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gff.cpp
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gff.cpp
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#include "gff.h"
GffNames* GffObj::names=NULL;
//global set of feature names, attribute names etc.
// -- common for all GffObjs in current application!
const uint GFF_MAX_LOCUS = 7000000; //longest known gene in human is ~2.2M, UCSC claims a gene for mouse of ~ 3.1 M
const uint GFF_MAX_EXON = 30000; //longest known exon in human is ~11K
const uint GFF_MAX_INTRON= 6000000; //Ensembl shows a >5MB mouse intron
const int GFF_MIN_INTRON = 4; //for mergeCloseExons option
//bool gff_show_warnings = false; //global setting, set by GffReader->showWarnings()
int gff_fid_mRNA=0; //mRNA (has CDS)
int gff_fid_transcript=1; // generic "transcript" feature
int gff_fid_exon=2; // generic "exon"-like feature (exon,CDS,UTR,start/stop codon)
int gff_fid_CDS=3; // CDS feature (CDS, start/stop codon)
const char* exonTypes[]={ "None", "StartCodon", "StopCodon",
"CDS", "UTR", "CDS+UTR", "exon" };
const GffScore GFFSCORE_NONE;
//const uint gfo_flag_LEVEL_MSK = 0x00FF0000;
//const byte gfo_flagShift_LEVEL = 16;
void gffnames_ref(GffNames* &n) {
if (n==NULL) n=new GffNames();
n->numrefs++;
}
void gffnames_unref(GffNames* &n) {
if (n==NULL) GError("Error: attempt to remove reference to null GffNames object!\n");
n->numrefs--;
if (n->numrefs==0) { delete n; n=NULL; }
}
const byte CLASSCODE_OVL_RANK = 14; //rank value just above 'o' class code
//rank value < this means exon overlap
const byte CLASSCODE_J_RANK = 6; // all junctional based overlaps
byte classcode_rank(char c) {
switch (c) {
case '=': return 0; //intron chain match or full exon chain match if strict matching is enabled
case '~': return 1; //intron chain match when strict matching is enabled
case 'c': return 4; //containment, perfect partial match (transfrag contained in reference)
case 'k': return 4; // reverse containment (reference contained in transfrag)
case 'm': return 6; // full span overlap with all reference introns either matching or retained
case 'n': return 6; // partial overlap transfrag with at least one intron retention
case 'j': return 6; // multi-exon transfrag overlap with at least one junction match OR intron overlap!
case 'e': return 12; // single exon transfrag partially overlapping an intron of reference (possible pre-mRNA fragment)
case 'o': return 12; // other generic exon overlap
//**** >14 => no exon overlaps (not on the same strand) from here on *****
case 's': return 16; //"shadow" - an intron overlaps with a ref intron on the opposite strand (wrong strand mapping?)
case 'x': return 18; // generic overlap on opposite strand (usually wrong strand mapping)
case 'i': return 20; // intra-intron (transfrag fully contained within a reference intron)
case 'y': return 30; // no exon overlap: ref exons fall within transfrag introns! (reverse of i)
case 'p': return 90; //polymerase run
case 'r': return 92; //repeats
case 'u': return 94; //intergenic
case 0 : return 100;
default: return 96;
}
}
const char* strExonType(char xtype) {
static const char* extbl[7]={"None", "start_codon", "stop_codon", "CDS", "UTR", "CDS_UTR", "exon"};
if (xtype>0 && xtype<7)
return extbl[(int)xtype];
else return "NULL";
}
int gfo_cmpByLoc(const pointer p1, const pointer p2) {
GffObj& g1=*((GffObj*)p1);
GffObj& g2=*((GffObj*)p2);
if (g1.gseq_id==g2.gseq_id) {
if (g1.start!=g2.start)
return (int)(g1.start-g2.start);
else if (g1.getLevel()!=g2.getLevel())
return (int)(g1.getLevel()-g2.getLevel());
else
if (g1.end!=g2.end)
return (int)(g1.end-g2.end);
else return strcmp(g1.getID(), g2.getID());
}
else //return (int)(g1.gseq_id-g2.gseq_id); // input order !
return strcmp(g1.getGSeqName(), g2.getGSeqName()); //lexicographic !
}
//comparator for ordering by reference sequence (chromosome) index
int gfo_cmpRefByID(const pointer p1, const pointer p2) {
GffObj& g1=*((GffObj*)p1);
GffObj& g2=*((GffObj*)p2);
if (g1.gseq_id==g2.gseq_id) {
if (g1.start!=g2.start)
return (int)(g1.start-g2.start);
else if (g1.getLevel()!=g2.getLevel())
return (int)(g1.getLevel()-g2.getLevel());
else
if (g1.end!=g2.end)
return (int)(g1.end-g2.end);
else return strcmp(g1.getID(), g2.getID());
}
else return (g1.gseq_id-g2.gseq_id); // sort refs by their id# order
}
char* GffLine::extractGFFAttr(char* & infostr, const char* oline, const char* attr, bool caseStrict,
bool enforce_GTF2, int* rlen, bool deleteAttr) {
//parse a key attribute and remove it from the info string
//(only works for attributes that have values following them after ' ' or '=')
static const char GTF2_ERR[]="Error parsing attribute %s ('\"' required for GTF) at line:\n%s\n";
int attrlen=strlen(attr);
char cend=attr[attrlen-1];
//char* pos = (caseStrict) ? strstr(info, attr) : strifind(info, attr);
//must make sure attr is not found in quoted text
char* pos=infostr;
char prevch=0;
bool in_str=false;
bool notfound=true;
int (*strcmpfn)(const char*, const char*, int) = caseStrict ? Gstrcmp : Gstricmp;
while (notfound && *pos) {
char ch=*pos;
if (ch=='"') {
in_str=!in_str;
pos++;
prevch=ch;
continue;
}
if (!in_str && (prevch==0 || prevch==' ' || prevch == ';')
&& strcmpfn(attr, pos, attrlen)==0) {
//attr match found
//check for word boundary on right
char* epos=pos+attrlen;
if (cend=='=' || cend==' ' || *epos==0 || *epos==' ') {
notfound=false;
break;
}
//not a perfect match, move on
pos=epos;
prevch=*(pos-1);
continue;
}
//not a match or in_str
prevch=ch;
pos++;
}
if (notfound) return NULL;
char* vp=pos+attrlen;
while (*vp==' ') vp++;
if (*vp==';' || *vp==0) {
GMessage("Warning: cannot parse value of GFF attribute \"%s\" at line:\n%s\n", attr, oline);
return NULL;
}
bool dq_enclosed=false; //value string enclosed by double quotes
if (*vp=='"') {
dq_enclosed=true;
vp++;
}
if (enforce_GTF2 && !dq_enclosed)
GError(GTF2_ERR, attr, oline);
char* vend=vp;
if (dq_enclosed) {
while (*vend!='"' && *vend!=';' && *vend!=0) vend++;
}
else {
while (*vend!=';' && *vend!=0) vend++;
}
if (enforce_GTF2 && *vend!='"')
GError(GTF2_ERR, attr, oline);
char *r=Gstrdup(vp, vend-1);
if (rlen) *rlen = vend-vp;
if (deleteAttr) {//-- remove this attribute from infostr
while (*vend!=0 && (*vend=='"' || *vend==';' || *vend==' ')) vend++;
if (*vend==0) vend--;
for (char *src=vend, *dest=pos;;src++,dest++) {
*dest=*src; //shift the rest of infostr (copy over)
if (*src==0) break;
}
}
return r;
}
BEDLine::BEDLine(GffReader* reader, const char* l): skip(true), dupline(NULL), line(NULL), llen(0),
gseqname(NULL), fstart(0), fend(0), strand(0), ID(NULL), info(NULL),
cds_start(0), cds_end(0), cds_phase(0), exons(1) {
if (reader==NULL || l==NULL) return;
llen=strlen(l);
GMALLOC(line,llen+1);
memcpy(line, l, llen+1);
GMALLOC(dupline, llen+1);
memcpy(dupline, l, llen+1);
char* t[14];
int i=0;
int tidx=1;
t[0]=line;
if (startsWith(line, "browser ") || startsWith(line, "track "))
return;
while (line[i]!=0) {
if (line[i]=='\t') {
line[i]=0;
t[tidx]=line+i+1;
tidx++;
//our custom BED-13+ format, with GFF3 attributes in 13th column
if (tidx>12) { info=t[12]; break; }
}
i++;
}
/* if (tidx<6) { // require BED-6+ lines
GMessage("Warning: 6+ BED columns expected, instead found:\n%s\n", l);
return;
}
*/
gseqname=t[0];
char* p=t[1];
if (!parseUInt(p,fstart)) {
GMessage("Warning: invalid BED start coordinate at line:\n%s\n",l);
return;
}
++fstart; //BED start is 0 based
p=t[2];
if (!parseUInt(p,fend)) {
GMessage("Warning: invalid BED end coordinate at line:\n%s\n",l);
return;
}
if (fend<fstart) Gswap(fend,fstart); //make sure fstart<=fend, always
if (tidx>5) {
strand=*t[5];
if (strand!='-' && strand !='.' && strand !='+') {
GMessage("Warning: unrecognized BED strand at line:\n%s\n",l);
return;
}
}
else strand='.';
//if (tidx>12) ID=t[12];
// else ID=t[3];
ID=t[3];
//now parse the exons, if any
if (tidx>11) {
int numexons=0;
p=t[9];
if (!parseInt(p, numexons) || numexons<=0) {
GMessage("Warning: invalid BED block count at line:\n%s\n",l);
return;
}
char** blen;
char** bstart;
GMALLOC(blen, numexons * sizeof(char*));
GMALLOC(bstart, numexons * sizeof(char*));
i=0;
int b=1;
blen[0]=t[10];
while (t[10][i]!=0 && b<=numexons) {
if (t[10][i]==',') {
t[10][i]=0;
if (b<numexons)
blen[b]=t[10]+i+1;
b++;
}
i++;
}
b=1;i=0;
bstart[0]=t[11];
while (t[11][i]!=0 && b<=numexons) {
if (t[11][i]==',') {
t[11][i]=0;
if (b<numexons)
bstart[b]=t[11]+i+1;
b++;
}
i++;
}
GSeg ex;
for (i=0;i<numexons;++i) {
int exonlen;
if (!strToInt(blen[i], exonlen) || exonlen<=0) {
GMessage("Warning: invalid BED block size %s at line:\n%s\n",blen[i], l);
return;
}
int exonstart;
if (!strToInt(bstart[i], exonstart) || exonstart<0) {
GMessage("Warning: invalid BED block start %s at line:\n%s\n",bstart[i], l);
return;
}
if (i==0 && exonstart!=0) {
GMessage("Warning: first BED block start is %d>0 at line:\n%s\n",exonstart, l);
return;
}
exonstart+=fstart;
uint exonend=exonstart+exonlen-1;
if ((uint)exonstart>fend || exonend>fend) {
GMessage("Warning: BED exon %d-%d is outside record boundary at line:\n%s\n",exonstart,exonend, l);
return;
}
ex.start=exonstart;ex.end=exonend;
exons.Add(ex);
}
GFREE(blen);
GFREE(bstart);
}
else { //take it as single-exon transcript
GSeg v(fstart, fend);
exons.Add(v);
}
if (info!=NULL) {
char* cdstr=GffLine::extractGFFAttr(info, dupline, "CDS=");
if (cdstr) {
char* p=strchr(cdstr, ':');
if (p!=NULL) {
*p='\0'; ++p;
}
if (strToUInt(cdstr, cds_start) && cds_start>=fstart-1) {
++cds_start;
if (!strToUInt(p, cds_end) || cds_end>fend) {
GMessage("Warning: invalid CDS (%d-%d) discarded for line:\n%s\n",
cds_start, cds_end, dupline);
cds_start=0;
cds_end=0; //invalid CDS coordinates
}
}
char* cdstr_phase=NULL;
if (cds_start>0 && (cdstr_phase=GffLine::extractGFFAttr(info, dupline, "CDSphase="))!=NULL) {
cds_phase=cdstr_phase[0];
GFREE(cdstr_phase);
}
GFREE(cdstr);
}
}
if (cds_start==0 && cds_end==0 && tidx>7) {
//check if columns 7,8 can be reasonably assumed to be CDS start-end coordinates
if (strToUInt(t[6], cds_start) && strToUInt(t[7], cds_end) && cds_end>cds_start) {
if (cds_start>=fstart-1 && cds_end<=fend)
cds_start++;
else { cds_start=0; cds_end=0; }
}
}
skip=false;
}
bool GffLine::parseSegmentList(GVec<GSeg>& segs, char* str) {
bool segs_valid=false;
char* p=strchr(str, '-');
if (p!=NULL && p>str) {
GDynArray<char*> ss;
strsplit(str, ss, ',');
GSeg seg;
segs_valid=true;
for (uint i=0;i<ss.Count();++i) {
char* p=strchr(ss[i], '-');
if (p==NULL) {
segs_valid=false;
break;
}
*p='\0'; ++p;
int xstart=0, xend=0;
if (!strToInt(ss[i], xstart) || xstart<(int)fstart || xstart>(int)fend){
segs_valid=false;
break;
}
if (!strToInt(p, xend) || xend<(int)fstart || xend>(int)fend) {
segs_valid=false;
break;
}
if (xstart>xend) { seg.start=(uint)xend;seg.end=(uint)xstart; }
else { seg.start=(uint)xstart;seg.end=(uint)xend; }
segs.Add(seg);
} //parse all CDS segments
if (segs_valid) {
if (segs.Count()>1) segs.Sort();
} else
segs.Clear();
}
return segs_valid;
}
void GffLine::ensembl_GFF_ID_process(char*& id) {
char* n=NULL;
if (startsWith(id, "gene:")) {
n=Gstrdup(id+5);
GFREE(id);
id=n;
}
else if (startsWith(id, "transcript:")) {
n=Gstrdup(id+11);
GFREE(id);
id=n;
}
}
void GffLine::ensembl_GTF_ID_process(char*& id, const char* ver_attr) {
char* v=NULL;
v=extractAttr(ver_attr);
if (v!=NULL) {
char* n=Gstrdup(id, strlen(v)+1);
strcat(n,".");strcat(n,v);
GFREE(v);
GFREE(id);
id=n;
}
}
GffLine::GffLine(GffReader* reader, const char* l): _parents(NULL), _parents_len(0),
dupline(NULL), line(NULL), llen(0), gseqname(NULL), track(NULL),
ftype(NULL), ftype_id(-1), info(NULL), fstart(0), fend(0), //qstart(0), qend(0), qlen(0),
score(0), score_decimals(-1), strand(0), flags(0), exontype(exgffNone), phase(0), cds_start(0), cds_end(0),
exons(), cdss(), gene_name(NULL), gene_id(NULL), parents(NULL), num_parents(0), ID(NULL) {
llen=strlen(l);
GMALLOC(line,llen+1);
memcpy(line, l, llen+1);
GMALLOC(dupline, llen+1);
memcpy(dupline, l, llen+1);
skipLine=true; //clear only if we make it to the end of this function
char* t[9];
int i=0;
int tidx=1;
t[0]=line;
char fnamelc[128];
while (line[i]!=0) {
if (line[i]=='\t') {
line[i]=0;
t[tidx]=line+i+1;
tidx++;
//if (tidx>8) break;
}
i++;
}
if (tidx<8) { // ignore non-GFF lines
return;
}
if (tidx>9) {
GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l);
}
gffWarnings=reader->gff_warns;
gseqname=t[0];
track=t[1];
ftype=t[2];
info=t[8];
char* p=t[3];
if (!parseUInt(p,fstart)) {
//chromosome_band entries in Flybase
GMessage("Warning: invalid start coordinate at line:\n%s\n",l);
return;
}
p=t[4];
if (!parseUInt(p,fend)) {
GMessage("Warning: invalid end coordinate at line:\n%s\n",l);
return;
}
if (fend<fstart) {
GMessage("Error: invalid feature coordinates (end<start!) at line:\n%s\n",l);
Gswap(fend,fstart); //make sure fstart<=fend, always
//return;
}
p=t[5];
if (p[0]=='.' && p[1]==0) {
score=0;
score_decimals=-1;
}
else {
score_decimals=0;
//count decimals
char* pd=strchr(p,'.');
if (pd) {
++pd;
char* pde=pd;
while ((*pde)!=0) ++pde;
score_decimals=pde-pd;
}
if (!parseFloat(p, score))
GError("Error parsing feature score from GFF line:\n%s\n",l);
}
strand=*t[6];
if (strand!='+' && strand!='-' && strand!='.')
GError("Error parsing strand (%c) from GFF line:\n%s\n",strand,l);
phase=*t[7]; // must be '.', '0', '1' or '2'
// exon/CDS/mrna filter
strncpy(fnamelc, ftype, 127);
fnamelc[127]=0;
strlower(fnamelc); //convert to lower case
if (endsWith(fnamelc, "match")) {
//TODO: do not discard generic cDNA_match/protein_match features, convert them internally
// (when a hit chain has multiple _match features with the same ID, e.g. multiple HSPs with the same subject)
// and set GffObj::flag_DISCONTINUOUS
return;
}
bool is_t_data=false;
bool someRNA=false;
if (strstr(fnamelc, "utr")!=NULL) {
exontype=exgffUTR;
is_exon=true;
is_t_data=true;
}
else if (endsWith(fnamelc, "exon")) {
exontype=exgffExon;
is_exon=true;
is_t_data=true;
}
else if (strstr(fnamelc, "stop")!=NULL &&
(strstr(fnamelc, "codon")!=NULL || strstr(fnamelc, "cds")!=NULL) &&
strstr(fnamelc, "redefined")==NULL && strstr(fnamelc, "selenocysteine")==NULL) {
exontype=exgffStopCodon;
is_exon=true;
is_cds=true; //though some place it outside the last CDS segment
is_t_data=true;
}
else if (strstr(fnamelc, "start") &&
((strstr(fnamelc, "codon")!=NULL) || strstr(fnamelc, "cds")!=NULL)){
exontype=exgffStartCodon;
is_exon=true;
is_cds=true;
is_t_data=true;
}
else if (strcmp(fnamelc, "cds")==0) {
exontype=exgffCDS;
is_exon=true;
is_cds=true;
is_t_data=true;
}
else if (startsWith(fnamelc, "intron") || endsWith(fnamelc, "intron")) {
exontype=exgffIntron;
}
else if ((someRNA=endsWith(fnamelc,"rna")) || endsWith(fnamelc,"transcript")) { // || startsWith(fnamelc+1, "rna")) {
is_transcript=true;
is_t_data=true;
if (someRNA) ftype_id=GffObj::names->feats.addName(ftype);
}
else if (endsWith(fnamelc, "_gene_segment")) {
is_transcript=true;
is_t_data=true;
is_gene_segment=true;
}
else if (endsWith(fnamelc, "gene") || startsWith(fnamelc, "gene")) {
is_gene=true;
is_t_data=true; //because its name will be attached to parented transcripts
}
char* Parent=NULL;
/*
Rejecting non-transcript lines early if only transcripts are requested ?!
It would be faster to do this here but there are GFF cases when we reject an
unusual parent feature here (e.g. protein with CDS children) and then
their exon/CDS children show up and get assigned to an implicit parent mRNA
The solution is to still load this parent as GffObj for now and BAN it later
so its children get dismissed/discarded as well.
*/
if (reader->ignoreLocus) {
if (strcmp(ftype, "locus")==0) return;
if (is_transcript || is_gene) {
char* locus=NULL;
if (reader->is_gff3 || reader->gff_type==0)
locus=extractAttr("locus=");
else locus=extractAttr("locus");
if (locus!=NULL) { GFREE(locus); }
}
}
char *gtf_tid=NULL;
char *gtf_gid=NULL;
if (reader->is_gff3 || reader->gff_type==0) {
ID=extractAttr("ID=",true);
if (ID!=NULL && reader->procEnsemblID()) {
ensembl_GFF_ID_process(ID);
}
Parent=extractAttr("Parent=",true);
if (Parent!=NULL && reader->procEnsemblID()) {
ensembl_GFF_ID_process(Parent);
}
if (reader->gff_type==0) {
if (ID!=NULL || Parent!=NULL) reader->is_gff3=true;
else { //check if it looks like a GTF
gtf_tid=extractAttr("transcript_id", true, true);
if (gtf_tid!=NULL) {
if (reader->procEnsemblID())
ensembl_GTF_ID_process(gtf_tid, "transcript_version");
}
else { //NULL gtf_tid, try gene_id
gtf_gid=extractAttr("gene_id", true, true);
if (gtf_gid!=NULL) {
if (reader->procEnsemblID())
ensembl_GTF_ID_process(gtf_gid, "gene_version");
}
else return; //cannot determine file type yet
}
reader->is_gtf=true;
}
}
}
if (reader->is_gff3) {
//parse as GFF3
//if (ID==NULL && Parent==NULL) return; //silently ignore unidentified/unlinked features
if (ID!=NULL) {
//has ID attr so it's likely to be a parent feature
//look for explicit gene name
gene_name=getAttrValue("gene_name=");
if (gene_name==NULL) {
gene_name=getAttrValue("geneName=");
if (gene_name==NULL) {
gene_name=getAttrValue("gene_sym=");
if (gene_name==NULL) {
gene_name=getAttrValue("gene=");
}
}
}
gene_id=getAttrValue("geneID=");
if (gene_id==NULL) {
gene_id=getAttrValue("gene_id=");
}
//--parse exons for TLF
char* segstr=extractAttr("exons=");
bool exons_valid=false;
if (segstr) {
exons_valid=parseSegmentList(exons, segstr);
char* exoncountstr=extractAttr("exonCount=");
if (exoncountstr) {
int exoncount=0;
if (!strToInt(exoncountstr, exoncount) || exoncount!=(int)exons.Count())
GMessage("Warning: exonCount attribute value doesn't match the exons attribute!\n");
GFREE(exoncountstr);
}
GFREE(segstr);
}
if (exons_valid) {
bool validCDS=false;
segstr=extractAttr("CDS=");
if (segstr) {
char* p=strchr(segstr, ':');
if (p!=NULL) { // CDS=start:end format
*p='\0'; ++p;
validCDS=true;
if (validCDS && strToUInt(segstr, cds_start) && cds_start>=fstart) {
if (!strToUInt(p, cds_end) || cds_end>fend) {
validCDS=false;
}
}
if (!validCDS || (int)cds_start<=0 || (int)cds_end<=0) {
GMessage("Warning: invalid CDS (%d-%d) discarded for line:\n%s\n",
cds_start, cds_end, dupline);
cds_start=0;
cds_end=0;
}
} //CDS=start:end format
else { //CDS = list of start-end segments, just like the exons
validCDS=parseSegmentList(cdss, segstr);
if (validCDS && cdss.Count()>0) {
if (cds_start==0) cds_start=cdss.First().start;
if (cds_end==0) cds_end=cdss.Last().end;
}
}
GFREE(segstr);
}
if (validCDS) {
char* cds_phase=NULL;
if ((cds_phase=extractAttr("CDSphase="))!=NULL) {
phase=cds_phase[0];
GFREE(cds_phase);
}
} //CDS found
}//has valid exons
}// has GFF3 ID
if (Parent!=NULL) {
//keep Parent attr
//parse multiple parents
num_parents=1;
p=Parent;
int last_delim_pos=-1;
while (*p!=';' && *p!=0) {
if (*p==',' && *(p+1)!=0 && *(p+1)!=';') {
num_parents++;
last_delim_pos=(p-Parent);
}
p++;
}
_parents_len=p-Parent+1;
_parents=Parent;
GMALLOC(parents, num_parents*sizeof(char*));
parents[0]=_parents;
int i=1;
if (last_delim_pos>0) {
for (p=_parents+1;p<=_parents+last_delim_pos;p++) {
if (*p==',') {
char* ep=p-1;
while (*ep==' ' && ep>_parents) ep--;
*(ep+1)=0; //end the string there
parents[i]=p+1;
i++;
}
}
}
} //has Parent field
//special case for gene_id: for genes, this is the ID
if (gene_id==NULL) {
if (is_gene) {
if (ID!=NULL) gene_id=Gstrdup(ID);
} else if (is_transcript) {
if (Parent!=NULL) gene_id=Gstrdup(Parent);
}
}
} //GFF3
else { // ----------------- GTF syntax ------------------
if (reader->transcripts_Only && !is_t_data) {
return; //alwasys skip unrecognized non-transcript features in GTF
}
if (is_gene) {
reader->gtf_gene=true;
ID = (gtf_tid!=NULL) ? gtf_tid : extractAttr("transcript_id", true, true);
//Ensemble GTF might lack transcript_id !
if (ID!=NULL) {
if (gtf_tid==NULL && reader->procEnsemblID())
ensembl_GTF_ID_process(ID, "transcript_version");
}
gene_id = (gtf_gid!=NULL) ? gtf_gid : extractAttr("gene_id", true, true);
if (gene_id!=NULL && gtf_gid==NULL && reader->procEnsemblID())
ensembl_GTF_ID_process(gene_id, "gene_version");
if (ID==NULL) {
//no transcript_id -- this should not be valid GTF2 format, but Ensembl (Gencode?)
//has being known to add "gene" features with only gene_id in their GTF
if (gene_id!=NULL) { //likely a gene feature line (Ensembl!)
ID=Gstrdup(gene_id); //take over as ID (for defective GTF lacking transcript_id)
}
}
// else if (strcmp(gene_id, ID)==0) //GENCODE v20 gene feature ?
}
else if (is_transcript) {
ID = (gtf_tid!=NULL) ? gtf_tid : extractAttr("transcript_id", true, true);
//gene_id=extractAttr("gene_id"); // for GTF this is the only attribute accepted as geneID
if (ID==NULL) {
//something is wrong here, cannot parse the GTF ID
GMessage("Warning: invalid GTF record, transcript_id not found:\n%s\n", l);
return;
} else if (gtf_tid==NULL && reader->procEnsemblID())
ensembl_GTF_ID_process(ID, "transcript_version");
gene_id = (gtf_gid!=NULL) ? gtf_gid : extractAttr("gene_id", true, true);
if (gene_id!=NULL) {
if (gtf_gid==NULL && reader->procEnsemblID())
ensembl_GTF_ID_process(gene_id, "gene_version");
Parent=Gstrdup(gene_id);
}
reader->gtf_transcript=true;
is_gtf_transcript=1;
} else { //must be an exon type ?
Parent = (gtf_tid!=NULL) ? gtf_tid : extractAttr("transcript_id", true, true);
if (Parent!=NULL && gtf_tid==NULL && reader->procEnsemblID())
ensembl_GTF_ID_process(Parent, "transcript_version");
gene_id = (gtf_gid!=NULL) ? gtf_gid : extractAttr("gene_id", true, true); // for GTF this is the only attribute accepted as geneID
if (gene_id!=NULL && gtf_gid==NULL && reader->procEnsemblID())
ensembl_GTF_ID_process(gene_id, "gene_version");
//old pre-GTF2 formats like Jigsaw's (legacy support)
if (Parent==NULL && exontype==exgffExon) {
if (startsWith(track,"jigsaw")) {
is_cds=true;
strcpy(track,"jigsaw");
p=strchr(info,';');
if (p==NULL) { Parent=Gstrdup(info); info=NULL; }
else { Parent=Gstrdup(info,p-1);
info=p+1;
}
}
}
if (Parent==NULL) {
//something is wrong here couldn't parse the transcript ID for this feature
GMessage("Warning: invalid GTF record, transcript_id not found:\n%s\n", l);
return;
}
}
//more GTF attribute parsing
if (is_gene && gene_id==NULL && ID!=NULL)
gene_id=Gstrdup(ID);
gene_name=getAttrValue("gene_name");
if (gene_name==NULL) {
gene_name=getAttrValue("gene_sym");
if (gene_name==NULL) {
gene_name=getAttrValue("gene");
if (gene_name==NULL)
gene_name=getAttrValue("genesymbol");
}
}
//*** IMPORTANT: prepare GTF for easy parseAttr by adding '=' character after the attribute name
// for ALL attributes
p=info;
bool noed=true; //not edited after the last delim
bool nsp=false; //non-space found after last delim
while (*p!=0) {
if (*p==' ') {
if (nsp && noed) {
*p='=';
noed=false;
p++;
continue;
}
}
else nsp=true; //non-space
if (*p==';') { noed=true; nsp=false; }
p++;
}
//-- GTF prepare parents[] if Parent found
if (Parent!=NULL) { //GTF transcript_id found as a parent
_parents=Parent;
num_parents=1;
_parents_len=strlen(Parent)+1;
GMALLOC(parents, sizeof(char*));
parents[0]=_parents;
}
} //GTF
if (ID==NULL && parents==NULL) {
if (gffWarnings)
GMessage("Warning: discarding unrecognized feature (no ID or Parent):\n%s\n",dupline);
return; //skip
}
skipLine=false;
}
//FIXME - this should only be used AFTER finalize() was called, and must have cdss=NULL of course
void GffObj::setCDS(uint cd_start, uint cd_end, char phase) {
if (cd_start<this->start) {
GMessage("Warning: setCDS() called for %s with an out of bounds CDS start %d!\n",
gffID, cd_start);
return;
}
if (cd_end>this->end) {
GMessage("Warning: setCDS() called for %s with an out of bounds CDS end %d!\n",
gffID, cd_end);
return;
}
this->CDstart=cd_start;
this->CDend=cd_end;
this->CDphase=phase;
isTranscript(true);
subftype_id=gff_fid_exon;
if (monoFeature()) {
if (exons.Count()==0) addExon(this->start, this->end, exgffExon);
else exons[0]->exontype=exgffExon;
}
}
void GffObj::setCDS(GffObj* t) {
//copy the cdss as well
uint cd_start=t->CDstart;
uint cd_end=t->CDend;
uint phase=t->CDphase;
if (cd_start<this->start) {
GMessage("Warning: setCDS() called for %s with an out of bounds CDS start %d!\n",
gffID, cd_start);
return;
}
if (cd_end>this->end) {
GMessage("Warning: setCDS() called for %s with an out of bounds CDS end %d!\n",
gffID, cd_end);
return;
}
this->CDstart=cd_start;
this->CDend=cd_end;
this->CDphase=phase;
isTranscript(true);
subftype_id=gff_fid_exon;
if (monoFeature()) {
if (exons.Count()==0) addExon(this->start, this->end, exgffExon);
else exons[0]->exontype=exgffExon;
}
if (t->cdss!=NULL) {
if (this->cdss!=NULL) delete cdss;
cdss=new GList<GffExon>(true, true, false);
for (int i=0;i<t->cdss->Count();i++) {
cdss->Add(new GffExon(*(t->cdss->Get(i))));
}
}
}
int GffObj::readExon(GffReader& reader, GffLine& gl) {
// -- this should only be called before ::finalize()!
//should make sure to get the right subftype_id!
if (!isTranscript() && gl.exontype>exgffNone) {
//subfeature recognized as exon-like, so this should be considered a transcript!
isTranscript(true);
}
if (isTranscript()) {
if (subftype_id<0) {//exon_ftype_id=gff_fid_exon;
if (gl.exontype>exgffNone) subftype_id=gff_fid_exon;
else subftype_id=names->feats.addName(gl.ftype);
}
//any recognized exon-like segment gets the generic "exon" type (also applies to CDS)
if (gl.exontype==exgffNone && !gl.is_transcript) {
//extraneous mRNA feature, discard
if (reader.gff_warns)
GMessage("Warning: discarding unrecognized transcript subfeature '%s' of %s\n",
gl.ftype, gffID);
return -1;
}
}
else { //non-mRNA parent feature, check this subf type
int subf_id=names->feats.addName(gl.ftype);
if (subftype_id<0 || exons.Count()==0) //never assigned a subfeature type before (e.g. first exon being added)
subftype_id=subf_id;
else {
if (subftype_id!=subf_id) {
if (subftype_id==ftype_id && exons.Count()==1 && exons[0]->start==start && exons[0]->end==end) {
//the existing exon was just a dummy one created by default, discard it?
exons.Clear();
covlen=0;
subftype_id=subf_id; //allow the new subfeature to completely takeover
}
else { //multiple subfeatures, prefer those exon-like
if (reader.gff_warns)
GMessage("Warning: multiple subfeatures (%s and %s) found for %s, discarding ",
names->feats.getName(subf_id), names->feats.getName(subftype_id),gffID);
if (gl.exontype>exgffNone) { //new feature is an exon, discard previously parsed subfeatures
if (reader.gff_warns) GMessage("%s.\n", names->feats.getName(subftype_id));
subftype_id=subf_id;
exons.Clear();
covlen=0;
}
else { //discard new feature
if (reader.gff_warns) GMessage("Warning: skipping subfeature %s.\n", names->feats.getName(subf_id));
return -1; //skip this 2nd subfeature type for this parent!
}
}
} //incoming subfeature is of different type
} //new subfeature type
} //non-mRNA parent
int eidx=-1;
GList<GffExon>* segs=NULL; //either cds or &exons
if (gl.is_cds) {
if (cdss==NULL)
cdss=new GList<GffExon>(true, true, false);
segs=cdss;
} else {
segs=&exons;
}
eidx=addExon(*segs, gl);
if (eidx<0) {
GMessage("Warning: addExon() failed for GFF line:\n%s\n",gl.dupline);
return eidx; //this should never happen!
}
if (reader.keep_Attrs) {
if (reader.noExonAttrs) {
parseAttrs(attrs, gl.info, true);
}
else { //need all exon-level attributes
parseAttrs((*segs)[eidx]->attrs, gl.info, true, gl.is_cds);
}
}
return eidx;
}
int GffObj::addExon(GList<GffExon>& segs, GffLine& gl, int8_t exontype_override) {
int ex_type=(exontype_override!=exgffNone) ? exontype_override : gl.exontype;
GffScore exon_score(gl.score, gl.score_decimals);
int eidx=addExon(gl.fstart, gl.fend, ex_type, gl.phase, exon_score, &segs);
if (&segs==cdss && isGene() && gl.ID!=NULL && eidx>=0) {
//special NCBI cases where CDS can be treated as discontiguous features, grouped by their ID
//-- used for genes with X_gene_segment features
//char* cds_id=Gstrdup(gl.ID);
//segs[eidx]->uptr=cds_id;
segs[eidx]->uptr=gl.ID;
gl.ID=NULL;
}
return eidx;
}
int GffObj::exonOverlapIdx(GList<GffExon>& segs, uint s, uint e, int* ovlen, int start_idx) {
//return the exons' index for the overlapping OR ADJACENT exon
//ovlen, if given, will return the overlap length
//if (s>e) Gswap(s,e);
for (int i=start_idx;i<segs.Count();i++) {
if (segs[i]->start>e+1) break;
if (s-1>segs[i]->end) continue;
//-- overlap/adjacent if we are here:
if (ovlen!=NULL) {
int ovlend= (segs[i]->end>e) ? e : segs[i]->end;
*ovlen= ovlend - ((s>segs[i]->start)? s : segs[i]->start)+1;
}
return i;
} //for each exon
*ovlen=0;
return -1;
}
void GffObj::transferCDS(GffExon* cds) {
//direct adding of a cds to the cdss pointer, without checking
if (cdss==NULL) cdss=new GList<GffExon>(true, true, false);
cdss->Add(cds); //now the caller must forget this exon!
if (CDstart==0 || CDstart>cds->start) CDstart=cds->start;
}
int GffObj::addExon(uint segstart, uint segend, int8_t exontype, char phase, GffScore exon_score, GList<GffExon>* segs) {
if (segstart>segend) { Gswap(segstart, segend); }
if (segs==NULL) segs=&exons;
if (exontype!=exgffNone) { //check for overlaps between exon/CDS-type segments
//addExonSegment(gl.fstart, gl.fend, gl.score, gl.phase, gl.is_cds, exontype_override);
int ovlen=0;
int oi=-1;
while ((oi=exonOverlapIdx(*segs, segstart, segend, &ovlen, oi+1))>=0) {
//note: ovlen==0 for adjacent segments
if ((*segs)[oi]->exontype>exgffNone &&
(*segs)[oi]->start<=segstart && (*segs)[oi]->end>=segend) {
//existing feature contains this segment, so we do NOT need to add it
//-- unless its the annoying NCBI exception: gene with multiple alternate
// _gene_segment CDS features!
if (!(this->isGene() && exontype==exgffCDS &&
(*segs)[oi]->exontype==exgffCDS ))
return oi;
}