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gff_utils.cpp
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gff_utils.cpp
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#include "gff_utils.h"
GHash<GeneInfo*> gene_ids;
bool verbose=false; //same with GffReader::showWarnings and GffLoader::beVserbose
bool debugMode=false;
bool ensembl_convert=false; //-L, assist in converting Ensembl GTF to GFF3
FILE* ffasta=NULL;
FILE* f_in=NULL;
FILE* f_out=NULL;
FILE* f_w=NULL; //writing fasta with spliced exons (transcripts)
FILE* f_u=NULL;
int wPadding = 0; //padding for -w option
FILE* f_x=NULL; //writing fasta with spliced CDS
FILE* f_y=NULL; //wrting fasta with translated CDS
FILE* f_j=NULL; //wrting junctions (intron coordinates)
int maxintron=999000000;
ID_Flt_Type IDflt=idFlt_None;
bool TFilters=false;
bool wCDSonly=false;
bool wNConly=false;
int minLen=0; //minimum transcript length
bool validCDSonly=false; // translation with no in-frame STOP
bool bothStrands=false; //for single-exon mRNA validation, check the other strand too
bool altPhases=false; //if original phase fails translation validation,
//try the other 2 phases until one makes it
bool addCDSattrs=false;
bool add_hasCDS=false;
//bool streamIn=false; // --stream option
bool adjustStop=false; //automatic adjust the CDS stop coordinate
bool covInfo=false; // --cov-info : only report genome coverage
GStr tableFormat; //list of "attributes" to print in tab delimited format
bool spliceCheck=false; //only known splice-sites
bool decodeChars=false; //decode url-encoded chars in attrs (-D)
bool StarStop=false; //use * instead of . for stop codon translation
bool fullCDSonly=false; // starts with START, ends with STOP codon
bool multiExon=false;
bool writeExonSegs=false;
char* tracklabel=NULL;
/*
char* rfltGSeq=NULL;
char rfltStrand=0;
uint rfltStart=0;
uint rfltEnd=MAX_UINT;*/
GRangeParser* fltRange=NULL;
GRangeParser* fltJunction=NULL;
bool rfltWithin=false; //check for full containment within given range
bool addDescr=false;
bool wfaNoCDS=false;
bool fmtGFF3=true; //default output: GFF3
//other formats only make sense in transcriptOnly mode
bool fmtGTF=false;
bool fmtBED=false;
bool fmtTLF=false;
bool fmtTable=false;
GffPrintMode exonPrinting=pgffAny;
GFastaDb gfasta;
GHash<SeqInfo*> seqinfo;
GVec<CTableField> tableCols;
GHash<RefTran*> reftbl;
GStrSet<> fltIDs;
GStrSet<> attrList;
GHash<int> isoCounter; //counts the valid isoforms
void printFasta(FILE* f, GStr* defline, const char* seq, int seqlen, bool useStar) {
//if seqlen is provided >0, seq does not have to be 0-terminated
if (seq==NULL) return;
int len=(seqlen>0)?seqlen:strlen(seq);
if (len<=0) return;
if (defline!=NULL)
fprintf(f, ">%s\n",defline->chars());
int ilen=0;
for (int i=0; i < len; i++, ilen++) {
if (ilen == 70) {
fputc('\n', f);
ilen = 0;
}
if (useStar && seq[i]=='.')
putc('*', f);
else putc(seq[i], f);
} //for
fputc('\n', f);
}
int qsearch_gloci(uint x, GList<GffLocus>& loci) {
//binary search
//do the simplest tests first:
if (loci[0]->start>x) return 0;
if (loci.Last()->start<x) return -1;
uint istart=0;
int i=0;
int idx=-1;
int maxh=loci.Count()-1;
int l=0;
int h = maxh;
while (l <= h) {
i = (l+h)>>1;
istart=loci[i]->start;
if (istart < x) l = i + 1;
else {
if (istart == x) { //found matching coordinate here
idx=i;
while (idx<=maxh && loci[idx]->start==x) {
idx++;
}
return (idx>maxh) ? -1 : idx;
}
h = i - 1;
}
} //while
idx = l;
while (idx<=maxh && loci[idx]->start<=x) {
idx++;
}
return (idx>maxh) ? -1 : idx;
}
int qsearch_rnas(uint x, GList<GffObj>& rnas) {
//binary search
//do the simplest tests first:
if (rnas[0]->start>x) return 0;
if (rnas.Last()->start<x) return -1;
uint istart=0;
int i=0;
int idx=-1;
int maxh=rnas.Count()-1;
int l=0;
int h = maxh;
while (l <= h) {
i = (l+h)>>1;
istart=rnas[i]->start;
if (istart < x) l = i + 1;
else {
if (istart == x) { //found matching coordinate here
idx=i;
while (idx<=maxh && rnas[idx]->start==x) {
idx++;
}
return (idx>maxh) ? -1 : idx;
}
h = i - 1;
}
} //while
idx = l;
while (idx<=maxh && rnas[idx]->start<=x) {
idx++;
}
return (idx>maxh) ? -1 : idx;
}
int cmpRedundant(GffObj& a, GffObj& b) {
if (a.exons.Count()==b.exons.Count()) {
if (a.covlen==b.covlen) {
return strcmp(a.getID(), b.getID());
}
else return (a.covlen>b.covlen)? 1 : -1;
}
else return (a.exons.Count()>b.exons.Count())? 1: -1;
}
bool tMatch(GffObj& a, GffObj& b) {
//strict intron chain match, or single-exon perfect match
int imax=a.exons.Count()-1;
int jmax=b.exons.Count()-1;
int ovlen=0;
if (imax!=jmax) return false; //different number of introns
if (imax==0) { //single-exon mRNAs
//if (equnspl) {
//fuzz match for single-exon transfrags:
// it's a match if they overlap at least 80% of max len
ovlen=a.exons[0]->overlapLen(b.exons[0]);
int maxlen=GMAX(a.covlen,b.covlen);
return (ovlen>=maxlen*0.8);
/*}
else {
//only exact match
ovlen=a.covlen;
return (a.exons[0]->start==b.exons[0]->start &&
a.exons[0]->end==b.exons[0]->end);
}*/
}
//check intron overlaps
ovlen=a.exons[0]->end-(GMAX(a.start,b.start))+1;
ovlen+=(GMIN(a.end,b.end))-a.exons.Last()->start;
for (int i=1;i<=imax;i++) {
if (i<imax) ovlen+=a.exons[i]->len();
if ((a.exons[i-1]->end!=b.exons[i-1]->end) ||
(a.exons[i]->start!=b.exons[i]->start)) {
return false; //intron mismatch
}
}
return true;
}
char* getSeqDescr(char* seqid) {
static char charbuf[128];
if (seqinfo.Count()==0) return NULL;
char* suf=rstrchr(seqid, '.');
if (suf!=NULL) *suf=0;
SeqInfo* seqd=seqinfo.Find(seqid);
if (suf!=NULL) *suf='.';
if (seqd!=NULL) {
GStr s(seqd->descr);
//cleanup some Uniref gunk
if (s[0]=='[') {
int r=s.index(']');
if (r>=0 && r<8 && isdigit(s[1]))
s.remove(0,r+1);
}
if (s.length()>80) {
int r=s.index(';');
if (r>5) s.cut(r);
}
if (s.length()>127) {
s.cut(127);
int r=s.rindex(' ');
if (r>0) s.cut(r);
}
strcpy(charbuf, s.chars());
return charbuf;
}
else return NULL;
}
char* getSeqName(char* seqid) {
static char charbuf[128];
char* suf=rstrchr(seqid, '.');
if (suf!=NULL) *suf=0;
strcpy(charbuf, seqid);
if (suf!=NULL) *suf='.';
return charbuf;
}
int adjust_stopcodon(GffObj& gffrec, int adj, GList<GSeg>* seglst) {
//adj>0, extend CDS to include a potential stop codon
//when CDS is expanded, the terminal exon might have to be adjusted too
int realadj=0;
if (gffrec.strand=='-') {
if ((int)gffrec.CDstart>adj) {
gffrec.CDstart-=adj;
realadj=adj;
if (gffrec.exons.First()->start>gffrec.CDstart) {
gffrec.covlen+=gffrec.exons.First()->start - gffrec.CDstart;
gffrec.exons.First()->start=gffrec.CDstart;
gffrec.start=gffrec.CDstart;
}
}
}
else { // forward strand
//expand beyond
realadj=adj;
gffrec.CDend+=adj;
if (adj<0) {//restore
if (gffrec.exons.Last()->end==gffrec.CDend-adj) {
gffrec.exons.Last()->end+=adj;
gffrec.end=gffrec.exons.Last()->end;
gffrec.covlen+=adj;
}
}
else if (gffrec.exons.Last()->end<gffrec.CDend) {
gffrec.covlen+=gffrec.CDend-gffrec.exons.Last()->end;
gffrec.exons.Last()->end=gffrec.CDend;
gffrec.end=gffrec.CDend;
}
}
if (seglst!=NULL) seglst->Last()->end+=realadj;
return realadj;
}
void printTableData(FILE* f, GffObj& g, bool inFasta) {
//using attribute list in tableCols
const int DBUF_LEN=1024; //there should not be attribute values larger than 1K!
char dbuf[DBUF_LEN];
char* av=NULL;
for(int i=0;i<tableCols.Count();i++) {
if (i>0 || inFasta) {
if (!inFasta || tableCols[i].type!=ctfGFF_ID)
fprintf(f,"\t");
}
switch(tableCols[i].type) {
case ctfGFF_Attr:
av=g.getAttr(tableCols[i].name.chars());
if (av) {
if (decodeChars) {
GffObj::decodeHexChars(dbuf, av, DBUF_LEN-1);
fprintf(f,"%s", dbuf);
} else fprintf(f,"%s",av);
} else fprintf(f,".");
break;
case ctfGFF_chr:
fprintf(f,"%s",g.getGSeqName());
break;
case ctfGFF_track:
fprintf(f,"%s",g.getTrackName());
break;
case ctfGFF_ID:
if (!inFasta)
fprintf(f,"%s",g.getID());
break;
case ctfGFF_geneID:
fprintf(f,"%s",g.getGeneID()!=NULL ? g.getGeneID() : ".");
break;
case ctfGFF_geneName:
fprintf(f,"%s",g.getGeneName()!=NULL ? g.getGeneName() : ".");
break;
case ctfGFF_Parent:
fprintf(f,"%s",g.parent!=NULL ? g.parent->getID() : ".");
break;
case ctfGFF_feature:
fprintf(f,"%s",g.getFeatureName());
break;
case ctfGFF_start:
fprintf(f,"%d",g.start);
break;
case ctfGFF_end:
fprintf(f,"%d",g.end);
break;
case ctfGFF_strand:
fprintf(f,"%c",g.strand);
break;
case ctfGFF_numexons:
fprintf(f,"%d",g.exons.Count());
break;
case ctfGFF_exons:
if (g.exons.Count()>0) {
for (int x=0;x<g.exons.Count();x++) {
if (x>0) fprintf(f,",");
fprintf(f,"%d-%d",g.exons[x]->start, g.exons[x]->end);
}
} else fprintf(f,".");
break;
case ctfGFF_introns:
if (g.exons.Count()>1) {
for (int i=0;i<g.exons.Count()-1;i++) {
if (i>0) fprintf(f,",");
fprintf(f,"%d-%d",g.exons[i]->end+1, g.exons[i+1]->start-1);
}
} else fprintf(f,".");
break;
case ctfGFF_cds:
if (g.hasCDS()) {
GVec<GffExon> cds;
g.getCDSegs(cds);
for (int x=0;x<cds.Count();x++) {
if (x>0) fprintf(f,",");
fprintf(f,"%d-%d",cds[x].start, cds[x].end);
}
}
else fprintf(f,".");
break;
case ctfGFF_covlen:
fprintf(f, "%d", g.covlen);
break;
case ctfGFF_cdslen:
if (g.hasCDS()) {
GVec<GffExon> cds;
g.getCDSegs(cds);
int clen=0;
for (int x=0;x<cds.Count();x++)
clen+=cds[x].end-cds[x].start+1;
fprintf(f, "%d", clen);
}
else fprintf(f, "0");
break;
} //switch
}
fprintf(f,"\n");
}
bool GffLoader::validateGffRec(GffObj* gffrec) {
if (!checkFilters(gffrec)) {
if (gffrec->isTranscript()) {
TFilters=true;
if (gffrec->parent!=NULL && keepGenes) {
GPVec<GffObj>& pchildren=gffrec->parent->children;
for (int c=0;c<pchildren.Count();c++) {
if (pchildren[c]==gffrec) {
pchildren.Delete(c);
break;
}
}
}
return false;
}
if (gffrec->isGene() && keepGenes) return true;
return false;
} //transcript rejected
return true;
}
bool GffLoader::checkFilters(GffObj* gffrec) {
if (reftbl.Count()>0) { //check if we need to reject by ref seq filter
GStr refname(gffrec->getRefName());
RefTran* rt=reftbl.Find(refname.chars());
if (rt==NULL && refname.length()>2 && refname[-2]=='.' && isdigit(refname[-1])) {
//try removing the version suffix
refname.cut(-2);
//GMessage("[DEBUG] Trying ref name '%s'...\n", refname.chars());
rt=reftbl.Find(refname.chars());
}
if (rt) {
gffrec->setRefName(rt->new_name);
}
/* //no, do not discard non-matching entries, let them pass through!
else {
if (verbose)
GMessage("Info: %s discarded due to reference %s not being mapped\n",
gffrec->getID(), refname.chars());
return false; //discard, ref seq not in the given translation table
}*/
}
if (transcriptsOnly && gffrec->isDiscarded()) {
//discard generic "locus" features with no other detailed subfeatures
//GMessage("Warning: discarding %s GFF generic gene/locus container %s\n",gffrec->getID());
return false;
}
if (IDflt) {
if (fltIDs.hasKey(gffrec->getID())) {
if (IDflt==idFlt_Exclude) return false;
}
else if (IDflt==idFlt_Only) return false;
}
if (minLen>0 && gffrec->covlen<minLen) {
if (verbose)
GMessage("Info: %s discarded due to minimum length threshold %d\n",
gffrec->getID(), minLen);
return false;
}
if (fltRange!=NULL) { //filter by gseqName
if (fltRange->refName!=NULL && strcmp(gffrec->getGSeqName(),fltRange->refName)!=0) {
return false;
}
if (fltRange->strand>0 && gffrec->strand!=fltRange->strand) {
return false;
}
//check coordinates
if (fltRange->start || fltRange->end<UINT_MAX) {
if (rfltWithin) {
if (gffrec->start<fltRange->start || gffrec->end>fltRange->end) {
return false; //not within query range
}
}
else {
if (gffrec->start>fltRange->end || gffrec->end<fltRange->start) {
return false;
}
}
}
}
if (this->attrsFilter) { //mostly relevant for transcripts and gene records
//remove attributes that are not in attrList
gffrec->removeAttrs(attrList);
}
if (gffrec->isTranscript()) { // && TFilters) ?
//these filters only apply to transcripts
if (multiExon && gffrec->exons.Count()<=1) {
return false;
}
if (wCDSonly && gffrec->CDstart==0) {
return false;
}
if (wNConly && gffrec->hasCDS()) return false;
if (fltJunction!=NULL) {
if (gffrec->exons.Count()<=1) return false;
if (fltJunction->refName!=NULL && strcmp(gffrec->getGSeqName(),fltJunction->refName)!=0) {
return false;
}
if (fltJunction->strand && gffrec->strand!=fltJunction->strand) {
return false;
}
//check coordinates
uint jstart=fltJunction->start;
uint jend=fltJunction->end;
if (jstart==0) jstart=jend;
if (jend==0) jend=jstart;
if (gffrec->start>=jstart || gffrec->end<=jend) {
return false;
}
bool noJMatch=true;
for (int i=0;i<gffrec->exons.Count()-1;++i) {
if (fltJunction->start && fltJunction->end) {
if (gffrec->exons[i]->end+1==fltJunction->start &&
gffrec->exons[i+1]->start-1==fltJunction->end)
{ noJMatch=false; break; }
} else if (fltJunction->start) { //end match not required
if (gffrec->exons[i]->end+1==fltJunction->start)
{ noJMatch=false; break; }
} else { //only end match required:
if (gffrec->exons[i+1]->start-1==fltJunction->end)
{ noJMatch=false; break; }
}
}
if (noJMatch) return false;
}
return process_transcript(gfasta, *gffrec);
} //transcript filters check
return true;
}
bool GffLoader::process_transcript(GFastaDb& gfasta, GffObj& gffrec) {
if (!gffrec.isTranscript()) return false; //shouldn't call this function unless it's a transcript
//returns true if the transcript passed the filter
char* gname=gffrec.getGeneName();
if (gname==NULL) gname=gffrec.getGeneID();
if (ensembl_convert && startsWith(gffrec.getID(), "ENS")) {
const char* biotype=gffrec.getAttr("gene_biotype");
if (biotype) {
gffrec.addAttr("type", biotype);
gffrec.removeAttr("gene_biotype");
}
else { //old Ensembl files lacking gene_biotype
gffrec.addAttr("type", gffrec.getTrackName());
}
//bool is_gene=false;
bool is_pseudo=false;
if (strcmp(biotype, "protein_coding")==0 || gffrec.hasCDS())
gffrec.setFeatureName("mRNA");
else {
if (strcmp(biotype, "processed_transcript")==0)
gffrec.setFeatureName("proc_RNA");
else {
//is_gene=endsWith(biotype, "gene");
is_pseudo=strifind(biotype, "pseudo");
if (is_pseudo) {
gffrec.setFeatureName("pseudo_RNA");
}
else if (endsWith(biotype, "RNA")) {
gffrec.setFeatureName(biotype);
} else gffrec.setFeatureName("misc_RNA");
}
}
}
if (gname && strcmp(gname, gffrec.getID())!=0) {
int* isonum=isoCounter.Find(gname);
if (isonum==NULL) {
//isonum=new int(1);
isoCounter.Add(gname,1);
}
else (*isonum)++;
//defline.appendfmt(" gene=%s", gname);
}
int seqlen=0;
const char* tlabel=tracklabel;
if (tlabel==NULL) tlabel=gffrec.getTrackName();
//defline.appendfmt(" track:%s",tlabel);
char* cdsnt = NULL;
char* cdsaa = NULL;
int aalen=0;
for (int i=1;i<gffrec.exons.Count();i++) {
int ilen=gffrec.exons[i]->start-gffrec.exons[i-1]->end-1;
if (verbose && ilen>4000000)
GMessage("Warning: very large intron (%d) for transcript %s\n",
ilen, gffrec.getID());
if (ilen>maxintron) {
return false;
}
}
GMapSegments seglst(gffrec.strand);
GFaSeqGet* faseq=NULL;
if (f_x!=NULL || f_y!=NULL || f_w!=NULL || f_u!=NULL || spliceCheck || validCDSonly || addCDSattrs) {
faseq=fastaSeqGet(gfasta, gffrec.getGSeqName());
if (faseq==NULL)
GError("Error: no genomic sequence available (check -g option!).\n");
}
if (spliceCheck && gffrec.exons.Count()>1) {
//check introns for splice site consensi ( GT-AG, GC-AG or AT-AC )
int glen=gffrec.end-gffrec.start+1;
const char* gseq=faseq->subseq(gffrec.start, glen);
if (gseq==NULL) {
GMessage("Error at GFF ID %s : could not retrieve subsequence %s:%d-%d !\n",
gffrec.getID(), gffrec.getRefName(), gffrec.start, gffrec.end);
return false;
}
bool revcompl=(gffrec.strand=='-');
bool ssValid=true;
for (int e=1;e<gffrec.exons.Count();e++) {
const char* intron=gseq+gffrec.exons[e-1]->end+1-gffrec.start;
int intronlen=gffrec.exons[e]->start-gffrec.exons[e-1]->end-1;
GSpliceSite acceptorSite(intron,intronlen,true, revcompl);
GSpliceSite donorSite(intron,intronlen, false, revcompl);
//GMessage("%c intron %d-%d : %s .. %s\n",
// gffrec.strand, istart, iend, donorSite.nt, acceptorSite.nt);
if (acceptorSite=="AG") { // GT-AG or GC-AG
if (!donorSite.canonicalDonor()) {
ssValid=false;break;
}
}
else if (acceptorSite=="AC") { //AT-AC also accepted
if (donorSite!="AT") { ssValid=false; break; }
}
else { ssValid=false; break; }
}
if (!ssValid) {
if (verbose)
GMessage("Unrecognized splice sites found for '%s'\n",gffrec.getID());
return false; //don't print this one!
}
}
bool trprint=true;
bool inframeStop=false;
//int stopCodonAdjust=0;
int mCDphase=0;
bool fullCDS=false;
bool endStop=false;
bool stopAdjusted=false;
if (add_hasCDS && gffrec.hasCDS()) gffrec.addAttr("hasCDS", "true");
if (gffrec.CDphase=='1' || gffrec.CDphase=='2')
mCDphase = gffrec.CDphase-'0';
//CDS partialness only added when -y -x -V options are given
if (gffrec.hasCDS() && (f_y!=NULL || f_x!=NULL || validCDSonly || addCDSattrs)) {
int strandNum=0;
int phaseNum=0;
CDS_CHECK:
uint cds_olen=0;
inframeStop=false;
cdsnt=gffrec.getSpliced(faseq, true, &seqlen, NULL, &cds_olen, &seglst, adjustStop);
//if adjustStop, seqlen has the CDS+3'UTR length, but cds_olen still has the original CDS length
if (cdsnt!=NULL && cdsnt[0]!='\0') { //has CDS
cdsaa=translateDNA(cdsnt, aalen, seqlen);
char* p=strchr(cdsaa,'.');
int cds_aalen=aalen;
if (adjustStop)
cds_aalen=cds_olen/3; //originally stated CDS length
endStop=false;
if (p!=NULL) { //stop codon found
if (p-cdsaa==cds_aalen-1) { //stop found as the stated last CDS codon
*p='\0';//remove it
endStop=true;
if (adjustStop) {
seqlen=cds_aalen*3;
aalen=cds_aalen;
}
cds_aalen--;
aalen--;
//no need to adjust stop codon
}
else {//stop found in a different position than the last codon
if (p-cdsaa<cds_aalen-1 && !adjustStop) {
inframeStop=true;
}
if (adjustStop) {
*p='\0';
cds_aalen=p-cdsaa+1; //adjusted CDS length
seqlen=cds_aalen*3;
aalen=cds_aalen;
uint gc=seglst.gmap(seqlen);
if (gffrec.strand=='-') gffrec.CDstart=gc;
else gffrec.CDend=gc;
endStop=true;
stopAdjusted=true;
}
}
}//stop codon found
//if (trprint==false) { //failed CDS validity check
if (inframeStop) {
//in-frame stop codon found
if (altPhases && phaseNum<3) {
phaseNum++; //try a different phase
gffrec.CDphase = '0'+((mCDphase+phaseNum)%3);
GFREE(cdsaa);
goto CDS_CHECK;
}
if (gffrec.exons.Count()==1 && bothStrands) {
strandNum++;
phaseNum=0;
if (strandNum<2) {
GFREE(cdsaa);
gffrec.strand = (gffrec.strand=='-') ? '+':'-';
goto CDS_CHECK; //repeat the CDS check for a different frame
}
}
if (verbose) GMessage("Warning: In-frame STOP found for '%s'\n",gffrec.getID());
if (addCDSattrs) gffrec.addAttr("InFrameStop", "true");
} //has in-frame STOP
if (stopAdjusted) {
if (addCDSattrs) gffrec.addAttr("CDStopAdjusted", "true");
inframeStop=false; //pretend it's OK now that we've adjusted it
}
if (!inframeStop) {
bool hasStart=(cdsaa[0]=='M'); //for the regular eukaryotic translation table
fullCDS=(endStop && hasStart);
if (!fullCDS) {
const char* partialness=NULL;
if (hasStart) partialness="3";
else {
partialness = endStop ? "5" : "5_3";
}
if (addCDSattrs) gffrec.addAttr("partialness", partialness);
}
}
if (trprint && ((fullCDSonly && !fullCDS) || (validCDSonly && inframeStop)) )
trprint=false;
//} // Valid CDS only requested?
} //has CDS
} //translation or codon check was requested
if (!trprint) {
GFREE(cdsnt);
GFREE(cdsaa);
//if (adjstop!=NULL) delete adjstop;
return false;
}
/*
if (validCDSonly) {
int stopCodonAdjust=adjstop->restore();
if (stopCodonAdjust!=0 && !endStop) {
//restore stop codon location
//adjust_stopcodon(gffrec, -stopCodonAdjust, &seglst);
if (seglst.Count()>0) seglst.Last()->end-=stopCodonAdjust;
if (cdsnt!=NULL && seqlen>0) {
seqlen-=stopCodonAdjust;
cdsnt[seqlen]=0;
}
if (cdsaa!=NULL) aalen--;
}
}
if (adjstop!=NULL) delete adjstop;
*/
if (cdsnt!=NULL) { // && !inframeStop) {
GStr defline(gffrec.getID(), 94);
if (writeExonSegs) {
defline.append(" loc:");
defline.append(gffrec.getGSeqName());
defline.appendfmt("(%c)",gffrec.strand);
//warning: not CDS coordinates are written here, but the exon ones
defline+=(int)gffrec.start;
defline+=(char)'-';
defline+=(int)gffrec.end;
// -- here these are CDS substring coordinates on the spliced sequence:
defline.append(" segs:");
for (int i=0;i<seglst.Count();i++) {
if (i>0) defline.append(",");
defline+=(int)seglst[i].start;
defline.append("-");
defline+=(int)seglst[i].end;
}
}
if (f_y!=NULL) { //CDS translation fasta output requested
if (cdsaa==NULL) { //translate now if not done before
cdsaa=translateDNA(cdsnt, aalen, seqlen);
}
if (aalen>0) {
if (cdsaa[aalen-1]=='.' || cdsaa[aalen-1]=='\0') --aalen; //avoid printing the stop codon
fprintf(f_y, ">%s", defline.chars());
if (fmtTable) printTableData(f_y, gffrec, true);
else {
if (gffrec.attrs!=NULL && gffrec.attrs->Count()>0) fprintf(f_y," ");
gffrec.printAttrs(f_y, ";", false, decodeChars, false);
fprintf(f_y, "\n");
}
printFasta(f_y, NULL, cdsaa, aalen, StarStop);
}
}
if (f_x!=NULL) { //CDS only
fprintf(f_x, ">%s", defline.chars());
if (fmtTable) printTableData(f_x, gffrec, true);
else {
if (gffrec.attrs!=NULL && gffrec.attrs->Count()>0) fprintf(f_x," ");
gffrec.printAttrs(f_x, ";", false, decodeChars, false);
fprintf(f_x, "\n");
}
printFasta(f_x, NULL, cdsnt, seqlen);
}
GFREE(cdsnt);
GFREE(cdsaa);
} //writing CDS or its translation
if (f_w!=NULL) { //write spliced exons
uint cds_start=0;
uint cds_end=0;
seglst.Clear();
int padLeft=0;
int padRight=0;
if (wPadding>0) {
padLeft= (gffrec.start>(uint)wPadding) ? wPadding : gffrec.start - 1;
int ediff=faseq->getseqlen()-gffrec.end;
padRight=(wPadding>ediff) ? ediff : wPadding;
gffrec.addPadding(padLeft, padRight);
}
char* exont=gffrec.getSpliced(faseq, false, &seqlen, &cds_start, &cds_end, &seglst);
//restore exons to normal (remove padding)
if (wPadding>0)
gffrec.removePadding(padLeft, padRight);
GStr defline(gffrec.getID());
if (exont!=NULL) {
if (!wfaNoCDS && gffrec.CDstart>0) {
defline.appendfmt(" CDS=%d-%d", cds_start, cds_end);
}
if (writeExonSegs) {
defline.append(" loc:");
defline.append(gffrec.getGSeqName());
defline+=(char)'|';
defline+=(int)gffrec.start;
defline+=(char)'-';
defline+=(int)gffrec.end;
defline+=(char)'|';
defline+=(char)gffrec.strand;
defline.append(" exons:");
for (int i=0;i<gffrec.exons.Count();i++) {
if (i>0) defline.append(",");
defline+=(int)gffrec.exons[i]->start;
defline.append("-");
defline+=(int)gffrec.exons[i]->end;
}
if (wPadding>0) {
defline.append(" padding:");
defline.append(padLeft);
defline+=(char)'|';
defline.append(padRight);
}
defline.append(" segs:");
for (int i=0;i<seglst.Count();i++) {
if (i>0) defline.append(",");
defline+=(int)seglst[i].start;
defline.append("-");
defline+=(int)seglst[i].end;
}
}
fprintf(f_w, ">%s", defline.chars());
if (fmtTable) printTableData(f_w, gffrec, true);
else {
if (gffrec.attrs!=NULL && gffrec.attrs->Count()>0) fprintf(f_w," ");
gffrec.printAttrs(f_w, ";", false, decodeChars, false);
fprintf(f_w, "\n");
}
printFasta(f_w, NULL, exont, seqlen);
GFREE(exont);
}
} //writing f_w (spliced exons)
if (f_u!=NULL) { //write unspliced transcript sequence
int padLeft=0;
int padRight=0;
if (wPadding>0) {
padLeft= (gffrec.start>(uint)wPadding) ? wPadding : gffrec.start - 1;
int ediff=faseq->getseqlen()-gffrec.end;
padRight=(wPadding>ediff) ? ediff : wPadding;
}
//char* exont=gffrec.getSpliced(faseq, false, &seqlen, &cds_start, &cds_end, &seglst);
int fspan=gffrec.end-gffrec.start+1+padLeft+padRight;
int fstart=gffrec.start-padLeft;
const char* tseq=faseq->subseq(fstart, fspan); //non-zero-terminated
//fspan will be updated with whatever was read
if (tseq==NULL) {
GError("Error getting transcripts seq for %s (%d : %d)!\n", gffrec.getID(), fstart, fspan);
}
GStr defline(gffrec.getID());
if (tseq!=NULL && fspan>0) {
fprintf(f_u, ">%s", defline.chars());
if (fmtTable) printTableData(f_u, gffrec, true);
else {
if (gffrec.attrs!=NULL && gffrec.attrs->Count()>0) fprintf(f_u," ");
gffrec.printAttrs(f_u, ";", false, decodeChars, false);
fprintf(f_u, "\n");
}
printFasta(f_u, NULL, tseq, fspan);
}
} //writing f_u (unspliced sequence)
return true;
}
GTData::GTData(GffObj* t, GenomicSeqData* gd):rna(t),gdata(gd), locus(NULL), replaced_by(NULL), geneinfo(NULL) {
if (rna!=NULL) {
//geneinfo=(GeneInfo*)rna->uptr; //take over geneinfo, if there
rna->uptr=this;
}
if (gdata!=NULL)
gdata->tdata.Add(this);
}
bool GffLoader::unsplContained(GffObj& ti, GffObj& tj) {
//returns true only if ti (which MUST be single-exon) is "almost" contained in any of tj's exons
//but it does not cross any intron-exon boundary of tj
int imax=ti.exons.Count()-1;
int jmax=tj.exons.Count()-1;
if (imax>0) GError("Error: bad unsplContained() call, 1st parameter must be single-exon transcript!\n");
if (ncSpan) {
int maxIntronOvl=dOvlSET ? 25 : 0;
//int minovl = dOvlSET ? 5 : (int)(0.8 * ti.len()); //minimum overlap to declare "redundancy"
for (int j=0;j<=jmax;j++) {
bool exonOverlap=false;
if (dOvlSET) {
exonOverlap= (tj.exons[j]->overlapLen(ti.start-1, ti.end+1) > 0);
} else {
exonOverlap=(ti.overlapLen(tj.exons[j])>=0.8 * ti.len());
}
if (exonOverlap) {
//must not overlap the introns
if ((j>0 && ti.start+maxIntronOvl<tj.exons[j]->start)
|| (j<jmax && ti.end>tj.exons[j]->end+maxIntronOvl))
return false;
return true;
}
} //for each exon
} else { // not fuzzSpan, strict containment required
for (int j=0;j<=jmax;j++) {
if (ti.end<=tj.exons[j]->end && ti.start>=tj.exons[j]->start)
return true;
}
}
return false;
}
GffObj* GffLoader::redundantTranscripts(GffObj& ti, GffObj& tj) {
// matchAllIntrons==true: transcripts are considered "redundant" only if
// they have the exact same number of introns and same splice sites (or none)
// (single-exon transcripts should be also fully contained to be considered matching)
// matchAllIntrons==false: an intron chain could be a subset of a "container" chain,
// as long as no intron-exon boundaries are violated;
// also, if --cset was given, a single-exon transcript will be collapsed
// if it's contained in one of the exons of the another transcript
// fuzzSpan==false: the genomic span of one transcript MUST BE contained in or equal with the genomic
// span of the other
//
// fuzzSpan==true: then genomic spans of transcripts are no longer required to be fully contained
// (i.e. they may extend each-other in opposite directions)
//if redundancy is detected, the "bigger" transcript is returned (otherwise NULL is returned)
int adj=dOvlSET ? 1 : 0;
if (ti.start>tj.end+adj || tj.start>ti.end+adj ||
(tj.strand!='.' && ti.strand!='.' && tj.strand!=ti.strand)) return NULL; //no span overlap
int imax=ti.exons.Count()-1;
int jmax=tj.exons.Count()-1;
GffObj* bigger=NULL;
GffObj* smaller=NULL;
if (matchAllIntrons) { //full intron chain match expected, or full containment for SET
if (imax!=jmax) return NULL; //must have the same number of exons!
if (ti.covlen>tj.covlen) {
bigger=&ti;
if (!ncSpan && (ti.start>tj.start || ti.end<tj.end))
return NULL; //no containment
}
else { //ti.covlen<=tj.covlen
bigger=&tj;
if (!ncSpan && (tj.start>ti.start || tj.end<ti.end))
return NULL; //no containment
}
//check that all introns really match
for (int i=0;i<imax;i++) {
if (ti.exons[i]->end!=tj.exons[i]->end ||
ti.exons[i+1]->start!=tj.exons[i+1]->start) return NULL;
}
return bigger;
}
//--- matchAllIntrons==false: intron-chain containment is also considered redundancy
int minlen=0;
if (ti.covlen>tj.covlen) {
if (tj.exons.Count()>ti.exons.Count()) {
//exon count override
bigger=&tj;
smaller=&ti;
} else {
bigger=&ti;
smaller=&tj;
}
//maxlen=ti.covlen;
minlen=tj.covlen;
} else { //tj has more bases covered
if (ti.exons.Count()>tj.exons.Count()) {
//exon count override
bigger=&ti;
smaller=&tj;
} else {
bigger=&tj;
smaller=&ti;
}
//maxlen=tj.covlen;
minlen=ti.covlen;
}
if (imax==0 && jmax==0) {
//single-exon transcripts: if fuzzSpan, at least 80% of the shortest one must be overlapped by the other
if (ncSpan) {
if (dOvlSET) {
return (ti.exons[0]->overlapLen(tj.exons[0]->start-1, tj.exons[0]->end+1)>0) ? bigger : NULL;
} else {