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root/gclib/tophat_cpp/gff.cpp
Revision: 29
Committed: Tue Aug 2 21:24:54 2011 UTC (8 years, 9 months ago) by gpertea
File size: 64074 byte(s)
Log Message:
adding tophat source work

Line User Rev File contents
1 gpertea 29 #include "gff.h"
2    
3     //GffNames* GffReader::names=NULL;
4     GffNames* GffObj::names=NULL;
5     //global set of feature names, attribute names etc.
6     // -- common for all GffObjs in current application!
7    
8     const uint GFF_MAX_LOCUS = 7000000; //longest known gene in human is ~2.2M, UCSC claims a gene for mouse of ~ 3.1 M
9     const uint GFF_MAX_EXON = 30000; //longest known exon in human is ~11K
10     const uint GFF_MAX_INTRON= 6000000;
11     bool gff_show_warnings = false; //global setting, set by GffReader->showWarnings()
12     const int gff_fid_mRNA=0;
13     const int gff_fid_transcript=1;
14     const int gff_fid_exon=2;
15     const int gff_fid_CDS=3; //never really used in GffObj ftype_id or subftype_id
16     const uint gfo_flag_HAS_ERRORS = 0x00000001;
17     const uint gfo_flag_CHILDREN_PROMOTED= 0x00000002;
18     const uint gfo_flag_IS_GENE = 0x00000004;
19     const uint gfo_flag_IS_TRANSCRIPT = 0x00000008;
20     const uint gfo_flag_FROM_GFF3 = 0x00000010;
21     const uint gfo_flag_BY_EXON = 0x00000020; //created by subfeature (exon) directly
22     const uint gfo_flag_DISCARDED = 0x00000100;
23     const uint gfo_flag_LST_KEEP = 0x00000200;
24     const uint gfo_flag_LEVEL_MSK = 0x00FF0000;
25     const byte gfo_flagShift_LEVEL = 16;
26    
27     void gffnames_ref(GffNames* &n) {
28     if (n==NULL) n=new GffNames();
29     n->numrefs++;
30     }
31    
32     void gffnames_unref(GffNames* &n) {
33     if (n==NULL) GError("Error: attempt to remove reference to null GffNames object!\n");
34     n->numrefs--;
35     if (n->numrefs==0) { delete n; n=NULL; }
36     }
37    
38     int gfo_cmpByLoc(const pointer p1, const pointer p2) {
39    
40     GffObj& g1=*((GffObj*)p1);
41     GffObj& g2=*((GffObj*)p2);
42     if (g1.gseq_id==g2.gseq_id) {
43     if (g1.start!=g2.start)
44     return (int)(g1.start-g2.start);
45     else if (g1.getLevel()!=g2.getLevel())
46     return (int)(g1.getLevel()-g2.getLevel());
47     else
48     if (g1.end!=g2.end)
49     return (int)(g1.end-g2.end);
50     else return strcmp(g1.getID(), g2.getID());
51     }
52     else return (int)(g1.gseq_id-g2.gseq_id);
53     }
54    
55     char* GffLine::extractAttr(const char* pre, bool caseStrict, bool enforce_GTF2) {
56     //parse a key attribute and remove it from the info string
57     //(only works for attributes that have values following them after ' ' or '=')
58     static const char GTF2_ERR[]="Error parsing attribute %s ('\"' required) at GTF line:\n%s\n";
59     int lpre=strlen(pre);
60     char cend=pre[lpre-1];
61     char* pos = (caseStrict) ? strstr(info, pre) : strifind(info, pre);
62     if (pos==NULL) return NULL;
63     char* findstart=info;
64     //require word boundary on the left:
65     while (pos!=NULL && pos!=info && *(pos-1)!=';' && *(pos-1)!=' ') {
66     findstart=pos+lpre;
67     pos = (caseStrict) ? strstr(findstart, pre) : strifind(findstart, pre);
68     }
69     if (pos==NULL) return NULL;
70     if (cend!=' ' && cend!='=') {
71     //require word boundary on the right:
72     while (pos!=NULL && *(pos+lpre)!=' ' && *(pos+lpre)!='=') {
73     findstart=pos+lpre;
74     pos = (caseStrict) ? strstr(findstart, pre) : strifind(findstart, pre);
75     }
76     }
77     if (pos==NULL) return NULL;
78     char* vp=pos+lpre;
79     while (*vp==' ') vp++;
80     if (*vp==';' || *vp==0)
81     GError("Error parsing value of GFF attribute \"%s\", line:\n%s\n", pre, dupline);
82     bool dq_enclosed=false; //value string enclosed by double quotes
83     if (*vp=='"') {
84     dq_enclosed=true;
85     vp++;
86     }
87     if (enforce_GTF2 && !dq_enclosed)
88     GError(GTF2_ERR,pre, dupline);
89     char* vend=vp;
90     if (dq_enclosed) {
91     while (*vend!='"' && *vend!=';' && *vend!=0) vend++;
92     }
93     else {
94     while (*vend!=';' && *vend!=0) vend++;
95     }
96     if (enforce_GTF2 && *vend!='"')
97     GError(GTF2_ERR, pre, dupline);
98     char *r=Gstrdup(vp, vend-1);
99     //-- now remove this attribute from the info string
100     while (*vend!=0 && (*vend=='"' || *vend==';' || *vend==' ')) vend++;
101     if (*vend==0) vend--;
102     for (char *src=vend, *dest=pos;;src++,dest++) {
103     *dest=*src;
104     if (*src==0) break;
105     }
106     return r;
107     }
108    
109     static char fnamelc[128];
110    
111     GffLine::GffLine(GffReader* reader, const char* l) {
112     llen=strlen(l);
113     GMALLOC(line,llen+1);
114     memcpy(line, l, llen+1);
115     GMALLOC(dupline, llen+1);
116     memcpy(dupline, l, llen+1);
117     skip=true;
118     gseqname=NULL;
119     track=NULL;
120     ftype=NULL;
121     info=NULL;
122     _parents=NULL;
123     _parents_len=0;
124     num_parents=0;
125     parents=NULL;
126     is_gff3=false;
127     is_cds=false;
128     is_transcript=false;
129     is_exon=false;
130     is_gene=false;
131     exontype=0;
132     gene_id=NULL;
133     gene_name=NULL;
134     qstart=0;
135     qend=0;
136     qlen=0;
137     ID=NULL;
138     char* t[9];
139     int i=0;
140     int tidx=1;
141     t[0]=line;
142    
143     while (line[i]!=0) {
144     if (line[i]=='\t') {
145     line[i]=0;
146     t[tidx]=line+i+1;
147     tidx++;
148     if (tidx>8) break;
149     }
150     i++;
151     }
152    
153     if (tidx<8) { // ignore non-GFF lines
154     // GMessage("Warning: error parsing GFF/GTF line:\n%s\n", l);
155     return;
156     }
157     gseqname=t[0];
158     track=t[1];
159     ftype=t[2];
160     info=t[8];
161     char* p=t[3];
162     if (!parseUInt(p,fstart))
163     GError("Error parsing start coordinate from GFF line:\n%s\n",l);
164     p=t[4];
165     if (!parseUInt(p,fend))
166     GError("Error parsing end coordinate from GFF line:\n%s\n",l);
167     if (fend<fstart) swap(fend,fstart); //make sure fstart>=fend, always
168     p=t[5];
169     if (p[0]=='.' && p[1]==0) {
170     score=0;
171     }
172     else {
173     if (!parseDouble(p,score))
174     GError("Error parsing feature score from GFF line:\n%s\n",l);
175     }
176     strand=*t[6];
177     if (strand!='+' && strand!='-' && strand!='.')
178     GError("Error parsing strand (%c) from GFF line:\n%s\n",strand,l);
179     phase=*t[7]; // must be '.', '0', '1' or '2'
180     ID=NULL;
181     // exon/CDS/mrna filter
182     strncpy(fnamelc, ftype, 127);
183     fnamelc[127]=0;
184     strlower(fnamelc); //convert to lower case
185     bool is_t_data=false;
186     if (strstr(fnamelc, "utr")!=NULL) {
187     exontype=exgffUTR;
188     is_exon=true;
189     is_t_data=true;
190     }
191     else if (strstr(fnamelc, "exon")!=NULL) {
192     exontype=exgffExon;
193     is_exon=true;
194     is_t_data=true;
195     }
196     else if (strstr(fnamelc, "stop") &&
197     (strstr(fnamelc, "codon") || strstr(fnamelc, "cds"))){
198     exontype=exgffStop;
199     is_cds=true; //though some place it outside the last CDS segment
200     is_t_data=true;
201     }
202     else if (strstr(fnamelc, "start") &&
203     ((strstr(fnamelc, "codon")!=NULL) || strstr(fnamelc, "cds")!=NULL)){
204     exontype=exgffStart;
205     is_cds=true;
206     is_t_data=true;
207     }
208     else if (strcmp(fnamelc, "cds")==0) {
209     exontype=exgffCDS;
210     is_cds=true;
211     is_t_data=true;
212     }
213     else if (endsWith(fnamelc, "gene") || startsWith(fnamelc, "gene")) {
214     is_gene=true;
215     is_t_data=true; //because its name will be attached to parented transcripts
216     }
217     else if (endsWith(fnamelc,"rna") || endsWith(fnamelc,"transcript")) {
218     is_transcript=true;
219     is_t_data=true;
220     }
221    
222     if (reader->transcriptsOnly && !is_t_data) {
223     char* id=extractAttr("ID=");
224     if (id==NULL) id=extractAttr("transcript_id");
225     //GMessage("Discarding non-transcript line:\n%s\n",l);
226     if (id!=NULL) {
227     reader->discarded_ids.Add(id, new int(1));
228     GFREE(id);
229     }
230     return; //skip this line, unwanted feature name
231     }
232     ID=extractAttr("ID=");
233     char* Parent=extractAttr("Parent=");
234     is_gff3=(ID!=NULL || Parent!=NULL);
235     if (is_gff3) {
236     //parse as GFF3
237     if (ID!=NULL) {
238     //has ID attr so it's likely to be a parent feature
239     //look for explicit gene name
240     gene_name=extractAttr("gene_name=",false);
241     if (gene_name==NULL) {
242     gene_name=extractAttr("geneName=",false);
243     if (gene_name==NULL) {
244     gene_name=extractAttr("gene_sym=",false);
245     if (gene_name==NULL) {
246     gene_name=extractAttr("gene=",false);
247     }
248     }
249     }
250     gene_id=extractAttr("geneID=",false);
251     if (gene_id==NULL) {
252     gene_id=extractAttr("gene_id=",false);
253     }
254     if (is_gene) {
255     //special case: keep the Name and ID attributes of the gene feature
256     if (gene_name==NULL)
257     gene_name=extractAttr("Name=");
258     if (gene_id==NULL) //the ID is also gene_id in this case
259     gene_id=Gstrdup(ID);
260     //skip=false;
261     //return;
262     GFREE(Parent); //TMI, we really don't care about gene Parents?
263     } //gene feature
264     }// has GFF3 ID
265     if (Parent!=NULL) {
266     //keep Parent attr
267     //parse multiple parents
268     num_parents=1;
269     p=Parent;
270     int last_delim_pos=-1;
271     while (*p!=';' && *p!=0) {
272     if (*p==',' && *(p+1)!=0 && *(p+1)!=';') {
273     num_parents++;
274     last_delim_pos=(p-Parent);
275     }
276     p++;
277     }
278     _parents_len=p-Parent+1;
279     _parents=Parent;
280     GMALLOC(parents, num_parents*sizeof(char*));
281     parents[0]=_parents;
282     int i=1;
283     if (last_delim_pos>0) {
284     for (p=_parents+1;p<=_parents+last_delim_pos;p++) {
285     if (*p==',') {
286     char* ep=p-1;
287     while (*ep==' ' && ep>_parents) ep--;
288     *(ep+1)=0; //end the string there
289     parents[i]=p+1;
290     i++;
291     }
292     }
293     }
294     } //has Parent field
295     } //GFF3
296     else { // GTF-like expected
297     Parent=extractAttr("transcript_id");
298     if (Parent!=NULL) { //GTF2 format detected
299     if (is_transcript) {
300     // atypical GTF with a parent transcript line declared
301     ID=Parent;
302     Parent=NULL;
303     }
304     gene_id=extractAttr("gene_id"); // for GTF this is the only attribute accepted as geneID
305     gene_name=extractAttr("gene_name");
306     if (gene_name==NULL) {
307     gene_name=extractAttr("gene_sym");
308     if (gene_name==NULL)
309     gene_name=extractAttr("gene");
310     }
311     //prepare for parseAttr by adding '=' character instead of spaces for all attributes
312     //after the attribute name
313     p=info;
314     bool noed=true; //not edited after the last delim
315     bool nsp=false; //non-space found after last delim
316     while (*p!=0) {
317     if (*p==' ') {
318     if (nsp && noed) {
319     *p='=';
320     noed=false;
321     p++;
322     continue;
323     }
324     }
325     else nsp=true; //non-space
326     if (*p==';') { noed=true; nsp=false; }
327     p++;
328     }
329     } //GTF2 detected (no parent line)
330     else {// Parent is NULL, check for jigsaw format or other pre-GTF2 format
331     //char* fexon=strstr(fnamelc, "exon");
332     //if (fexon!=NULL) {
333     if (exontype==exgffExon) {
334     if (startsWith(track,"jigsaw")) {
335     is_cds=true;
336     strcpy(track,"jigsaw");
337     p=strchr(info,';');
338     if (p==NULL) { Parent=Gstrdup(info); info=NULL; }
339     else { Parent=Gstrdup(info,p-1);
340     info=p+1;
341     }
342     }
343     } //exon feature?
344     if (Parent==NULL && exontype>=exgffCDS &&
345     (i=strcspn(info,"; \t\n\r"))<=(int)(strlen(info)+1)) {
346     //one word ID ? really desperate attempt to parse it here
347     Parent=Gstrdup(info,info+i-1);
348     info=NULL; //discard anything else on the line
349     }
350     }
351     if (Parent!=NULL) { //GTF transcript_id for exon/CDS feature
352     _parents=Parent;
353     GMALLOC(parents,sizeof(char*));
354     num_parents=1;
355     parents[0]=_parents;
356     }
357     } //GTF-like
358    
359     //parse other potentially useful features
360     if (is_gff3) {
361     if ((p=strstr(info,"Target="))!=NULL) { //has Target attr
362     p+=7;
363     while (*p!=';' && *p!=0 && *p!=' ') p++;
364     if (*p!=' ') {
365     GError("Error parsing target coordinates from GFF line:\n%s\n",l);
366     }
367     if (!parseUInt(p,qstart))
368     GError("Error parsing target start coordinate from GFF line:\n%s\n",l);
369     if (*p!=' ') {
370     GError("Error parsing next target coordinate from GFF line:\n%s\n",l);
371     }
372     p++;
373     if (!parseUInt(p,qend))
374     GError("Error parsing target end coordinate from GFF line:\n%s\n",l);
375     }
376     if ((p=strifind(info,"Qreg="))!=NULL) { //has Qreg attr
377     p+=5;
378     if (!parseUInt(p,qstart))
379     GError("Error parsing target start coordinate from GFF line:\n%s\n",l);
380     if (*p!='-') {
381     GError("Error parsing next target coordinate from GFF line:\n%s\n",l);
382     }
383     p++;
384     if (!parseUInt(p,qend))
385     GError("Error parsing target end coordinate from GFF line:\n%s\n",l);
386     if (*p=='|' || *p==':') {
387     p++;
388     if (!parseUInt(p,qlen))
389     GError("Error parsing target length from GFF Qreg|: \n%s\n",l);
390     }
391     }//has Qreg attr
392     if (qlen==0 && (p=strifind(info,"Qlen="))!=NULL) {
393     p+=5;
394     if (!parseUInt(p,qlen))
395     GError("Error parsing target length from GFF Qlen:\n%s\n",l);
396     }
397     }//parsing some useful attributes in GFF3 records
398     if (ID==NULL && parents==NULL) {
399     if (reader->gff_warns)
400     GMessage("Warning: could not parse ID or Parent from GFF line:\n%s\n",dupline);
401     return; //skip
402     }
403     skip=false;
404     }
405    
406     int GffObj::addExon(GffReader* reader, GffLine* gl, bool keepAttr, bool noExonAttr) {
407     //this will make sure we have the right subftype_id!
408     int subf_id=-1;
409     //if (ftype_id==gff_fid_mRNA) { //for mRNAs only parse known subfeatures!
410     if (isTranscript()) {
411     if (exon_ftype_id<0) {//exon_ftype_id=gff_fid_exon;
412     if (gl->exontype>0) exon_ftype_id=gff_fid_exon;
413     else exon_ftype_id=names->feats.addName(gl->ftype);
414     }
415     //any recognized mRNA segment gets the generic "exon" type (also applies to CDS)
416     if (gl->exontype==0 && !gl->is_transcript) {
417     //extraneous mRNA feature, discard
418     if (reader->gff_warns)
419     GMessage("Warning: discarding unrecognized transcript subfeature %s of %s\n",
420     gl->ftype, gffID);
421     return -1;
422     }
423     }
424     else { //non-mRNA parent feature, check this subf type
425     subf_id=names->feats.addName(gl->ftype);
426     if (exon_ftype_id<0 || exons.Count()==0) //never assigned a subfeature type before (e.g. first exon being added)
427     exon_ftype_id=subf_id;
428     else {
429     if (exon_ftype_id!=subf_id) {
430     //if (subftype_id==ftype_id && exons.Count()==1 && exons[0]->start==start && exons[0]->end==end) {
431     if (exon_ftype_id==ftype_id && exons.Count()==1 && exons[0]->start==start && exons[0]->end==end) {
432     //the existing exon was just a dummy one created by default, discard it
433     exons.Clear();
434     covlen=0;
435     exon_ftype_id=subf_id; //allow the new subfeature to completely takeover
436     }
437     else { //multiple subfeatures, prefer those with
438     if (reader->gff_warns)
439     GMessage("GFF Warning: multiple subfeatures (%s and %s) found for %s, discarding ",
440     names->feats.getName(subf_id), names->feats.getName(exon_ftype_id),gffID);
441     if (gl->exontype!=0) { //new feature is an exon, discard previously parsed subfeatures
442     if (reader->gff_warns) GMessage("%s.\n", names->feats.getName(exon_ftype_id));
443     exon_ftype_id=subf_id;
444     exons.Clear();
445     covlen=0;
446     }
447     else { //discard new feature
448     if (reader->gff_warns) GMessage("%s.\n", names->feats.getName(subf_id));
449     return -1; //skip this 2nd subfeature type for this parent!
450     }
451     }
452     } //incoming subfeature is of different type
453     } //new subfeature type
454     } //non-mRNA parent
455     int eidx=addExon(gl->fstart, gl->fend, gl->score, gl->phase,
456     gl->qstart,gl->qend, gl->is_cds, gl->exontype);
457     if (eidx<0) return eidx; //this should never happen
458     if (keepAttr) {
459     if (noExonAttr) {
460     if (attrs==NULL) //place the parsed attributes directly at transcript level
461     parseAttrs(attrs, gl->info);
462     }
463     else { //need all exon-level attributes
464     parseAttrs(exons[eidx]->attrs, gl->info, true);
465     }
466     }
467     return eidx;
468     }
469    
470    
471     int GffObj::addExon(uint segstart, uint segend, double sc, char fr, int qs, int qe, bool iscds, char exontype) {
472     if (exons.Count()==0) {
473     if (iscds) isCDS=true; //for now, assume CDS only if first "exon" given is a CDS
474     if (exon_ftype_id<0) {
475     exon_ftype_id = isTranscript() ? gff_fid_exon : ftype_id;
476     }
477     }
478     //special treatment of start/stop codon features, they might be broken/split between exons
479     //and in that case some providers will still give the wrong end coordinate as start+2 (e.g. UCSC)
480     //so we should not trust the end coordinate for such features
481     if (exontype==exgffStart || exontype==exgffStop) {
482     if (strand=='-') segstart=segend;
483     else segend=segstart;
484     if (exontype==exgffStart) {
485     if (CDstart==0 || segstart<CDstart) CDstart=segstart;
486     }
487     else {
488     if (segstart>CDend) CDend=segstart;
489     }
490     }
491     else if (iscds) { //update CDS anchors:
492     if (CDstart==0 || segstart<CDstart) {
493     CDstart=segstart;
494     if (exontype==exgffCDS && strand=='+') CDphase=fr;
495     }
496     if (segend>CDend) {
497     if (exontype==exgffCDS && strand=='-') CDphase=fr;
498     CDend=segend;
499     }
500     }
501     else { // not a CDS/start/stop
502     isCDS=false;
503     }
504     if (qs || qe) {
505     if (qs>qe) swap(qs,qe);
506     if (qs==0) qs=1;
507     }
508     if (exontype>0) { //check for overlaps between exon-type segments
509     int ovlen=0;
510     int oi=exonOverlapIdx(segstart, segend, &ovlen);
511     if (oi>=0) { //overlap existing segment
512     if (ovlen==0) {
513     //adjacent segments will be merged
514     if ((exons[oi]->exontype==exgffUTR && exontype==exgffCDS) ||
515     (exons[oi]->exontype==exgffCDS && exontype==exgffUTR)) {
516     expandExon(oi, segstart, segend, exgffCDSUTR, sc, fr, qs, qe);
517     return oi;
518     }
519     }
520     //only allow this for CDS within exon, stop_codon within exon, stop_codon within UTR,
521     // start_codon within CDS or stop_codon within CDS
522     if (exons[oi]->exontype>exontype &&
523     exons[oi]->start<=segstart && exons[oi]->end>=segend &&
524     !(exons[oi]->exontype==exgffUTR && exontype==exgffCDS)) {
525     //larger segment given first, now the smaller included one is redundant
526     return oi; //only used to store attributes from current GffLine
527     }
528     if (exontype>exons[oi]->exontype &&
529     segstart<=exons[oi]->start && segend>=exons[oi]->end &&
530     !(exontype==exgffUTR && exons[oi]->exontype==exgffCDS)) {
531     //smaller segment given first, so we have to enlarge it
532     expandExon(oi, segstart, segend, exontype, sc, fr, qs, qe);
533     //this should also check for overlapping next exon (oi+1) ?
534     return oi;
535     }
536     //there is also the special case of "ribosomal slippage exception" (programmed frameshift)
537     //where two CDS segments may actually overlap for 1 or 2 bases, but there should be only one encompassing exon
538     //if (ovlen>2 || exons[oi]->exontype!=exgffCDS || exontype!=exgffCDS) {
539     // --> had to relax this because of some weird UCSC annotations with exons partially overlapping the CDS segments
540     if (ovlen>2 && exons[oi]->exontype!=exgffUTR && exontype!=exgffUTR) {
541     //important structural warning, will always print:
542     if (gff_show_warnings)
543     GMessage("GFF Warning: discarding overlapping feature segment (%d-%d) (vs %d-%d (%s)) for GFF ID %s on %s\n",
544     segstart, segend, exons[oi]->start, exons[oi]->end, getSubfName(), gffID, getGSeqName());
545     hasErrors(true);
546     return -1; //segment NOT added
547     }
548     // else add the segment if the overlap is small and between two CDS segments
549     //TODO: we might want to add an attribute here with the slippage coordinate and size?
550     }//overlap of existing segment
551     } //check for overlap
552     // --- no overlap, or accepted micro-overlap (ribosomal slippage)
553     // create & add the new segment
554     GffExon* enew=new GffExon(segstart, segend, sc, fr, qs, qe, exontype);
555     int eidx=exons.Add(enew);
556     if (eidx<0) {
557     //this would actually be acceptable if the object is a "Gene" and "exons" are in fact isoforms
558     if (gff_show_warnings)
559     GMessage("GFF Warning: failed adding segment %d-%d for %s (discarded)!\n",
560     segstart, segend, gffID);
561     delete enew;
562     hasErrors(true);
563     return -1;
564     }
565     covlen+=(int)(exons[eidx]->end-exons[eidx]->start)+1;
566     start=exons.First()->start;
567     end=exons.Last()->end;
568     if (uptr!=NULL) { //collect stats about the underlying genomic sequence
569     GSeqStat* gsd=(GSeqStat*)uptr;
570     if (start<gsd->mincoord) gsd->mincoord=start;
571     if (end>gsd->maxcoord) gsd->maxcoord=end;
572     if (this->len()>gsd->maxfeat_len) {
573     gsd->maxfeat_len=this->len();
574     gsd->maxfeat=this;
575     }
576     }
577     return eidx;
578     }
579    
580     void GffObj::expandExon(int oi, uint segstart, uint segend, char exontype, double sc, char fr, int qs, int qe) {
581     //oi is the index of the *first* overlapping segment found that must be enlarged
582     covlen-=exons[oi]->len();
583     if (segstart<exons[oi]->start)
584     exons[oi]->start=segstart;
585     if (qs && qs<exons[oi]->qstart) exons[oi]->qstart=qs;
586     if (segend>exons[oi]->end)
587     exons[oi]->end=segend;
588     if (qe && qe>exons[oi]->qend) exons[oi]->qend=qe;
589     //warning: score cannot be properly adjusted! e.g. if it's a p-value it's just going to get worse
590     if (sc!=0) exons[oi]->score=sc;
591     covlen+=exons[oi]->len();
592     //if (exons[oi]->exontype< exontype) -- always true
593     exons[oi]->exontype = exontype;
594     if (exontype==exgffCDS) exons[oi]->phase=fr;
595     //we must check if any more exons are also overlapping this
596     int ni=oi+1; //next exon index after oi
597     while (ni<exons.Count() && segend>=exons[ni]->start) { // next segment overlaps new enlarged segment
598     //only allow this if next segment is fully included, and a subordinate
599     if (exons[ni]->exontype<exontype && exons[ni]->end<=segend) {
600     /* I guess we have to relax this due to stupid UCSC hg18 files having a start_codon sticking out
601     chr1 hg18_knownGene start_codon 69806911 69806913 0.000000 + .
602     chr1 hg18_knownGene CDS 69806911 69806912 0.000000 + 0
603     chr1 hg18_knownGene exon 69805456 69806912 0.000000 + .
604     */
605     if (exons[ni]->qstart<exons[oi]->qstart) exons[oi]->qstart=exons[ni]->qstart;
606     if (exons[ni]->qend>exons[oi]->qend) exons[oi]->qend=exons[ni]->qend;
607     exons.Delete(ni);
608     }
609     else {
610     if (gff_show_warnings) GMessage("GFF Warning: overlapping existing exon(%d-%d) while expanding to %d-%d for GFF ID %s\n",
611     exons[ni]->start, exons[ni]->end, segstart, segend, gffID);
612     //hasErrors(true);
613     break;
614     }
615     }
616     // -- make sure any other related boundaries are updated:
617     start=exons.First()->start;
618     end=exons.Last()->end;
619     if (uptr!=NULL) { //collect stats about the underlying genomic sequence
620     GSeqStat* gsd=(GSeqStat*)uptr;
621     if (start<gsd->mincoord) gsd->mincoord=start;
622     if (end>gsd->maxcoord) gsd->maxcoord=end;
623     if (this->len()>gsd->maxfeat_len) {
624     gsd->maxfeat_len=this->len();
625     gsd->maxfeat=this;
626     }
627     }
628     }
629    
630     void GffObj::removeExon(int idx) {
631     /*
632     if (idx==0 && segs[0].start==gstart)
633     gstart=segs[1].start;
634     if (idx==segcount && segs[segcount].end==gend)
635     gend=segs[segcount-1].end;
636     */
637     if (idx<0 || idx>=exons.Count()) return;
638     int segstart=exons[idx]->start;
639     int segend=exons[idx]->end;
640     exons.Delete(idx);
641     covlen -= (int)(segend-segstart)+1;
642     start=exons.First()->start;
643     end=exons.Last()->end;
644     if (isCDS) { CDstart=start; CDend=end; }
645     }
646    
647     void GffObj::removeExon(GffExon* p) {
648     for (int idx=0;idx<exons.Count();idx++) {
649     if (exons[idx]==p) {
650     int segstart=exons[idx]->start;
651     int segend=exons[idx]->end;
652     exons.Delete(idx);
653     covlen -= (int)(segend-segstart)+1;
654     start=exons.First()->start;
655     end=exons.Last()->end;
656     if (isCDS) { CDstart=start; CDend=end; }
657     return;
658     }
659     }
660     }
661    
662    
663    
664     GffObj::GffObj(GffReader *gfrd, GffLine* gffline, bool keepAttr, bool noExonAttr):
665     GSeg(0,0), exons(true,true,false), children(1,false) {
666     xstart=0;
667     xend=0;
668     xstatus=0;
669     partial=false;
670     isCDS=false;
671     uptr=NULL;
672     ulink=NULL;
673     parent=NULL;
674     udata=0;
675     flags=0;
676     CDstart=0;
677     CDend=0;
678     CDphase=0;
679     geneID=NULL;
680     gene_name=NULL;
681     attrs=NULL;
682     gffID=NULL;
683     track_id=-1;
684     gseq_id=-1;
685     ftype_id=-1;
686     exon_ftype_id=-1;
687     strand='.';
688     if (gfrd==NULL)
689     GError("Cannot use this GffObj constructor with a NULL GffReader!\n");
690     gffnames_ref(names);
691     if (gfrd->names==NULL) gfrd->names=names;
692     //qlen=0;qstart=0;qend=0;
693     gscore=0;
694     uscore=0;
695     covlen=0;
696     qcov=0;
697     start=gffline->fstart;
698     end=gffline->fend;
699     gseq_id=names->gseqs.addName(gffline->gseqname);
700     track_id=names->tracks.addName(gffline->track);
701     strand=gffline->strand;
702     qlen=gffline->qlen;
703     qstart=gffline->qstart;
704     qend=gffline->qend;
705     //setup flags from gffline
706     isCDS=gffline->is_cds; //for now
707     isGene(gffline->is_gene);
708     isTranscript(gffline->is_transcript || gffline->exontype!=0);
709     fromGff3(gffline->is_gff3);
710    
711     if (gffline->parents!=NULL) {
712     //GTF style -- create a GffObj directly by subfeature
713     //(also possible orphan GFF3 exon line, or an exon given before its parent (chado))
714     if (gffline->exontype!=0) { //recognized exon-like feature
715     ftype_id=gff_fid_transcript; //so this is some sort of transcript
716     exon_ftype_id=gff_fid_exon; //subfeatures MUST be exons
717     }
718     else {//unrecognized subfeatures
719     //make this GffObj of the same feature type
720     ftype_id=names->feats.addName(gffline->ftype);
721     }
722     if (gffline->ID==NULL) { //typical GTF
723     gffID=Gstrdup(gffline->parents[0]);
724     this->createdByExon(true);
725     //this is likely the first exon/segment of the feature
726     addExon(gfrd, gffline, keepAttr, noExonAttr);
727     }
728     else { //a parented feature with an ID -- probably an orphan GFF3 line
729     if (gffline->is_gff3 && gffline->exontype!=0) {
730     //premature exon given before its parent transcript
731     //create the transcript entry here
732     gffID=Gstrdup(gffline->parents[0]);
733     this->createdByExon(true);
734     //this is the first exon/segment of the transcript
735     addExon(gfrd, gffline, keepAttr, noExonAttr);
736     }
737     else { //unrecognized non-exon feature ? use the ID instead
738     gffID=Gstrdup(gffline->ID);
739     if (keepAttr) this->parseAttrs(attrs, gffline->info);
740     }
741     }
742     } //subfeature given directly
743     else { //gffline->parents==NULL
744     //create a parent feature in its own right
745     gscore=gffline->score;
746     if (gffline->ID==NULL || gffline->ID[0]==0)
747     GError("Error: no ID found for GFF record start\n");
748     gffID=Gstrdup(gffline->ID); //there must be an ID here
749     //if (gffline->is_transcript) ftype_id=gff_fid_mRNA;
750     //else
751     ftype_id=names->feats.addName(gffline->ftype);
752     if (gffline->is_transcript)
753     exon_ftype_id=gff_fid_exon;
754    
755     if (keepAttr) this->parseAttrs(attrs, gffline->info);
756     }//no parent
757    
758     if (gffline->gene_name!=NULL) {
759     gene_name=Gstrdup(gffline->gene_name);
760     }
761     if (gffline->gene_id!=NULL) {
762     geneID=Gstrdup(gffline->gene_id);
763     }
764    
765     GSeqStat* gsd=gfrd->gseqstats.AddIfNew(new GSeqStat(gseq_id,names->gseqs.lastNameUsed()),true);
766     uptr=gsd;
767     if (start<gsd->mincoord) gsd->mincoord=start;
768     if (end>gsd->maxcoord) gsd->maxcoord=end;
769     if (this->len()>gsd->maxfeat_len) {
770     gsd->maxfeat_len=this->len();
771     gsd->maxfeat=this;
772     }
773     }
774    
775     GffLine* GffReader::nextGffLine() {
776     if (gffline!=NULL) return gffline; //caller should free gffline after processing
777     while (gffline==NULL) {
778     int llen=0;
779     buflen=GFF_LINELEN-1;
780     char* l=fgetline(linebuf, buflen, fh, &fpos, &llen);
781     if (l==NULL) {
782     return NULL; //end of file
783     }
784     int ns=0; //first nonspace position
785     while (l[ns]!=0 && isspace(l[ns])) ns++;
786     if (l[ns]=='#' || llen<10) continue;
787     gffline=new GffLine(this, l);
788     if (gffline->skip) {
789     delete gffline;
790     gffline=NULL;
791     continue;
792     }
793     if (gffline->ID==NULL && gffline->parents==NULL) { //it must have an ID
794     //this might not be needed, already checked in the GffLine constructor
795     if (gff_warns)
796     GMessage("Warning: malformed GFF line, no parent or record Id (kipping\n");
797     delete gffline;
798     gffline=NULL;
799     //continue;
800     }
801     }
802     return gffline;
803     }
804    
805     char* GffReader::gfoBuildId(const char* id, const char* ctg) {
806     //caller must free the returned pointer
807     char* buf=NULL;
808     int idlen=strlen(id);
809     GMALLOC(buf, idlen+strlen(ctg)+2);
810     strcpy(buf, id);
811     buf[idlen]='~';
812     strcpy(buf+idlen+1, ctg);
813     return buf;
814     }
815    
816     void GffReader::gfoRemove(const char* id, const char* ctg) {
817     char* buf=gfoBuildId(id,ctg);
818     phash.Remove(buf);
819     GFREE(buf);
820     }
821    
822     //Warning: if gflst gets altered, idx becomes obsolete
823     GfoHolder* GffReader::gfoAdd(const char* id, const char* ctg, GffObj* gfo, int idx) {
824     char* buf=gfoBuildId(id,ctg);
825     GfoHolder* r=new GfoHolder(gfo,idx);
826     phash.Add(buf, r);
827     GFREE(buf);
828     return r;
829     }
830    
831     GfoHolder* GffReader::gfoFind(const char* id, const char* ctg) {
832     char* buf=gfoBuildId(id,ctg);
833     GfoHolder* r=phash.Find(buf);
834     GFREE(buf);
835     return r;
836     }
837    
838     GfoHolder* GffReader::replaceGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr, int replaceidx) {
839     GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
840     GfoHolder* r=NULL;
841     if (replaceidx>=0) {
842     gflst.Put(replaceidx,newgfo);
843     r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, replaceidx);
844     }
845     else {
846     int gfoidx=gflst.Add(newgfo);
847     r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, gfoidx);
848     }
849     if (gff_warns) {
850     int* pcount=tids.Find(newgfo->gffID);
851     if (pcount!=NULL) {
852     if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
853     (*pcount)++;
854     }
855     else {
856     tids.Add(newgfo->gffID,new int(1));
857     }
858     }
859     return r;
860     }
861    
862     GfoHolder* GffReader::updateParent(GfoHolder* newgfh, GffObj* parent) {
863     //assert(parent);
864     //assert(newgfo);
865     parent->children.Add(newgfh->gffobj);
866     if (newgfh->gffobj->parent==NULL) newgfh->gffobj->parent=parent;
867     newgfh->gffobj->setLevel(parent->getLevel()+1);
868     if (parent->isGene()) {
869     if (parent->gene_name!=NULL && newgfh->gffobj->gene_name==NULL)
870     newgfh->gffobj->gene_name=Gstrdup(parent->gene_name);
871     if (parent->geneID!=NULL && newgfh->gffobj->geneID==NULL)
872     newgfh->gffobj->geneID=Gstrdup(parent->geneID);
873     }
874    
875     return newgfh;
876     }
877    
878     GfoHolder* GffReader::newGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr,
879     GffObj* parent, GffExon* pexon) {
880     GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
881     GfoHolder* r=NULL;
882     int gfoidx=gflst.Add(newgfo);
883     r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, gfoidx);
884     if (parent!=NULL) {
885     updateParent(r, parent);
886     if (pexon!=NULL) parent->removeExon(pexon);
887     }
888     if (gff_warns) {
889     int* pcount=tids.Find(newgfo->gffID);
890     if (pcount!=NULL) {
891     if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
892     (*pcount)++;
893     }
894     else {
895     tids.Add(newgfo->gffID,new int(1));
896     }
897     }
898     return r;
899     }
900    
901     GfoHolder* GffReader::updateGffRec(GfoHolder* prevgfo, GffLine* gffline,
902     bool keepAttr) {
903     if (prevgfo==NULL) return NULL;
904     prevgfo->gffobj->createdByExon(false);
905     prevgfo->gffobj->ftype_id=prevgfo->gffobj->names->feats.addName(gffline->ftype);
906     prevgfo->gffobj->start=gffline->fstart;
907     prevgfo->gffobj->end=gffline->fend;
908     prevgfo->gffobj->isGene(gffline->is_gene);
909     prevgfo->gffobj->isTranscript(gffline->is_transcript || gffline->exontype!=0);
910     prevgfo->gffobj->fromGff3(gffline->is_gff3);
911     if (keepAttr) {
912     if (prevgfo->gffobj->attrs!=NULL) prevgfo->gffobj->attrs->Clear();
913     prevgfo->gffobj->parseAttrs(prevgfo->gffobj->attrs, gffline->info);
914     }
915     return prevgfo;
916     }
917    
918    
919     bool GffReader::addExonFeature(GfoHolder* prevgfo, GffLine* gffline, GHash<CNonExon>& pex, bool noExonAttr) {
920     bool r=true;
921     if (gffline->strand!=prevgfo->gffobj->strand) {
922     GMessage("GFF Error: duplicate GFF ID '%s' (exons found on different strands of %s)\n",
923     prevgfo->gffobj->gffID, prevgfo->gffobj->getGSeqName());
924     r=false;
925     }
926     int gdist=(gffline->fstart>prevgfo->gffobj->end) ? gffline->fstart-prevgfo->gffobj->end :
927     ((gffline->fend<prevgfo->gffobj->start)? prevgfo->gffobj->start-gffline->fend :
928     0 );
929     if (gdist>(int)GFF_MAX_LOCUS) { //too far apart, most likely this is a duplicate ID
930     GMessage("Error: duplicate GFF ID '%s' (or exons too far apart)!\n",prevgfo->gffobj->gffID);
931     //validation_errors = true;
932     r=false;
933     if (!gff_warns) exit(1);
934     }
935     int eidx=prevgfo->gffobj->addExon(this, gffline, !noExonAttr, noExonAttr);
936     if (eidx>=0 && gffline->ID!=NULL && gffline->exontype==0)
937     subfPoolAdd(pex, prevgfo);
938     return r;
939     }
940    
941     CNonExon* GffReader::subfPoolCheck(GffLine* gffline, GHash<CNonExon>& pex, char*& subp_name) {
942     CNonExon* subp=NULL;
943     subp_name=NULL;
944     for (int i=0;i<gffline->num_parents;i++) {
945     if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
946     continue;
947     subp_name=gfoBuildId(gffline->parents[i], gffline->gseqname); //e.g. mRNA name
948     subp=pex.Find(subp_name);
949     if (subp!=NULL)
950     return subp;
951     GFREE(subp_name);
952     }
953     return NULL;
954     }
955    
956     void GffReader::subfPoolAdd(GHash<CNonExon>& pex, GfoHolder* newgfo) {
957     //this might become a parent feature later
958     if (newgfo->gffobj->exons.Count()>0) {
959     char* xbuf=gfoBuildId(gffline->ID, gffline->gseqname);
960     pex.Add(xbuf, new CNonExon(newgfo->idx, newgfo->gffobj,
961     newgfo->gffobj->exons[0], gffline));
962     GFREE(xbuf);
963     }
964     }
965    
966     GfoHolder* GffReader::promoteFeature(CNonExon* subp, char*& subp_name, GHash<CNonExon>& pex,
967     bool keepAttr, bool noExonAttr) {
968     GffObj* prevp=subp->parent; //grandparent of gffline (e.g. gene)
969     if (prevp!=gflst[subp->idx])
970     GError("Error promoting subfeature %s, gflst index mismatch?!\n", subp->gffline->ID);
971     subp->gffline->discardParent();
972     GfoHolder* gfoh=newGffRec(subp->gffline, keepAttr, noExonAttr, prevp, subp->exon);
973     pex.Remove(subp_name); //no longer a potential parent, moved it to phash already
974     prevp->promotedChildren(true);
975     return gfoh; //returns the holder of newly promoted feature
976     }
977    
978     //have to parse the whole file because exons can be scattered all over
979     void GffReader::readAll(bool keepAttr, bool mergeCloseExons, bool noExonAttr) {
980     bool validation_errors = false;
981     //loc_debug=false;
982     GHash<CNonExon> pex; //keep track of any "exon"-like features that have an ID
983     //and thus could become promoted to parent features
984     while (nextGffLine()!=NULL) {
985     //seen this gff ID before?
986     GfoHolder* prevseen=NULL;
987     if (gffline->ID) //GFF3
988     prevseen=gfoFind(gffline->ID, gffline->gseqname);
989     if (prevseen!=NULL) {
990     if (prevseen->gffobj->createdByExon()) {
991     updateGffRec(prevseen, gffline, keepAttr);
992     }
993     else {
994     GMessage("Error: duplicate GFF ID '%s' encountered!\n",gffline->ID);
995     validation_errors = true;
996     if (gff_warns) {
997     delete gffline; gffline=NULL; continue;
998     }
999     else exit(1);
1000     }
1001     }
1002     if (gffline->parents==NULL) {//start GFF3-like record with no parent (mRNA, gene)
1003     if (!prevseen) newGffRec(gffline, keepAttr, noExonAttr);
1004     }
1005     else { //--- it's a parented feature (could still be a mRNA)
1006     bool found_parent=false;
1007     GfoHolder* newgfo=prevseen;
1008     for (int i=0;i<gffline->num_parents;i++) {
1009     if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
1010     continue; //skipping discarded parent feature
1011     GfoHolder* parentgfo=gfoFind(gffline->parents[i], gffline->gseqname);
1012     if (parentgfo!=NULL) { //parent GffObj parsed earlier
1013     found_parent=true;
1014     if (parentgfo->gffobj->isGene() && gffline->is_transcript
1015     && gffline->exontype==0) {
1016     //not an exon, but a transcript parented by a gene
1017     if (newgfo) {
1018     updateParent(newgfo, parentgfo->gffobj);
1019     }
1020     else {
1021     newgfo=newGffRec(gffline, keepAttr, noExonAttr, parentgfo->gffobj);
1022     }
1023     }
1024     else { //potential exon subfeature
1025     if (!addExonFeature(parentgfo, gffline, pex, noExonAttr))
1026     validation_errors=true;
1027     }
1028     }
1029     } //for each parsed parent Id
1030     if (!found_parent) { //new GTF-like record starting here with a subfeature directly
1031     //or it could be some chado GFF3 barf with exons declared BEFORE their parent :(
1032     //check if this feature isn't parented by a previously stored "exon" subfeature
1033     char* subp_name=NULL;
1034     CNonExon* subp=subfPoolCheck(gffline, pex, subp_name);
1035     if (subp!=NULL) { //found a subfeature that is the parent of this gffline
1036     //promote that subfeature to a full GffObj
1037     GfoHolder* gfoh=promoteFeature(subp, subp_name, pex, keepAttr, noExonAttr);
1038     //add current gffline as an exon of the newly promoted subfeature
1039     if (!addExonFeature(gfoh, gffline, pex, noExonAttr))
1040     validation_errors=true;
1041     }
1042     else { //no parent seen before, create one directly with this exon
1043     //loc_debug=true;
1044     GfoHolder* newgfo=prevseen ? prevseen : newGffRec(gffline, keepAttr, noExonAttr);
1045     if (gffline->ID!=NULL && gffline->exontype==0)
1046     subfPoolAdd(pex, newgfo);
1047     //even those with errors will be added here!
1048     }
1049     GFREE(subp_name);
1050     } //no previous parent found
1051     } //parented feature
1052     //--
1053     delete gffline;
1054     gffline=NULL;
1055     }//while gff lines
1056     gflst.finalize(this, mergeCloseExons, keepAttr, noExonAttr); //force sorting by locus if so constructed
1057     // all gff records are now loaded in GList gflst
1058     // so we can free the hash
1059     phash.Clear();
1060     tids.Clear();
1061     if (validation_errors) {
1062     exit(1);
1063     }
1064     }
1065    
1066     GffObj* GffObj::finalize(GffReader* gfr, bool mergeCloseExons, bool keepAttrs, bool noExonAttr) {
1067     //merge
1068     //always merge adjacent or overlapping segments
1069     //but if mergeCloseExons then merge even when distance is up to 5 bases
1070     udata=0;
1071     uptr=NULL;
1072     if (gfr->transcriptsOnly && !(isTranscript() || (isGene() && children.Count()==0))) {
1073     isDiscarded(true);
1074     }
1075     if (ftype_id==gff_fid_transcript && CDstart>0) {
1076     ftype_id=gff_fid_mRNA;
1077     //exon_ftype_id=gff_fid_exon;
1078     }
1079     //if (ftype_id==gff_fid_mRNA || exon_ftype_id==gff_fid_exon || mergeCloseExons) {
1080     if (isTranscript() || exon_ftype_id==gff_fid_exon || mergeCloseExons) {
1081     int mindist=mergeCloseExons ? 5:1;
1082     for (int i=0;i<exons.Count()-1;i++) {
1083     int ni=i+1;
1084     uint mend=exons[i]->end;
1085     while (ni<exons.Count()) {
1086     int dist=(int)(exons[ni]->start-mend);
1087     if (dist>mindist) break; //no merging with next segment
1088     if (gfr!=NULL && gfr->gff_warns && dist!=0 && (exons[ni]->exontype!=exgffUTR && exons[i]->exontype!=exgffUTR)) {
1089     GMessage("GFF warning: merging adjacent/overlapping segments of %s on %s (%d-%d, %d-%d)\n",
1090     gffID, getGSeqName(), exons[i]->start, exons[i]->end,exons[ni]->start, exons[ni]->end);
1091     }
1092     mend=exons[ni]->end;
1093     covlen-=exons[i]->len();
1094     exons[i]->end=mend;
1095     covlen+=exons[i]->len();
1096     covlen-=exons[ni]->len();
1097     if (exons[ni]->attrs!=NULL && (exons[i]->attrs==NULL ||
1098     exons[i]->attrs->Count()<exons[ni]->attrs->Count())) {
1099     //use the other exon attributes, if more
1100     delete(exons[i]->attrs);
1101     exons[i]->attrs=exons[ni]->attrs;
1102     exons[ni]->attrs=NULL;
1103     }
1104     exons.Delete(ni);
1105     } //check for merge with next exon
1106     } //for each exon
1107     }
1108     //attribute reduction for GTF records
1109     if (keepAttrs && !noExonAttr && !fromGff3()
1110     && exons.Count()>0 && exons[0]->attrs!=NULL) {
1111     bool attrs_discarded=false;
1112     for (int a=0;a<exons[0]->attrs->Count();a++) {
1113     int attr_name_id=exons[0]->attrs->Get(a)->attr_id;
1114     char* attr_name=names->attrs.getName(attr_name_id);
1115     char* attr_val =exons[0]->attrs->Get(a)->attr_val;
1116     bool sameExonAttr=true;
1117     for (int i=1;i<exons.Count();i++) {
1118     char* ov=exons[i]->getAttr(attr_name_id);
1119     if (ov==NULL || (strcmp(ov,attr_val)!=0)) {
1120     sameExonAttr=false;
1121     break;
1122     }
1123     }
1124     if (sameExonAttr) {
1125     //delete this attribute from exons level
1126     attrs_discarded=true;
1127     this->addAttr(attr_name, attr_val);
1128     for (int i=1;i<exons.Count();i++) {
1129     removeExonAttr(*(exons[i]), attr_name_id);
1130     }
1131     exons[0]->attrs->freeItem(a);
1132     }
1133     }
1134     if (attrs_discarded) exons[0]->attrs->Pack();
1135     }
1136     return this;
1137     }
1138    
1139     void GffObj::parseAttrs(GffAttrs*& atrlist, char* info, bool isExon) {
1140     if (names==NULL)
1141     GError(ERR_NULL_GFNAMES, "parseAttrs()");
1142     if (atrlist==NULL)
1143     atrlist=new GffAttrs();
1144     char* endinfo=info+strlen(info);
1145     char* start=info;
1146     char* pch=start;
1147     while (start<endinfo) {
1148     //skip spaces
1149     while (*start==' ' && start<endinfo) start++;
1150     pch=strchr(start, ';');
1151     if (pch==NULL) pch=endinfo;
1152     else {
1153     *pch='\0';
1154     pch++;
1155     }
1156     char* ech=strchr(start,'=');
1157     if (ech!=NULL) { // attr=value format found
1158     *ech='\0';
1159     //if (noExonAttr && (strcmp(start, "exon_number")==0 || strcmp(start, "exon")==0)) { start=pch; continue; }
1160     if (strcmp(start, "exon_number")==0 || strcmp(start, "exon")==0 ||
1161     strcmp(start, "exon_id")==0)
1162     { start=pch; continue; }
1163     ech++;
1164     while (*ech==' ' && ech<endinfo) ech++;//skip extra spaces after the '='
1165     //atrlist->Add(new GffAttr(names->attrs.addName(start),ech));
1166     //make sure we don't add the same attribute more than once
1167     if (isExon && (strcmp(start, "protein_id")==0)) {
1168     //Ensembl special case
1169     this->addAttr(start, ech);
1170     start=pch;
1171     continue;
1172     }
1173     atrlist->add_or_update(names, start, ech);
1174     }
1175     /*
1176     else { //not an attr=value format
1177     atrlist->Add(new GffAttr(names->attrs.addName(start),"1"));
1178     }
1179     */
1180     start=pch;
1181     }
1182     if (atrlist->Count()==0) { delete atrlist; atrlist=NULL; }
1183     }
1184    
1185     void GffObj::addAttr(const char* attrname, const char* attrvalue) {
1186     if (this->attrs==NULL)
1187     this->attrs=new GffAttrs();
1188     //this->attrs->Add(new GffAttr(names->attrs.addName(attrname),attrvalue));
1189     this->attrs->add_or_update(names, attrname, attrvalue);
1190     }
1191    
1192    
1193     void GffObj::setFeatureName(const char* feature) {
1194     //change the feature name/type for a transcript
1195     int fid=names->feats.addName(feature);
1196     if (monoFeature() && exons.Count()>0)
1197     this->exon_ftype_id=fid;
1198     this->ftype_id=fid;
1199     }
1200    
1201     void GffObj::setRefName(const char* newname) {
1202     //change the feature name/type for a transcript
1203     int rid=names->gseqs.addName(newname);
1204     this->gseq_id=rid;
1205     }
1206    
1207    
1208    
1209     int GffObj::removeAttr(const char* attrname, const char* attrval) {
1210     if (this->attrs==NULL || attrname==NULL || attrname[0]==0) return 0;
1211     int aid=this->names->attrs.getId(attrname);
1212     if (aid<0) return 0;
1213     int delcount=0; //could be more than one ?
1214     for (int i=0;i<this->attrs->Count();i++) {
1215     if (aid==this->attrs->Get(i)->attr_id) {
1216     if (attrval==NULL ||
1217     strcmp(attrval, this->attrs->Get(i)->attr_val)==0) {
1218     delcount++;
1219     this->attrs->freeItem(i);
1220     }
1221     }
1222     }
1223     if (delcount>0) this->attrs->Pack();
1224     return delcount;
1225     }
1226    
1227     int GffObj::removeAttr(int aid, const char* attrval) {
1228     if (this->attrs==NULL || aid<0) return 0;
1229     int delcount=0; //could be more than one ?
1230     for (int i=0;i<this->attrs->Count();i++) {
1231     if (aid==this->attrs->Get(i)->attr_id) {
1232     if (attrval==NULL ||
1233     strcmp(attrval, this->attrs->Get(i)->attr_val)==0) {
1234     delcount++;
1235     this->attrs->freeItem(i);
1236     }
1237     }
1238     }
1239     if (delcount>0) this->attrs->Pack();
1240     return delcount;
1241     }
1242    
1243    
1244     int GffObj::removeExonAttr(GffExon& exon, const char* attrname, const char* attrval) {
1245     if (exon.attrs==NULL || attrname==NULL || attrname[0]==0) return 0;
1246     int aid=this->names->attrs.getId(attrname);
1247     if (aid<0) return 0;
1248     int delcount=0; //could be more than one
1249     for (int i=0;i<exon.attrs->Count();i++) {
1250     if (aid==exon.attrs->Get(i)->attr_id) {
1251     if (attrval==NULL ||
1252     strcmp(attrval, exon.attrs->Get(i)->attr_val)==0) {
1253     delcount++;
1254     exon.attrs->freeItem(i);
1255     }
1256     }
1257     }
1258     if (delcount>0) exon.attrs->Pack();
1259     return delcount;
1260     }
1261    
1262     int GffObj::removeExonAttr(GffExon& exon, int aid, const char* attrval) {
1263     if (exon.attrs==NULL || aid<0) return 0;
1264     int delcount=0; //could be more than one
1265     for (int i=0;i<exon.attrs->Count();i++) {
1266     if (aid==exon.attrs->Get(i)->attr_id) {
1267     if (attrval==NULL ||
1268     strcmp(attrval, exon.attrs->Get(i)->attr_val)==0) {
1269     delcount++;
1270     exon.attrs->freeItem(i);
1271     }
1272     }
1273     }
1274     if (delcount>0) exon.attrs->Pack();
1275     return delcount;
1276     }
1277    
1278    
1279     void GffObj::getCDS_ends(uint& cds_start, uint& cds_end) {
1280     cds_start=0;
1281     cds_end=0;
1282     if (CDstart==0 || CDend==0) return; //no CDS info
1283     int cdsadj=0;
1284     if (CDphase=='1' || CDphase=='2') {
1285     cdsadj=CDphase-'0';
1286     }
1287     cds_start=CDstart;
1288     cds_end=CDend;
1289     if (strand=='-') cds_end-=cdsadj;
1290     else cds_start+=cdsadj;
1291     }
1292    
1293     void GffObj::mRNA_CDS_coords(uint& cds_mstart, uint& cds_mend) {
1294     //sets cds_start and cds_end to the CDS start,end coordinates on the spliced mRNA transcript
1295     cds_mstart=0;
1296     cds_mend=0;
1297     if (CDstart==0 || CDend==0) return; //no CDS info
1298     //restore normal coordinates, just in case
1299     unxcoord();
1300     int cdsadj=0;
1301     if (CDphase=='1' || CDphase=='2') {
1302     cdsadj=CDphase-'0';
1303     }
1304     /*
1305     uint seqstart=CDstart;
1306     uint seqend=CDend;
1307     */
1308     uint seqstart=exons.First()->start;
1309     uint seqend=exons.Last()->end;
1310     int s=0; //resulting nucleotide counter
1311     if (strand=='-') {
1312     for (int x=exons.Count()-1;x>=0;x--) {
1313     uint sgstart=exons[x]->start;
1314     uint sgend=exons[x]->end;
1315     if (seqend<sgstart || seqstart>sgend) continue;
1316     if (seqstart>=sgstart && seqstart<=sgend)
1317     sgstart=seqstart; //seqstart within this segment
1318     if (seqend>=sgstart && seqend<=sgend)
1319     sgend=seqend; //seqend within this segment
1320     s+=(int)(sgend-sgstart)+1;
1321     if (CDstart>=sgstart && CDstart<=sgend) {
1322     //CDstart in this segment
1323     //and we are getting the whole transcript
1324     cds_mend=s-(int)(CDstart-sgstart);
1325     }
1326     if (CDend>=sgstart && CDend<=sgend) {
1327     //CDstart in this segment
1328     //and we are getting the whole transcript
1329     cds_mstart=s-(int)(CDend-cdsadj-sgstart);
1330     }
1331     } //for each exon
1332     } // - strand
1333     else { // + strand
1334     for (int x=0;x<exons.Count();x++) {
1335     uint sgstart=exons[x]->start;
1336     uint sgend=exons[x]->end;
1337     if (seqend<sgstart || seqstart>sgend) continue;
1338     if (seqstart>=sgstart && seqstart<=sgend)
1339     sgstart=seqstart; //seqstart within this segment
1340     if (seqend>=sgstart && seqend<=sgend)
1341     sgend=seqend; //seqend within this segment
1342     s+=(int)(sgend-sgstart)+1;
1343     /* for (uint i=sgstart;i<=sgend;i++) {
1344     spliced[s]=gsubseq[i-gstart];
1345     s++;
1346     }//for each nt
1347     */
1348     if (CDstart>=sgstart && CDstart<=sgend) {
1349     //CDstart in this segment
1350     cds_mstart=s-(int)(sgend-CDstart-cdsadj);
1351     }
1352     if (CDend>=sgstart && CDend<=sgend) {
1353     //CDend in this segment
1354     cds_mend=s-(int)(sgend-CDend);
1355     }
1356     } //for each exon
1357     } // + strand
1358     //spliced[s]=0;
1359     //if (rlen!=NULL) *rlen=s;
1360     //return spliced;
1361     }
1362    
1363     char* GffObj::getUnspliced(GFaSeqGet* faseq, int* rlen, GList<GSeg>* seglst)
1364     {
1365     if (faseq==NULL) { GMessage("Warning: getUnspliced(NULL,.. ) called!\n");
1366     return NULL;
1367     }
1368     //restore normal coordinates:
1369     unxcoord();
1370     if (exons.Count()==0) return NULL;
1371     int fspan=end-start+1;
1372     const char* gsubseq=faseq->subseq(start, fspan);
1373     if (gsubseq==NULL) {
1374     GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1375     }
1376     char* unspliced=NULL;
1377    
1378     int seqstart=exons.First()->start;
1379     int seqend=exons.Last()->end;
1380    
1381     int unsplicedlen = 0;
1382    
1383     unsplicedlen += seqend - seqstart + 1;
1384    
1385     GMALLOC(unspliced, unsplicedlen+1); //allocate more here
1386     //uint seqstart, seqend;
1387    
1388     int s = 0; //resulting nucleotide counter
1389     if (strand=='-')
1390     {
1391     if (seglst!=NULL)
1392     seglst->Add(new GSeg(s+1,s+1+seqend-seqstart));
1393     for (int i=seqend;i>=seqstart;i--)
1394     {
1395     unspliced[s] = ntComplement(gsubseq[i-start]);
1396     s++;
1397     }//for each nt
1398     } // - strand
1399     else
1400     { // + strand
1401     if (seglst!=NULL)
1402     seglst->Add(new GSeg(s+1,s+1+seqend-seqstart));
1403     for (int i=seqstart;i<=seqend;i++)
1404     {
1405     unspliced[s]=gsubseq[i-start];
1406     s++;
1407     }//for each nt
1408     } // + strand
1409     //assert(s <= unsplicedlen);
1410     unspliced[s]=0;
1411     if (rlen!=NULL) *rlen=s;
1412     return unspliced;
1413     }
1414    
1415     char* GffObj::getSpliced(GFaSeqGet* faseq, bool CDSonly, int* rlen, uint* cds_start, uint* cds_end,
1416     GList<GSeg>* seglst) {
1417     if (CDSonly && CDstart==0) return NULL;
1418     if (faseq==NULL) { GMessage("Warning: getSpliced(NULL,.. ) called!\n");
1419     return NULL;
1420     }
1421     //restore normal coordinates:
1422     unxcoord();
1423     if (exons.Count()==0) return NULL;
1424     int fspan=end-start+1;
1425     const char* gsubseq=faseq->subseq(start, fspan);
1426     if (gsubseq==NULL) {
1427     GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1428     }
1429     if (fspan<(int)(end-start+1)) { //special case: stop coordinate was extended past the gseq length, must adjust
1430     int endadj=end-start+1-fspan;
1431     uint prevend=end;
1432     end-=endadj;
1433     if (CDend>end) CDend=end;
1434     if (exons.Last()->end>end) {
1435     exons.Last()->end=end; //this could get us into trouble if exon start is also > end
1436     if (exons.Last()->start>exons.Last()->end) {
1437     GError("GffObj::getSpliced() error: improper genomic coordinate %d on %s for %s\n",
1438     prevend,getGSeqName(), getID());
1439     }
1440     covlen-=endadj;
1441     }
1442     }
1443     char* spliced=NULL;
1444     GMALLOC(spliced, covlen+1); //allocate more here
1445     uint seqstart, seqend;
1446     int cdsadj=0;
1447     if (CDphase=='1' || CDphase=='2') {
1448     cdsadj=CDphase-'0';
1449     }
1450     if (CDSonly) {
1451     seqstart=CDstart;
1452     seqend=CDend;
1453     if (strand=='-') seqend-=cdsadj;
1454     else seqstart+=cdsadj;
1455     }
1456     else {
1457     seqstart=exons.First()->start;
1458     seqend=exons.Last()->end;
1459     }
1460     int s=0; //resulting nucleotide counter
1461     if (strand=='-') {
1462     for (int x=exons.Count()-1;x>=0;x--) {
1463     uint sgstart=exons[x]->start;
1464     uint sgend=exons[x]->end;
1465     if (seqend<sgstart || seqstart>sgend) continue;
1466     if (seqstart>=sgstart && seqstart<=sgend)
1467     sgstart=seqstart; //seqstart within this segment
1468     if (seqend>=sgstart && seqend<=sgend)
1469     sgend=seqend; //seqend within this segment
1470     if (seglst!=NULL)
1471     seglst->Add(new GSeg(s+1,s+1+sgend-sgstart));
1472     for (uint i=sgend;i>=sgstart;i--) {
1473     spliced[s] = ntComplement(gsubseq[i-start]);
1474     s++;
1475     }//for each nt
1476    
1477     if (!CDSonly && cds_start!=NULL && CDstart>0) {
1478     if (CDstart>=sgstart && CDstart<=sgend) {
1479     //CDstart in this segment
1480     //and we are getting the whole transcript
1481     *cds_end=s-(CDstart-sgstart);
1482     }
1483     if (CDend>=sgstart && CDend<=sgend) {
1484     //CDstart in this segment
1485     //and we are getting the whole transcript
1486     *cds_start=s-(CDend-cdsadj-sgstart);
1487     }
1488     }//update local CDS coordinates
1489     } //for each exon
1490     } // - strand
1491     else { // + strand
1492     for (int x=0;x<exons.Count();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=sgstart;i<=sgend;i++) {
1503     spliced[s]=gsubseq[i-start];
1504     s++;
1505     }//for each nt
1506     if (!CDSonly && cds_start!=NULL && CDstart>0) {
1507     if (CDstart>=sgstart && CDstart<=sgend) {
1508     //CDstart in this segment
1509     //and we are getting the whole transcript
1510     *cds_start=s-(sgend-CDstart-cdsadj);
1511     }
1512     if (CDend>=sgstart && CDend<=sgend) {
1513     //CDstart in this segment
1514     //and we are getting the whole transcript
1515     *cds_end=s-(sgend-CDend);
1516     }
1517     }//update local CDS coordinates
1518     } //for each exon
1519     } // + strand
1520     spliced[s]=0;
1521     if (rlen!=NULL) *rlen=s;
1522     return spliced;
1523     }
1524    
1525     char* GffObj::getSplicedTr(GFaSeqGet* faseq, bool CDSonly, int* rlen) {
1526     if (CDSonly && CDstart==0) return NULL;
1527     //restore normal coordinates:
1528     unxcoord();
1529     if (exons.Count()==0) return NULL;
1530     int fspan=end-start+1;
1531     const char* gsubseq=faseq->subseq(start, fspan);
1532     if (gsubseq==NULL) {
1533     GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
1534     }
1535    
1536     char* translation=NULL;
1537     GMALLOC(translation, (int)(covlen/3)+1);
1538     uint seqstart, seqend;
1539     int cdsadj=0;
1540     if (CDphase=='1' || CDphase=='2') {
1541     cdsadj=CDphase-'0';
1542     }
1543     if (CDSonly) {
1544     seqstart=CDstart;
1545     seqend=CDend;
1546     if (strand=='-') seqend-=cdsadj;
1547     else seqstart+=cdsadj;
1548     }
1549     else {
1550     seqstart=exons.First()->start;
1551     seqend=exons.Last()->end;
1552     }
1553     Codon codon;
1554     int nt=0; //codon nucleotide counter (0..2)
1555     int aa=0; //aminoacid count
1556     if (strand=='-') {
1557     for (int x=exons.Count()-1;x>=0;x--) {
1558     uint sgstart=exons[x]->start;
1559     uint sgend=exons[x]->end;
1560     if (seqend<sgstart || seqstart>sgend) continue;
1561     if (seqstart>=sgstart && seqstart<=sgend)
1562     sgstart=seqstart; //seqstart within this segment
1563     if (seqend>=sgstart && seqend<=sgend) {
1564     sgend=seqend; //seqend within this segment
1565     }
1566     for (uint i=sgend;i>=sgstart;i--) {
1567     codon.nuc[nt]=ntComplement(gsubseq[i-start]);
1568     nt++;
1569     if (nt==3) {
1570     nt=0;
1571     translation[aa]=codon.translate();
1572     aa++;
1573     }
1574     }//for each nt
1575     } //for each exon
1576     } // - strand
1577     else { // + strand
1578     for (int x=0;x<exons.Count();x++) {
1579     uint sgstart=exons[x]->start;
1580     uint sgend=exons[x]->end;
1581     if (seqend<sgstart || seqstart>sgend) continue;
1582     if (seqstart>=sgstart && seqstart<=sgend)
1583     sgstart=seqstart; //seqstart within this segment
1584     if (seqend>=sgstart && seqend<=sgend)
1585     sgend=seqend; //seqend within this segment
1586     for (uint i=sgstart;i<=sgend;i++) {
1587     codon.nuc[nt]=gsubseq[i-start];
1588     nt++;
1589     if (nt==3) {
1590     nt=0;
1591     translation[aa]=codon.translate();
1592     aa++;
1593     }
1594     }//for each nt
1595     } //for each exon
1596     } // + strand
1597     translation[aa]=0;
1598     if (rlen!=NULL) *rlen=aa;
1599     return translation;
1600     }
1601    
1602     void GffObj::printSummary(FILE* fout) {
1603     if (fout==NULL) fout=stdout;
1604     fprintf(fout, "%s\t%c\t%d\t%d\t%4.2f\t%4.1f\n", gffID,
1605     strand, start, end, gscore, (float)qcov/10.0);
1606     }
1607    
1608     void GffObj::printGxfLine(FILE* fout, const char* tlabel, const char* gseqname, bool iscds,
1609     uint segstart, uint segend, int exidx, char phase, bool gff3) {
1610     static char scorestr[14];
1611     strcpy(scorestr,".");
1612     GffAttrs* xattrs=NULL;
1613     if (exidx>=0) {
1614     if (exons[exidx]->score) sprintf(scorestr,"%.2f", exons[exidx]->score);
1615     xattrs=exons[exidx]->attrs;
1616     }
1617     if (phase==0 || !iscds) phase='.';
1618     const char* ftype=iscds ? "CDS" : getSubfName();
1619     if (gff3) {
1620     fprintf(fout,
1621     "%s\t%s\t%s\t%d\t%d\t%s\t%c\t%c\tParent=%s",
1622     gseqname, tlabel, ftype, segstart, segend, scorestr, strand,
1623     phase, gffID);
1624     if (xattrs!=NULL) {
1625     for (int i=0;i<xattrs->Count();i++)
1626     fprintf(fout, ";%s=%s",names->attrs.getName(xattrs->Get(i)->attr_id),
1627     xattrs->Get(i)->attr_val);
1628     }
1629     fprintf(fout, "\n");
1630     } //GFF
1631     else {//for GTF -- we print only transcripts
1632     //if (isValidTranscript())
1633     fprintf(fout, "%s\t%s\t%s\t%d\t%d\t%s\t%c\t%c\ttranscript_id \"%s\";",
1634     gseqname, tlabel, ftype, segstart, segend, scorestr, strand, phase, gffID);
1635     //char* geneid=(geneID!=NULL)? geneID : gffID;
1636     if (geneID)
1637     fprintf(fout," gene_id \"%s\";",geneID);
1638     if (gene_name!=NULL) {
1639     //fprintf(fout, " gene_name ");
1640     //if (gene_name[0]=='"') fprintf (fout, "%s;",gene_name);
1641     // else fprintf(fout, "\"%s\";",gene_name);
1642     fprintf(fout," gene_name \"%s\";",gene_name);
1643     }
1644     if (xattrs!=NULL) {
1645     for (int i=0;i<xattrs->Count();i++) {
1646     if (xattrs->Get(i)->attr_val==NULL) continue;
1647     const char* attrname=names->attrs.getName(xattrs->Get(i)->attr_id);
1648     fprintf(fout, " %s ",attrname);
1649     if (xattrs->Get(i)->attr_val[0]=='"')
1650     fprintf(fout, "%s;",xattrs->Get(i)->attr_val);
1651     else fprintf(fout, "\"%s\";",xattrs->Get(i)->attr_val);
1652     }
1653     }
1654     //for GTF, also append the GffObj attributes to each exon line
1655     if ((xattrs=this->attrs)!=NULL) {
1656     for (int i=0;i<xattrs->Count();i++) {
1657     if (xattrs->Get(i)->attr_val==NULL) continue;
1658     const char* attrname=names->attrs.getName(xattrs->Get(i)->attr_id);
1659     fprintf(fout, " %s ",attrname);
1660     if (xattrs->Get(i)->attr_val[0]=='"')
1661     fprintf(fout, "%s;",xattrs->Get(i)->attr_val);
1662     else fprintf(fout, "\"%s\";",xattrs->Get(i)->attr_val);
1663     }
1664     }
1665     fprintf(fout, "\n");
1666     }//GTF
1667     }
1668    
1669     void GffObj::printGxf(FILE* fout, GffPrintMode gffp,
1670     const char* tlabel, const char* gfparent) {
1671     static char tmpstr[255];
1672     if (tlabel==NULL) {
1673     tlabel=track_id>=0 ? names->tracks.Get(track_id)->name :
1674     (char*)"gffobj" ;
1675     }
1676     unxcoord();
1677     //if (exons.Count()==0) return;
1678     const char* gseqname=names->gseqs.Get(gseq_id)->name;
1679     bool gff3 = (gffp>=pgffAny);
1680     bool showCDS = (gffp==pgtfAny || gffp==pgtfCDS || gffp==pgffCDS || gffp==pgffAny || gffp==pgffBoth);
1681     bool showExon = (gffp<=pgtfExon || gffp==pgffAny || gffp==pgffExon || gffp==pgffBoth);
1682     if (gff3) {
1683     //print GFF3 mRNA line:
1684     if (gscore>0.0) sprintf(tmpstr,"%.2f", gscore);
1685     else strcpy(tmpstr,".");
1686     uint pstart, pend;
1687     if (gffp==pgffCDS) {
1688     pstart=CDstart;
1689     pend=CDend;
1690     }
1691     else { pstart=start;pend=end; }
1692     //const char* ftype=isTranscript() ? "mRNA" : getFeatureName();
1693     const char* ftype=getFeatureName();
1694     fprintf(fout,
1695     "%s\t%s\t%s\t%d\t%d\t%s\t%c\t.\tID=%s",
1696     gseqname, tlabel, ftype, pstart, pend, tmpstr, strand, gffID);
1697     if (CDstart>0 && !showCDS && !isCDS) fprintf(fout,";CDS=%d-%d",CDstart,CDend);
1698     if (gfparent!=NULL) {
1699     //parent override
1700     fprintf(fout, ";Parent=%s",gfparent);
1701     }
1702     else {
1703     if (parent!=NULL && !parent->isDiscarded())
1704     fprintf(fout, ";Parent=%s",parent->getID());
1705     }
1706     if (geneID!=NULL)
1707     fprintf(fout, ";geneID=%s",geneID);
1708     if (gene_name!=NULL)
1709     fprintf(fout, ";gene_name=%s",gene_name);
1710     if (attrs!=NULL) {
1711     for (int i=0;i<attrs->Count();i++) {
1712     const char* attrname=names->attrs.getName(attrs->Get(i)->attr_id);
1713     fprintf(fout,";%s=%s", attrname,
1714     attrs->Get(i)->attr_val);
1715     }
1716     }
1717     fprintf(fout,"\n");
1718     }// gff3 mRNA line
1719     if (showExon) {
1720     //print exons
1721     if (isCDS && exons.Count()>0 &&
1722     ((strand=='-' && exons.Last()->phase<'0') || (strand=='+' && exons.Last()->phase<'0')))
1723     updateExonPhase();
1724    
1725     for (int i=0;i<exons.Count();i++) {
1726     printGxfLine(fout, tlabel, gseqname, isCDS, exons[i]->start, exons[i]->end, i, exons[i]->phase, gff3);
1727     }
1728     }//printing exons
1729     if (showCDS && !isCDS && CDstart>0) {
1730     GArray<GffCDSeg> cds(true,true);
1731     getCDSegs(cds);
1732     for (int i=0;i<cds.Count();i++) {
1733     printGxfLine(fout, tlabel, gseqname, true, cds[i].start, cds[i].end, -1, cds[i].phase, gff3);
1734     }
1735     } //showCDS
1736     }
1737    
1738     void GffObj::updateExonPhase() {
1739     if (!isCDS) return;
1740     int cdsacc=0;
1741     if (CDphase=='1' || CDphase=='2') {
1742     cdsacc+= 3-(CDphase-'0');
1743     }
1744     if (strand=='-') { //reverse strand
1745     for (int i=exons.Count()-1;i>=0;i--) {
1746     exons[i]->phase='0'+ (3-cdsacc%3)%3;
1747     cdsacc+=exons[i]->end-exons[i]->start+1;
1748     }
1749     }
1750     else { //forward strand
1751     for (int i=0;i<exons.Count();i++) {
1752     exons[i]->phase='0'+ (3-cdsacc%3)%3;
1753     cdsacc+=exons[i]->end-exons[i]->start+1;
1754     }
1755     }
1756     }
1757    
1758    
1759     void GffObj::getCDSegs(GArray<GffCDSeg>& cds) {
1760     GffCDSeg cdseg;
1761     int cdsacc=0;
1762     if (CDphase=='1' || CDphase=='2') {
1763     cdsacc+= 3-(CDphase-'0');
1764     }
1765     if (strand=='-') {
1766     for (int x=exons.Count()-1;x>=0;x--) {
1767     uint sgstart=exons[x]->start;
1768     uint sgend=exons[x]->end;
1769     if (CDend<sgstart || CDstart>sgend) continue;
1770     if (CDstart>=sgstart && CDstart<=sgend)
1771     sgstart=CDstart; //cdstart within this segment
1772     if (CDend>=sgstart && CDend<=sgend)
1773     sgend=CDend; //cdend within this segment
1774     cdseg.start=sgstart;
1775     cdseg.end=sgend;
1776     cdseg.exonidx=x;
1777     //cdseg.phase='0'+(cdsacc>0 ? (3-cdsacc%3)%3 : 0);
1778     cdseg.phase='0'+ (3-cdsacc%3)%3;
1779     cdsacc+=sgend-sgstart+1;
1780     cds.Add(cdseg);
1781     } //for each exon
1782     } // - strand
1783     else { // + strand
1784     for (int x=0;x<exons.Count();x++) {
1785     uint sgstart=exons[x]->start;
1786     uint sgend=exons[x]->end;
1787     if (CDend<sgstart || CDstart>sgend) continue;
1788     if (CDstart>=sgstart && CDstart<=sgend)
1789     sgstart=CDstart; //seqstart within this segment
1790     if (CDend>=sgstart && CDend<=sgend)
1791     sgend=CDend; //seqend within this segment
1792     cdseg.start=sgstart;
1793     cdseg.end=sgend;
1794     cdseg.exonidx=x;
1795     //cdseg.phase='0'+(cdsacc>0 ? (3-cdsacc%3)%3 : 0);
1796     cdseg.phase='0' + (3-cdsacc%3)%3 ;
1797     cdsacc+=sgend-sgstart+1;
1798     cds.Add(cdseg);
1799     } //for each exon
1800     } // + strand
1801     }