx) {
913     GfoHolder gh(gfo,idx);
914     int i=glst.Add(gh);
915     return &(glst[i]);
916 gpertea 2 }
917    
918 gpertea 151 GfoHolder* GffReader::gfoFind(const char* id, const char* ctg, char strand, uint start, GVec<GfoHolder>** glst) {
919     GVec<GfoHolder>* gl=phash.Find(id);
920     GfoHolder* gh=NULL;
921     if (gl) {
922     for (int i=0;i<gl->Count();i++) {
923     GfoHolder& gfo = gl->Get(i);
924     if (ctg!=NULL && strcmp(ctg,gfo.gffobj->getGSeqName())!=0)
925     continue;
926     if (strand && strand != gfo.gffobj->strand)
927     continue;
928     if (start>0 && abs((int)start-(int)gfo.gffobj->start)>GFF_MAX_LOCUS)
929     continue;
930     //must be the same transcript, according to given comparison criteria
931     gh=&gfo;
932     break;
933     }
934     }
935     if (glst) *glst=gl;
936     return gh;
937     }
938    
939 gpertea 16 GfoHolder* GffReader::replaceGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr, int replaceidx) {
940     GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
941     GfoHolder* r=NULL;
942     if (replaceidx>=0) {
943     gflst.Put(replaceidx,newgfo);
944 gpertea 151 r=gfoAdd(newgfo, replaceidx);
945 gpertea 16 }
946     else {
947     int gfoidx=gflst.Add(newgfo);
948 gpertea 151 r=gfoAdd(newgfo, gfoidx);
949 gpertea 16 }
950     if (gff_warns) {
951     int* pcount=tids.Find(newgfo->gffID);
952     if (pcount!=NULL) {
953 gpertea 151 if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
954 gpertea 16 (*pcount)++;
955     }
956     else {
957     tids.Add(newgfo->gffID,new int(1));
958     }
959     }
960     return r;
961     }
962 gpertea 2
963 gpertea 16 GfoHolder* GffReader::updateParent(GfoHolder* newgfh, GffObj* parent) {
964     //assert(parent);
965     //assert(newgfo);
966     parent->children.Add(newgfh->gffobj);
967     if (newgfh->gffobj->parent==NULL) newgfh->gffobj->parent=parent;
968     newgfh->gffobj->setLevel(parent->getLevel()+1);
969     if (parent->isGene()) {
970     if (parent->gene_name!=NULL && newgfh->gffobj->gene_name==NULL)
971     newgfh->gffobj->gene_name=Gstrdup(parent->gene_name);
972     if (parent->geneID!=NULL && newgfh->gffobj->geneID==NULL)
973     newgfh->gffobj->geneID=Gstrdup(parent->geneID);
974     }
975    
976     return newgfh;
977 gpertea 2 }
978    
979 gpertea 16 GfoHolder* GffReader::newGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr,
980 gpertea 151 GffObj* parent, GffExon* pexon, GVec<GfoHolder>* glst) {
981 gpertea 16 GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
982     GfoHolder* r=NULL;
983     int gfoidx=gflst.Add(newgfo);
984 gpertea 151 r=(glst) ? gfoAdd(*glst, newgfo, gfoidx) :gfoAdd(newgfo, gfoidx);
985 gpertea 16 if (parent!=NULL) {
986     updateParent(r, parent);
987     if (pexon!=NULL) parent->removeExon(pexon);
988     }
989     if (gff_warns) {
990     int* pcount=tids.Find(newgfo->gffID);
991     if (pcount!=NULL) {
992     if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
993     (*pcount)++;
994     }
995     else {
996     tids.Add(newgfo->gffID,new int(1));
997     }
998     }
999     return r;
1000     }
1001 gpertea 2
1002 gpertea 16 GfoHolder* GffReader::updateGffRec(GfoHolder* prevgfo, GffLine* gffline,
1003     bool keepAttr) {
1004     if (prevgfo==NULL) return NULL;
1005     prevgfo->gffobj->createdByExon(false);
1006     prevgfo->gffobj->ftype_id=prevgfo->gffobj->names->feats.addName(gffline->ftype);
1007     prevgfo->gffobj->start=gffline->fstart;
1008     prevgfo->gffobj->end=gffline->fend;
1009     prevgfo->gffobj->isGene(gffline->is_gene);
1010     prevgfo->gffobj->isTranscript(gffline->is_transcript || gffline->exontype!=0);
1011     prevgfo->gffobj->fromGff3(gffline->is_gff3);
1012     if (keepAttr) {
1013     if (prevgfo->gffobj->attrs!=NULL) prevgfo->gffobj->attrs->Clear();
1014     prevgfo->gffobj->parseAttrs(prevgfo->gffobj->attrs, gffline->info);
1015     }
1016     return prevgfo;
1017     }
1018    
1019    
1020     bool GffReader::addExonFeature(GfoHolder* prevgfo, GffLine* gffline, GHash<CNonExon>& pex, bool noExonAttr) {
1021     bool r=true;
1022     if (gffline->strand!=prevgfo->gffobj->strand) {
1023 gpertea 115 //TODO: add support for trans-splicing and even inter-chromosomal fusions
1024     if (prevgfo->gffobj->strand=='.') {
1025     prevgfo->gffobj->strand=gffline->strand;
1026     }
1027     else {
1028     GMessage("GFF Error at %s (%c): exon %d-%d (%c) found on different strand; discarded.\n",
1029     prevgfo->gffobj->gffID, prevgfo->gffobj->strand,
1030     gffline->fstart, gffline->fend, gffline->strand, prevgfo->gffobj->getGSeqName());
1031     //r=false;
1032     return true; //FIXME: split trans-spliced mRNAs by strand
1033     }
1034     }
1035 gpertea 16 int gdist=(gffline->fstart>prevgfo->gffobj->end) ? gffline->fstart-prevgfo->gffobj->end :
1036     ((gffline->fend<prevgfo->gffobj->start)? prevgfo->gffobj->start-gffline->fend :
1037     0 );
1038     if (gdist>(int)GFF_MAX_LOCUS) { //too far apart, most likely this is a duplicate ID
1039     GMessage("Error: duplicate GFF ID '%s' (or exons too far apart)!\n",prevgfo->gffobj->gffID);
1040     //validation_errors = true;
1041     r=false;
1042     if (!gff_warns) exit(1);
1043     }
1044     int eidx=prevgfo->gffobj->addExon(this, gffline, !noExonAttr, noExonAttr);
1045     if (eidx>=0 && gffline->ID!=NULL && gffline->exontype==0)
1046     subfPoolAdd(pex, prevgfo);
1047     return r;
1048     }
1049    
1050     CNonExon* GffReader::subfPoolCheck(GffLine* gffline, GHash<CNonExon>& pex, char*& subp_name) {
1051     CNonExon* subp=NULL;
1052     subp_name=NULL;
1053     for (int i=0;i<gffline->num_parents;i++) {
1054     if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
1055     continue;
1056     subp_name=gfoBuildId(gffline->parents[i], gffline->gseqname); //e.g. mRNA name
1057     subp=pex.Find(subp_name);
1058     if (subp!=NULL)
1059     return subp;
1060     GFREE(subp_name);
1061     }
1062     return NULL;
1063     }
1064    
1065     void GffReader::subfPoolAdd(GHash<CNonExon>& pex, GfoHolder* newgfo) {
1066     //this might become a parent feature later
1067     if (newgfo->gffobj->exons.Count()>0) {
1068     char* xbuf=gfoBuildId(gffline->ID, gffline->gseqname);
1069     pex.Add(xbuf, new CNonExon(newgfo->idx, newgfo->gffobj,
1070     newgfo->gffobj->exons[0], gffline));
1071     GFREE(xbuf);
1072     }
1073     }
1074    
1075     GfoHolder* GffReader::promoteFeature(CNonExon* subp, char*& subp_name, GHash<CNonExon>& pex,
1076     bool keepAttr, bool noExonAttr) {
1077     GffObj* prevp=subp->parent; //grandparent of gffline (e.g. gene)
1078     if (prevp!=gflst[subp->idx])
1079     GError("Error promoting subfeature %s, gflst index mismatch?!\n", subp->gffline->ID);
1080     subp->gffline->discardParent();
1081     GfoHolder* gfoh=newGffRec(subp->gffline, keepAttr, noExonAttr, prevp, subp->exon);
1082     pex.Remove(subp_name); //no longer a potential parent, moved it to phash already
1083     prevp->promotedChildren(true);
1084     return gfoh; //returns the holder of newly promoted feature
1085     }
1086    
1087     //have to parse the whole file because exons can be scattered all over
1088 gpertea 2 void GffReader::readAll(bool keepAttr, bool mergeCloseExons, bool noExonAttr) {
1089 gpertea 16 bool validation_errors = false;
1090     //loc_debug=false;
1091     GHash<CNonExon> pex; //keep track of any "exon"-like features that have an ID
1092     //and thus could become promoted to parent features
1093 gpertea 2 while (nextGffLine()!=NULL) {
1094 gpertea 16 //seen this gff ID before?
1095     GfoHolder* prevseen=NULL;
1096 gpertea 151 if (gffline->ID) //GFF3 parent-like feature (mRNA, gene, etc.)
1097 gpertea 16 prevseen=gfoFind(gffline->ID, gffline->gseqname);
1098     if (prevseen!=NULL) {
1099     if (prevseen->gffobj->createdByExon()) {
1100 gpertea 151 //just in case the exon was found before (shouldn't happen)
1101 gpertea 16 updateGffRec(prevseen, gffline, keepAttr);
1102     }
1103     else {
1104     GMessage("Error: duplicate GFF ID '%s' encountered!\n",gffline->ID);
1105     validation_errors = true;
1106     if (gff_warns) {
1107     delete gffline; gffline=NULL; continue;
1108     }
1109     else exit(1);
1110     }
1111 gpertea 2 }
1112 gpertea 16 if (gffline->parents==NULL) {//start GFF3-like record with no parent (mRNA, gene)
1113     if (!prevseen) newGffRec(gffline, keepAttr, noExonAttr);
1114 gpertea 2 }
1115 gpertea 151 else { //--- it's a parented feature (exon/CDS, but might still be a mRNA)
1116 gpertea 16 bool found_parent=false;
1117     GfoHolder* newgfo=prevseen;
1118 gpertea 151 GVec<GfoHolder>* newgflst=NULL;
1119 gpertea 16 for (int i=0;i<gffline->num_parents;i++) {
1120     if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
1121     continue; //skipping discarded parent feature
1122 gpertea 151 GfoHolder* parentgfo=gfoFind(gffline->parents[i], gffline->gseqname, gffline->strand, gffline->fstart, &newgflst);
1123 gpertea 16 if (parentgfo!=NULL) { //parent GffObj parsed earlier
1124     found_parent=true;
1125     if (parentgfo->gffobj->isGene() && gffline->is_transcript
1126     && gffline->exontype==0) {
1127     //not an exon, but a transcript parented by a gene
1128     if (newgfo) {
1129     updateParent(newgfo, parentgfo->gffobj);
1130     }
1131     else {
1132     newgfo=newGffRec(gffline, keepAttr, noExonAttr, parentgfo->gffobj);
1133     }
1134     }
1135     else { //potential exon subfeature
1136     if (!addExonFeature(parentgfo, gffline, pex, noExonAttr))
1137     validation_errors=true;
1138     }
1139 gpertea 2 }
1140 gpertea 16 } //for each parsed parent Id
1141     if (!found_parent) { //new GTF-like record starting here with a subfeature directly
1142     //or it could be some chado GFF3 barf with exons declared BEFORE their parent :(
1143     //check if this feature isn't parented by a previously stored "exon" subfeature
1144     char* subp_name=NULL;
1145     CNonExon* subp=subfPoolCheck(gffline, pex, subp_name);
1146     if (subp!=NULL) { //found a subfeature that is the parent of this gffline
1147     //promote that subfeature to a full GffObj
1148     GfoHolder* gfoh=promoteFeature(subp, subp_name, pex, keepAttr, noExonAttr);
1149     //add current gffline as an exon of the newly promoted subfeature
1150     if (!addExonFeature(gfoh, gffline, pex, noExonAttr))
1151     validation_errors=true;
1152     }
1153     else { //no parent seen before, create one directly with this exon
1154     //loc_debug=true;
1155 gpertea 151 GfoHolder* newgfo=prevseen ? prevseen : newGffRec(gffline, keepAttr, noExonAttr, NULL, NULL, newgflst);
1156 gpertea 16 if (gffline->ID!=NULL && gffline->exontype==0)
1157     subfPoolAdd(pex, newgfo);
1158     //even those with errors will be added here!
1159     }
1160     GFREE(subp_name);
1161     } //no previous parent found
1162     } //parented feature
1163     //--
1164     delete gffline;
1165     gffline=NULL;
1166     }//while gff lines
1167     gflst.finalize(this, mergeCloseExons, keepAttr, noExonAttr); //force sorting by locus if so constructed
1168 gpertea 2 // all gff records are now loaded in GList gflst
1169     // so we can free the hash
1170     phash.Clear();
1171 gpertea 16 tids.Clear();
1172     if (validation_errors) {
1173     exit(1);
1174     }
1175 gpertea 2 }
1176    
1177 gpertea 16 GffObj* GffObj::finalize(GffReader* gfr, bool mergeCloseExons, bool keepAttrs, bool noExonAttr) {
1178     //merge
1179     //always merge adjacent or overlapping segments
1180     //but if mergeCloseExons then merge even when distance is up to 5 bases
1181 gpertea 2 udata=0;
1182     uptr=NULL;
1183 gpertea 16 if (gfr->transcriptsOnly && !(isTranscript() || (isGene() && children.Count()==0))) {
1184     isDiscarded(true);
1185     }
1186     if (ftype_id==gff_fid_transcript && CDstart>0) {
1187     ftype_id=gff_fid_mRNA;
1188     //exon_ftype_id=gff_fid_exon;
1189     }
1190     //if (ftype_id==gff_fid_mRNA || exon_ftype_id==gff_fid_exon || mergeCloseExons) {
1191     if (isTranscript() || exon_ftype_id==gff_fid_exon || mergeCloseExons) {
1192 gpertea 2 int mindist=mergeCloseExons ? 5:1;
1193     for (int i=0;i<exons.Count()-1;i++) {
1194     int ni=i+1;
1195     uint mend=exons[i]->end;
1196     while (ni<exons.Count()) {
1197     int dist=(int)(exons[ni]->start-mend);
1198 gpertea 16 if (dist>mindist) break; //no merging with next segment
1199     if (gfr!=NULL && gfr->gff_warns && dist!=0 && (exons[ni]->exontype!=exgffUTR && exons[i]->exontype!=exgffUTR)) {
1200     GMessage("GFF warning: merging adjacent/overlapping segments of %s on %s (%d-%d, %d-%d)\n",
1201     gffID, getGSeqName(), exons[i]->start, exons[i]->end,exons[ni]->start, exons[ni]->end);
1202     }
1203 gpertea 2 mend=exons[ni]->end;
1204 gpertea 16 covlen-=exons[i]->len();
1205 gpertea 2 exons[i]->end=mend;
1206 gpertea 16 covlen+=exons[i]->len();
1207     covlen-=exons[ni]->len();
1208 gpertea 2 if (exons[ni]->attrs!=NULL && (exons[i]->attrs==NULL ||
1209     exons[i]->attrs->Count()<exons[ni]->attrs->Count())) {
1210     //use the other exon attributes, if more
1211     delete(exons[i]->attrs);
1212     exons[i]->attrs=exons[ni]->attrs;
1213     exons[ni]->attrs=NULL;
1214     }
1215     exons.Delete(ni);
1216     } //check for merge with next exon
1217     } //for each exon
1218     }
1219 gpertea 16 //attribute reduction for GTF records
1220     if (keepAttrs && !noExonAttr && !fromGff3()
1221     && exons.Count()>0 && exons[0]->attrs!=NULL) {
1222     bool attrs_discarded=false;
1223     for (int a=0;a<exons[0]->attrs->Count();a++) {
1224     int attr_name_id=exons[0]->attrs->Get(a)->attr_id;
1225     char* attr_name=names->attrs.getName(attr_name_id);
1226     char* attr_val =exons[0]->attrs->Get(a)->attr_val;
1227     bool sameExonAttr=true;
1228     for (int i=1;i<exons.Count();i++) {
1229     char* ov=exons[i]->getAttr(attr_name_id);
1230     if (ov==NULL || (strcmp(ov,attr_val)!=0)) {
1231     sameExonAttr=false;
1232     break;
1233     }
1234     }
1235     if (sameExonAttr) {
1236     //delete this attribute from exons level
1237     attrs_discarded=true;
1238     this->addAttr(attr_name, attr_val);
1239     for (int i=1;i<exons.Count();i++) {
1240     removeExonAttr(*(exons[i]), attr_name_id);
1241     }
1242     exons[0]->attrs->freeItem(a);
1243     }
1244     }
1245     if (attrs_discarded) exons[0]->attrs->Pack();
1246     }
1247 gpertea 2 return this;
1248     }
1249    
1250 gpertea 16 void GffObj::parseAttrs(GffAttrs*& atrlist, char* info, bool isExon) {
1251 gpertea 2 if (names==NULL)
1252     GError(ERR_NULL_GFNAMES, "parseAttrs()");
1253     if (atrlist==NULL)
1254     atrlist=new GffAttrs();
1255     char* endinfo=info+strlen(info);
1256     char* start=info;
1257     char* pch=start;
1258     while (start<endinfo) {
1259     //skip spaces
1260     while (*start==' ' && start<endinfo) start++;
1261     pch=strchr(start, ';');
1262     if (pch==NULL) pch=endinfo;
1263     else {
1264     *pch='\0';
1265     pch++;
1266     }
1267     char* ech=strchr(start,'=');
1268     if (ech!=NULL) { // attr=value format found
1269     *ech='\0';
1270 gpertea 16 //if (noExonAttr && (strcmp(start, "exon_number")==0 || strcmp(start, "exon")==0)) { start=pch; continue; }
1271     if (strcmp(start, "exon_number")==0 || strcmp(start, "exon")==0 ||
1272     strcmp(start, "exon_id")==0)
1273     { start=pch; continue; }
1274 gpertea 2 ech++;
1275     while (*ech==' ' && ech<endinfo) ech++;//skip extra spaces after the '='
1276 gpertea 16 //atrlist->Add(new GffAttr(names->attrs.addName(start),ech));
1277     //make sure we don't add the same attribute more than once
1278     if (isExon && (strcmp(start, "protein_id")==0)) {
1279     //Ensembl special case
1280     this->addAttr(start, ech);
1281     start=pch;
1282     continue;
1283     }
1284     atrlist->add_or_update(names, start, ech);
1285 gpertea 2 }
1286     /*
1287     else { //not an attr=value format
1288     atrlist->Add(new GffAttr(names->attrs.addName(start),"1"));
1289     }
1290     */
1291     start=pch;
1292     }
1293     if (atrlist->Count()==0) { delete atrlist; atrlist=NULL; }
1294     }
1295    
1296 gpertea 16 void GffObj::addAttr(const char* attrname, const char* attrvalue) {
1297 gpertea 2 if (this->attrs==NULL)
1298     this->attrs=new GffAttrs();
1299 gpertea 16 //this->attrs->Add(new GffAttr(names->attrs.addName(attrname),attrvalue));
1300     this->attrs->add_or_update(names, attrname, attrvalue);
1301 gpertea 2 }
1302    
1303 gpertea 16
1304     void GffObj::setFeatureName(const char* feature) {
1305     //change the feature name/type for a transcript
1306     int fid=names->feats.addName(feature);
1307     if (monoFeature() && exons.Count()>0)
1308     this->exon_ftype_id=fid;
1309     this->ftype_id=fid;
1310     }
1311    
1312     void GffObj::setRefName(const char* newname) {
1313     //change the feature name/type for a transcript
1314     int rid=names->gseqs.addName(newname);
1315     this->gseq_id=rid;
1316     }
1317    
1318    
1319    
1320     int GffObj::removeAttr(const char* attrname, const char* attrval) {
1321     if (this->attrs==NULL || attrname==NULL || attrname[0]==0) return 0;
1322     int aid=this->names->attrs.getId(attrname);
1323     if (aid<0) return 0;
1324     int delcount=0; //could be more than one ?
1325     for (int i=0;i<this->attrs->Count();i++) {
1326     if (aid==this->attrs->Get(i)->attr_id) {
1327     if (attrval==NULL ||
1328     strcmp(attrval, this->attrs->Get(i)->attr_val)==0) {
1329     delcount++;
1330     this->attrs->freeItem(i);
1331     }
1332     }
1333     }
1334     if (delcount>0) this->attrs->Pack();
1335     return delcount;
1336     }
1337    
1338     int GffObj::removeAttr(int aid, const char* attrval) {
1339     if (this->attrs==NULL || aid<0) return 0;
1340     int delcount=0; //could be more than one ?
1341     for (int i=0;i<this->attrs->Count();i++) {
1342     if (aid==this->attrs->Get(i)->attr_id) {
1343     if (attrval==NULL ||
1344     strcmp(attrval, this->attrs->Get(i)->attr_val)==0) {
1345     delcount++;
1346     this->attrs->freeItem(i);
1347     }
1348     }
1349     }
1350     if (delcount>0) this->attrs->Pack();
1351     return delcount;
1352     }
1353    
1354    
1355     int GffObj::removeExonAttr(GffExon& exon, const char* attrname, const char* attrval) {
1356     if (exon.attrs==NULL || attrname==NULL || attrname[0]==0) return 0;
1357     int aid=this->names->attrs.getId(attrname);
1358     if (aid<0) return 0;
1359     int delcount=0; //could be more than one
1360     for (int i=0;i<exon.attrs->Count();i++) {
1361     if (aid==exon.attrs->Get(i)->attr_id) {
1362     if (attrval==NULL ||
1363     strcmp(attrval, exon.attrs->Get(i)->attr_val)==0) {
1364     delcount++;
1365     exon.attrs->freeItem(i);
1366     }
1367     }
1368     }
1369     if (delcount>0) exon.attrs->Pack();
1370     return delcount;
1371     }
1372    
1373     int GffObj::removeExonAttr(GffExon& exon, int aid, const char* attrval) {
1374     if (exon.attrs==NULL || aid<0) return 0;
1375     int delcount=0; //could be more than one
1376     for (int i=0;i<exon.attrs->Count();i++) {
1377     if (aid==exon.attrs->Get(i)->attr_id) {
1378     if (attrval==NULL ||
1379     strcmp(attrval, exon.attrs->Get(i)->attr_val)==0) {
1380     delcount++;
1381     exon.attrs->freeItem(i);
1382     }
1383     }
1384     }
1385     if (delcount>0) exon.attrs->Pack();
1386     return delcount;
1387     }
1388    
1389    
1390 gpertea 2 void GffObj::getCDS_ends(uint& cds_start, uint& cds_end) {
1391     cds_start=0;
1392     cds_end=0;
1393     if (CDstart==0 || CDend==0) return; //no CDS info
1394     int cdsadj=0;
1395     if (CDphase=='1' || CDphase=='2') {
1396     cdsadj=CDphase-'0';
1397     }
1398     cds_start=CDstart;
1399     cds_end=CDend;
1400     if (strand=='-') cds_end-=cdsadj;
1401     else cds_start+=cdsadj;
1402     }
1403    
1404     void GffObj::mRNA_CDS_coords(uint& cds_mstart, uint& cds_mend) {
1405     //sets cds_start and cds_end to the CDS start,end coordinates on the spliced mRNA transcript
1406     cds_mstart=0;
1407     cds_mend=0;
1408     if (CDstart==0 || CDend==0) return; //no CDS info
1409     //restore normal coordinates, just in case
1410     unxcoord();
1411     int cdsadj=0;
1412     if (CDphase=='1' || CDphase=='2') {
1413     cdsadj=CDphase-'0';
1414     }
1415     /*
1416     uint seqstart=CDstart;
1417     uint seqend=CDend;
1418     */
1419     uint seqstart=exons.First()->start;
1420     uint seqend=exons.Last()->end;
1421     int s=0; //resulting nucleotide counter
1422     if (strand=='-') {
1423     for (int x=exons.Count()-1;x>=0;x--) {
1424     uint sgstart=exons[x]->start;
1425     uint sgend=exons[x]->end;
1426     if (seqend<sgstart || seqstart>sgend) continue;
1427     if (seqstart>=sgstart && seqstart<=sgend)
1428     sgstart=seqstart; //seqstart within this segment
1429     if (seqend>=sgstart && seqend<=sgend)
1430     sgend=seqend; //seqend within this segment
1431     s+=(int)(sgend-sgstart)+1;
1432     if (CDstart>=sgstart && CDstart<=sgend) {
1433     //CDstart in this segment
1434     //and we are getting the whole transcript
1435     cds_mend=s-(int)(CDstart-sgstart);
1436     }
1437     if (CDend>=sgstart && CDend<=sgend) {
1438     //CDstart in this segment
1439     //and we are getting the whole transcript
1440     cds_mstart=s-(int)(CDend-cdsadj-sgstart);
1441     }
1442     } //for each exon
1443     } // - strand
1444     else { // + strand
1445     for (int x=0;x<exons.Count();x++) {
1446     uint sgstart=exons[x]->start;
1447     uint sgend=exons[x]->end;
1448     if (seqend<sgstart || seqstart>sgend) continue;
1449     if (seqstart>=sgstart && seqstart<=sgend)
1450     sgstart=seqstart; //seqstart within this segment
1451     if (seqend>=sgstart && seqend<=sgend)
1452     sgend=seqend; //seqend within this segment
1453     s+=(int)(sgend-sgstart)+1;
1454     /* for (uint i=sgstart;i<=sgend;i++) {
1455     spliced[s]=gsubseq[i-gstart];
1456     s++;
1457     }//for each nt
1458     */
1459     if (CDstart>=sgstart && CDstart<=sgend) {
1460     //CDstart in this segment
1461     cds_mstart=s-(int)(sgend-CDstart-cdsadj);
1462     }
1463     if (CDend>=sgstart && CDend<=sgend) {
1464     //CDend in this segment
1465     cds_mend=s-(int)(sgend-CDend);
1466     }
1467     } //for each exon
1468     } // + strand
1469     //spliced[s]=0;
1470     //if (rlen!=NULL) *rlen=s;
1471     //return spliced;
1472     }
1473    
1474 gpertea 16 char* GffObj::getUnspliced(GFaSeqGet* faseq, int* rlen, GList<GSeg>* seglst)
1475     {
1476     if (faseq==NULL) { GMessage("Warning: getUnspliced(NULL,.. ) called!\n");
1477     return NULL;
1478     }
1479     //restore normal coordinates:
1480     unxcoord();
1481     if (exons.Count()==0) return NULL;
1482     int fspan=end-start+1;
1483     const char* gsubseq=faseq->subseq(start, fspan);
1484     if (gsubseq==NULL) {
1485     GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1486     }
1487     char* unspliced=NULL;
1488    
1489     int seqstart=exons.First()->start;
1490     int seqend=exons.Last()->end;
1491    
1492     int unsplicedlen = 0;
1493    
1494     unsplicedlen += seqend - seqstart + 1;
1495    
1496     GMALLOC(unspliced, unsplicedlen+1); //allocate more here
1497     //uint seqstart, seqend;
1498    
1499     int s = 0; //resulting nucleotide counter
1500     if (strand=='-')
1501     {
1502     if (seglst!=NULL)
1503     seglst->Add(new GSeg(s+1,s+1+seqend-seqstart));
1504     for (int i=seqend;i>=seqstart;i--)
1505     {
1506     unspliced[s] = ntComplement(gsubseq[i-start]);
1507     s++;
1508     }//for each nt
1509     } // - strand
1510     else
1511     { // + strand
1512     if (seglst!=NULL)
1513     seglst->Add(new GSeg(s+1,s+1+seqend-seqstart));
1514     for (int i=seqstart;i<=seqend;i++)
1515     {
1516     unspliced[s]=gsubseq[i-start];
1517     s++;
1518     }//for each nt
1519     } // + strand
1520     //assert(s <= unsplicedlen);
1521     unspliced[s]=0;
1522     if (rlen!=NULL) *rlen=s;
1523     return unspliced;
1524     }
1525    
1526 gpertea 2 char* GffObj::getSpliced(GFaSeqGet* faseq, bool CDSonly, int* rlen, uint* cds_start, uint* cds_end,
1527     GList<GSeg>* seglst) {
1528     if (CDSonly && CDstart==0) return NULL;
1529     if (faseq==NULL) { GMessage("Warning: getSpliced(NULL,.. ) called!\n");
1530     return NULL;
1531     }
1532     //restore normal coordinates:
1533     unxcoord();
1534     if (exons.Count()==0) return NULL;
1535     int fspan=end-start+1;
1536     const char* gsubseq=faseq->subseq(start, fspan);
1537     if (gsubseq==NULL) {
1538     GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1539     }
1540 gpertea 16 if (fspan<(int)(end-start+1)) { //special case: stop coordinate was extended past the gseq length, must adjust
1541     int endadj=end-start+1-fspan;
1542     uint prevend=end;
1543     end-=endadj;
1544     if (CDend>end) CDend=end;
1545     if (exons.Last()->end>end) {
1546     exons.Last()->end=end; //this could get us into trouble if exon start is also > end
1547     if (exons.Last()->start>exons.Last()->end) {
1548     GError("GffObj::getSpliced() error: improper genomic coordinate %d on %s for %s\n",
1549     prevend,getGSeqName(), getID());
1550     }
1551     covlen-=endadj;
1552     }
1553     }
1554 gpertea 2 char* spliced=NULL;
1555     GMALLOC(spliced, covlen+1); //allocate more here
1556     uint seqstart, seqend;
1557     int cdsadj=0;
1558     if (CDphase=='1' || CDphase=='2') {
1559     cdsadj=CDphase-'0';
1560     }
1561     if (CDSonly) {
1562     seqstart=CDstart;
1563     seqend=CDend;
1564     if (strand=='-') seqend-=cdsadj;
1565     else seqstart+=cdsadj;
1566     }
1567     else {
1568     seqstart=exons.First()->start;
1569     seqend=exons.Last()->end;
1570     }
1571     int s=0; //resulting nucleotide counter
1572     if (strand=='-') {
1573     for (int x=exons.Count()-1;x>=0;x--) {
1574     uint sgstart=exons[x]->start;
1575     uint sgend=exons[x]->end;
1576     if (seqend<sgstart || seqstart>sgend) continue;
1577     if (seqstart>=sgstart && seqstart<=sgend)
1578     sgstart=seqstart; //seqstart within this segment
1579     if (seqend>=sgstart && seqend<=sgend)
1580     sgend=seqend; //seqend within this segment
1581     if (seglst!=NULL)
1582     seglst->Add(new GSeg(s+1,s+1+sgend-sgstart));
1583     for (uint i=sgend;i>=sgstart;i--) {
1584     spliced[s] = ntComplement(gsubseq[i-start]);
1585     s++;
1586     }//for each nt
1587    
1588     if (!CDSonly && cds_start!=NULL && CDstart>0) {
1589     if (CDstart>=sgstart && CDstart<=sgend) {
1590     //CDstart in this segment
1591     //and we are getting the whole transcript
1592     *cds_end=s-(CDstart-sgstart);
1593     }
1594     if (CDend>=sgstart && CDend<=sgend) {
1595     //CDstart in this segment
1596     //and we are getting the whole transcript
1597     *cds_start=s-(CDend-cdsadj-sgstart);
1598     }
1599     }//update local CDS coordinates
1600     } //for each exon
1601     } // - strand
1602     else { // + strand
1603     for (int x=0;x<exons.Count();x++) {
1604     uint sgstart=exons[x]->start;
1605     uint sgend=exons[x]->end;
1606     if (seqend<sgstart || seqstart>sgend) continue;
1607     if (seqstart>=sgstart && seqstart<=sgend)
1608     sgstart=seqstart; //seqstart within this segment
1609     if (seqend>=sgstart && seqend<=sgend)
1610     sgend=seqend; //seqend within this segment
1611     if (seglst!=NULL)
1612     seglst->Add(new GSeg(s+1,s+1+sgend-sgstart));
1613     for (uint i=sgstart;i<=sgend;i++) {
1614     spliced[s]=gsubseq[i-start];
1615     s++;
1616     }//for each nt
1617     if (!CDSonly && cds_start!=NULL && CDstart>0) {
1618     if (CDstart>=sgstart && CDstart<=sgend) {
1619     //CDstart in this segment
1620     //and we are getting the whole transcript
1621     *cds_start=s-(sgend-CDstart-cdsadj);
1622     }
1623     if (CDend>=sgstart && CDend<=sgend) {
1624     //CDstart in this segment
1625     //and we are getting the whole transcript
1626     *cds_end=s-(sgend-CDend);
1627     }
1628     }//update local CDS coordinates
1629     } //for each exon
1630     } // + strand
1631     spliced[s]=0;
1632     if (rlen!=NULL) *rlen=s;
1633     return spliced;
1634     }
1635    
1636     char* GffObj::getSplicedTr(GFaSeqGet* faseq, bool CDSonly, int* rlen) {
1637     if (CDSonly && CDstart==0) return NULL;
1638     //restore normal coordinates:
1639     unxcoord();
1640     if (exons.Count()==0) return NULL;
1641     int fspan=end-start+1;
1642     const char* gsubseq=faseq->subseq(start, fspan);
1643     if (gsubseq==NULL) {
1644     GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1645     }
1646    
1647     char* translation=NULL;
1648     GMALLOC(translation, (int)(covlen/3)+1);
1649     uint seqstart, seqend;
1650     int cdsadj=0;
1651     if (CDphase=='1' || CDphase=='2') {
1652     cdsadj=CDphase-'0';
1653     }
1654     if (CDSonly) {
1655     seqstart=CDstart;
1656     seqend=CDend;
1657     if (strand=='-') seqend-=cdsadj;
1658     else seqstart+=cdsadj;
1659     }
1660     else {
1661     seqstart=exons.First()->start;
1662     seqend=exons.Last()->end;
1663     }
1664     Codon codon;
1665     int nt=0; //codon nucleotide counter (0..2)
1666     int aa=0; //aminoacid count
1667     if (strand=='-') {
1668     for (int x=exons.Count()-1;x>=0;x--) {
1669     uint sgstart=exons[x]->start;
1670     uint sgend=exons[x]->end;
1671     if (seqend<sgstart || seqstart>sgend) continue;
1672     if (seqstart>=sgstart && seqstart<=sgend)
1673     sgstart=seqstart; //seqstart within this segment
1674     if (seqend>=sgstart && seqend<=sgend) {
1675     sgend=seqend; //seqend within this segment
1676     }
1677     for (uint i=sgend;i>=sgstart;i--) {
1678     codon.nuc[nt]=ntComplement(gsubseq[i-start]);
1679     nt++;
1680     if (nt==3) {
1681     nt=0;
1682     translation[aa]=codon.translate();
1683     aa++;
1684     }
1685     }//for each nt
1686     } //for each exon
1687     } // - strand
1688     else { // + strand
1689     for (int x=0;x<exons.Count();x++) {
1690     uint sgstart=exons[x]->start;
1691     uint sgend=exons[x]->end;
1692     if (seqend<sgstart || seqstart>sgend) continue;
1693     if (seqstart>=sgstart && seqstart<=sgend)
1694     sgstart=seqstart; //seqstart within this segment
1695     if (seqend>=sgstart && seqend<=sgend)
1696     sgend=seqend; //seqend within this segment
1697     for (uint i=sgstart;i<=sgend;i++) {
1698     codon.nuc[nt]=gsubseq[i-start];
1699     nt++;
1700     if (nt==3) {
1701     nt=0;
1702     translation[aa]=codon.translate();
1703     aa++;
1704     }
1705     }//for each nt
1706     } //for each exon
1707     } // + strand
1708     translation[aa]=0;
1709     if (rlen!=NULL) *rlen=aa;
1710     return translation;
1711     }
1712    
1713     void GffObj::printSummary(FILE* fout) {
1714     if (fout==NULL) fout=stdout;
1715     fprintf(fout, "%s\t%c\t%d\t%d\t%4.2f\t%4.1f\n", gffID,
1716     strand, start, end, gscore, (float)qcov/10.0);
1717     }
1718    
1719 gpertea 16 void GffObj::printGxfLine(FILE* fout, const char* tlabel, const char* gseqname, bool iscds,
1720 gpertea 2 uint segstart, uint segend, int exidx, char phase, bool gff3) {
1721     static char scorestr[14];
1722     strcpy(scorestr,".");
1723     GffAttrs* xattrs=NULL;
1724     if (exidx>=0) {
1725     if (exons[exidx]->score) sprintf(scorestr,"%.2f", exons[exidx]->score);
1726     xattrs=exons[exidx]->attrs;
1727     }
1728     if (phase==0 || !iscds) phase='.';
1729     const char* ftype=iscds ? "CDS" : getSubfName();
1730     if (gff3) {
1731     fprintf(fout,
1732     "%s\t%s\t%s\t%d\t%d\t%s\t%c\t%c\tParent=%s",
1733     gseqname, tlabel, ftype, segstart, segend, scorestr, strand,
1734     phase, gffID);
1735     if (xattrs!=NULL) {
1736     for (int i=0;i<xattrs->Count();i++)
1737     fprintf(fout, ";%s=%s",names->attrs.getName(xattrs->Get(i)->attr_id),
1738     xattrs->Get(i)->attr_val);
1739     }
1740     fprintf(fout, "\n");
1741     } //GFF
1742 gpertea 16 else {//for GTF -- we print only transcripts
1743     //if (isValidTranscript())
1744     fprintf(fout, "%s\t%s\t%s\t%d\t%d\t%s\t%c\t%c\ttranscript_id \"%s\";",
1745     gseqname, tlabel, ftype, segstart, segend, scorestr, strand, phase, gffID);
1746     //char* geneid=(geneID!=NULL)? geneID : gffID;
1747     if (geneID)
1748     fprintf(fout," gene_id \"%s\";",geneID);
1749     if (gene_name!=NULL) {
1750     //fprintf(fout, " gene_name ");
1751     //if (gene_name[0]=='"') fprintf (fout, "%s;",gene_name);
1752     // else fprintf(fout, "\"%s\";",gene_name);
1753     fprintf(fout," gene_name \"%s\";",gene_name);
1754     }
1755 gpertea 2 if (xattrs!=NULL) {
1756 gpertea 16 for (int i=0;i<xattrs->Count();i++) {
1757     if (xattrs->Get(i)->attr_val==NULL) continue;
1758     const char* attrname=names->attrs.getName(xattrs->Get(i)->attr_id);
1759     fprintf(fout, " %s ",attrname);
1760     if (xattrs->Get(i)->attr_val[0]=='"')
1761     fprintf(fout, "%s;",xattrs->Get(i)->attr_val);
1762     else fprintf(fout, "\"%s\";",xattrs->Get(i)->attr_val);
1763     }
1764 gpertea 2 }
1765 gpertea 16 //for GTF, also append the GffObj attributes to each exon line
1766     if ((xattrs=this->attrs)!=NULL) {
1767     for (int i=0;i<xattrs->Count();i++) {
1768     if (xattrs->Get(i)->attr_val==NULL) continue;
1769     const char* attrname=names->attrs.getName(xattrs->Get(i)->attr_id);
1770     fprintf(fout, " %s ",attrname);
1771     if (xattrs->Get(i)->attr_val[0]=='"')
1772     fprintf(fout, "%s;",xattrs->Get(i)->attr_val);
1773     else fprintf(fout, "\"%s\";",xattrs->Get(i)->attr_val);
1774     }
1775     }
1776 gpertea 2 fprintf(fout, "\n");
1777     }//GTF
1778     }
1779    
1780 gpertea 16 void GffObj::printGxf(FILE* fout, GffPrintMode gffp,
1781     const char* tlabel, const char* gfparent) {
1782 gpertea 2 static char tmpstr[255];
1783     if (tlabel==NULL) {
1784     tlabel=track_id>=0 ? names->tracks.Get(track_id)->name :
1785     (char*)"gffobj" ;
1786     }
1787     unxcoord();
1788 gpertea 16 //if (exons.Count()==0) return;
1789     const char* gseqname=names->gseqs.Get(gseq_id)->name;
1790 gpertea 2 bool gff3 = (gffp>=pgffAny);
1791     bool showCDS = (gffp==pgtfAny || gffp==pgtfCDS || gffp==pgffCDS || gffp==pgffAny || gffp==pgffBoth);
1792     bool showExon = (gffp<=pgtfExon || gffp==pgffAny || gffp==pgffExon || gffp==pgffBoth);
1793     if (gff3) {
1794     //print GFF3 mRNA line:
1795     if (gscore>0.0) sprintf(tmpstr,"%.2f", gscore);
1796     else strcpy(tmpstr,".");
1797     uint pstart, pend;
1798     if (gffp==pgffCDS) {
1799     pstart=CDstart;
1800     pend=CDend;
1801     }
1802     else { pstart=start;pend=end; }
1803 gpertea 16 //const char* ftype=isTranscript() ? "mRNA" : getFeatureName();
1804     const char* ftype=getFeatureName();
1805 gpertea 2 fprintf(fout,
1806     "%s\t%s\t%s\t%d\t%d\t%s\t%c\t.\tID=%s",
1807     gseqname, tlabel, ftype, pstart, pend, tmpstr, strand, gffID);
1808 gpertea 16 if (CDstart>0 && !showCDS && !isCDS) fprintf(fout,";CDS=%d-%d",CDstart,CDend);
1809     if (gfparent!=NULL) {
1810     //parent override
1811     fprintf(fout, ";Parent=%s",gfparent);
1812     }
1813     else {
1814     if (parent!=NULL && !parent->isDiscarded())
1815     fprintf(fout, ";Parent=%s",parent->getID());
1816     }
1817     if (geneID!=NULL)
1818     fprintf(fout, ";geneID=%s",geneID);
1819     if (gene_name!=NULL)
1820     fprintf(fout, ";gene_name=%s",gene_name);
1821 gpertea 2 if (attrs!=NULL) {
1822     for (int i=0;i<attrs->Count();i++) {
1823 gpertea 16 const char* attrname=names->attrs.getName(attrs->Get(i)->attr_id);
1824     fprintf(fout,";%s=%s", attrname,
1825 gpertea 2 attrs->Get(i)->attr_val);
1826     }
1827     }
1828     fprintf(fout,"\n");
1829     }// gff3 mRNA line
1830     if (showExon) {
1831     //print exons
1832 gpertea 16 if (isCDS && exons.Count()>0 &&
1833     ((strand=='-' && exons.Last()->phase<'0') || (strand=='+' && exons.Last()->phase<'0')))
1834     updateExonPhase();
1835    
1836     for (int i=0;i<exons.Count();i++) {
1837     printGxfLine(fout, tlabel, gseqname, isCDS, exons[i]->start, exons[i]->end, i, exons[i]->phase, gff3);
1838     }
1839     }//printing exons
1840 gpertea 2 if (showCDS && !isCDS && CDstart>0) {
1841     GArray<GffCDSeg> cds(true,true);
1842     getCDSegs(cds);
1843     for (int i=0;i<cds.Count();i++) {
1844     printGxfLine(fout, tlabel, gseqname, true, cds[i].start, cds[i].end, -1, cds[i].phase, gff3);
1845     }
1846     } //showCDS
1847     }
1848    
1849 gpertea 16 void GffObj::updateExonPhase() {
1850     if (!isCDS) return;
1851     int cdsacc=0;
1852     if (CDphase=='1' || CDphase=='2') {
1853     cdsacc+= 3-(CDphase-'0');
1854     }
1855     if (strand=='-') { //reverse strand
1856     for (int i=exons.Count()-1;i>=0;i--) {
1857     exons[i]->phase='0'+ (3-cdsacc%3)%3;
1858     cdsacc+=exons[i]->end-exons[i]->start+1;
1859     }
1860     }
1861     else { //forward strand
1862     for (int i=0;i<exons.Count();i++) {
1863     exons[i]->phase='0'+ (3-cdsacc%3)%3;
1864     cdsacc+=exons[i]->end-exons[i]->start+1;
1865     }
1866     }
1867     }
1868 gpertea 2
1869 gpertea 16
1870 gpertea 2 void GffObj::getCDSegs(GArray<GffCDSeg>& cds) {
1871     GffCDSeg cdseg;
1872     int cdsacc=0;
1873     if (CDphase=='1' || CDphase=='2') {
1874     cdsacc+= 3-(CDphase-'0');
1875     }
1876     if (strand=='-') {
1877     for (int x=exons.Count()-1;x>=0;x--) {
1878     uint sgstart=exons[x]->start;
1879     uint sgend=exons[x]->end;
1880     if (CDend<sgstart || CDstart>sgend) continue;
1881     if (CDstart>=sgstart && CDstart<=sgend)
1882     sgstart=CDstart; //cdstart within this segment
1883     if (CDend>=sgstart && CDend<=sgend)
1884     sgend=CDend; //cdend within this segment
1885     cdseg.start=sgstart;
1886     cdseg.end=sgend;
1887     cdseg.exonidx=x;
1888     //cdseg.phase='0'+(cdsacc>0 ? (3-cdsacc%3)%3 : 0);
1889     cdseg.phase='0'+ (3-cdsacc%3)%3;
1890     cdsacc+=sgend-sgstart+1;
1891     cds.Add(cdseg);
1892     } //for each exon
1893     } // - strand
1894     else { // + strand
1895     for (int x=0;x<exons.Count();x++) {
1896     uint sgstart=exons[x]->start;
1897     uint sgend=exons[x]->end;
1898     if (CDend<sgstart || CDstart>sgend) continue;
1899     if (CDstart>=sgstart && CDstart<=sgend)
1900     sgstart=CDstart; //seqstart within this segment
1901     if (CDend>=sgstart && CDend<=sgend)
1902     sgend=CDend; //seqend within this segment
1903     cdseg.start=sgstart;
1904     cdseg.end=sgend;
1905     cdseg.exonidx=x;
1906     //cdseg.phase='0'+(cdsacc>0 ? (3-cdsacc%3)%3 : 0);
1907     cdseg.phase='0' + (3-cdsacc%3)%3 ;
1908     cdsacc+=sgend-sgstart+1;
1909     cds.Add(cdseg);
1910     } //for each exon
1911     } // + strand
1912     }