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gffread.cpp
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gffread.cpp
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#include "GArgs.h"
#include "gff_utils.h"
#include <ctype.h>
#define VERSION "0.9.4"
#define USAGE "Usage:\n\
gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] \n\
[-o <outfile.gff>] [-t <tname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]\n\
[-CTVNJMKQAFGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]\n\
[-i <maxintron>] \n\
Filters and/or converts GFF3/GTF2 records.\n\
<input_gff> is a GFF file, use '-' if the GFF records will be given at stdin\n\
\n\
Options:\n\
-g full path to a multi-fasta file with the genomic sequences\n\
for all input mappings, OR a directory with single-fasta files\n\
(one per genomic sequence, with file names matching sequence names)\n\
-s <seq_info.fsize> is a tab-delimited file providing this info\n\
for each of the mapped sequences:\n\
<seq-name> <seq-length> <seq-description>\n\
(useful for -A option with mRNA/EST/protein mappings)\n\
-i discard transcripts having an intron larger than <maxintron>\n\
-r only show transcripts overlapping coordinate range <start>..<end>\n\
(on chromosome/contig <chr>, strand <strand> if provided)\n\
-R for -r option, discard all transcripts that are not fully \n\
contained within the given range\n\
-U discard single-exon transcripts\n\
-C coding only: discard mRNAs that have no CDS feature\n\
-F full GFF attribute preservation (all attributes are shown)\n\
-G only parse additional exon attributes from the first exon\n\
and move them to the mRNA level (useful for GTF input)\n\
-A use the description field from <seq_info.fsize> and add it\n\
as the value for a 'descr' attribute to the GFF record\n\
\n\
-O process also non-transcript GFF records (by default non-transcript\n\
records are ignored)\n\
-V discard any mRNAs with CDS having in-frame stop codons\n\
-H for -V option, check and adjust the starting CDS phase\n\
if the original phase leads to a translation with an \n\
in-frame stop codon\n\
-B for -V option, single-exon transcripts are also checked on the\n\
opposite strand\n\
-N discard multi-exon mRNAs that have any intron with a non-canonical\n\
splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)\n\
-J discard any mRNAs that either lack initial START codon\n\
or the terminal STOP codon, or have an in-frame stop codon\n\
(only print mRNAs with a fulll, valid CDS)\n\
--no-pseudo: filter out records matching the 'pseudo' keyword\n\
\n\
-M/--merge : cluster the input transcripts into loci, collapsing matching\n\
transcripts (those with the same exact introns and fully contained)\n\
-d <dupinfo> : for -M option, write collapsing info to file <dupinfo>\n\
--cluster-only: same as --merge but without collapsing matching transcripts\n\
-K for -M option: also collapse shorter, fully contained transcripts\n\
with fewer introns than the container\n\
-Q for -M option, remove the containment restriction:\n\
(multi-exon transcripts will be collapsed if just their introns match,\n\
while single-exon transcripts can partially overlap (80%))\n\
\n\
--force-exons: make sure that the lowest level GFF features are printed as \n\
\"exon\" features\n\
-E expose (warn about) duplicate transcript IDs and other potential \n\
problems with the given GFF/GTF records\n\
-D decode url encoded characters within attributes\n\
-Z merge close exons into a single exon (for intron size<4)\n\
-w write a fasta file with spliced exons for each GFF transcript\n\
-x write a fasta file with spliced CDS for each GFF transcript\n\
-W for -w and -x options, also write for each fasta record the exon\n\
coordinates projected onto the spliced sequence\n\
-y write a protein fasta file with the translation of CDS for each record\n\
-L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)\n\
-m <chr_replace> is a reference (genomic) sequence replacement table with\n\
this format:\n\
<original_ref_ID> <new_ref_ID>\n\
GFF records on reference sequences that are not found among the\n\
<original_ref_ID> entries in this file will be filtered out\n\
-o the \"filtered\" GFF records will be written to <outfile.gff>\n\
(use -o- for printing to stdout)\n\
-t use <trackname> in the second column of each GFF output line\n\
-T -o option will output GTF format instead of GFF3\n\
"
class SeqInfo { //populated from the -s option of gffread
public:
int len;
char* descr;
SeqInfo( int l, char* s) {
len=l;
if (s==NULL) {
descr=NULL;
} else {
descr=Gstrdup(s);
}
}
~SeqInfo() {
GFREE(descr);
}
};
class RefTran {
public:
char* new_name;
RefTran(char *ns) {
new_name=NULL;
if (ns!=NULL)
new_name=Gstrdup(ns);
}
~RefTran() {
GFREE(new_name);
}
};
FILE* ffasta=NULL;
FILE* f_in=NULL;
FILE* f_out=NULL;
FILE* f_w=NULL; //fasta with spliced exons (transcripts)
FILE* f_x=NULL; //fasta with spliced CDS
FILE* f_y=NULL; //fasta with translated CDS
bool wCDSonly=false;
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 mRNAOnly=true;
bool NoPseudo=false;
bool forceExons=false;
bool spliceCheck=false; //only known splice-sites
bool decodeChars=false; //decode url-encoded chars in attrs (-D)
bool fullCDSonly=false; // starts with START, ends with STOP codon
bool fullattr=false;
//bool sortByLoc=false; // if the GFF output should be sorted by location
bool ensembl_convert=false; //-L, assist in converting Ensembl GTF to GFF3
//GStr gseqpath;
//GStr gcdbfa;
//bool multiGSeq=false; //if a directory or a .cidx file was given to -g option
//GFaSeqGet* faseq=NULL;
//GCdbYank* gcdb=NULL;
//int gseq_id=-1; //current genome sequence ID -- the current GffObj::gseq_id
bool fmtGTF=false;
bool addDescr=false;
//bool protmap=false;
bool multiExon=false;
bool writeExonSegs=false;
char* tracklabel=NULL;
int maxintron=999000000;
bool mergeCloseExons=false;
//range filter:
char* rfltGSeq=NULL;
char rfltStrand=0;
uint rfltStart=0;
uint rfltEnd=MAX_UINT;
bool rfltWithin=false; //check for full containment within given range
bool noExonAttr=false;
bool doCluster=false;
bool doCollapseRedundant=false;
GList<GenomicSeqData> g_data(true,true,true); //list of GFF records by genomic seq
//hash with sequence info
GHash<SeqInfo> seqinfo;
GHash<int> isoCounter; //counts the valid isoforms
GHash<RefTran> reftbl;
GHash<GeneInfo> gene_ids;
//min-max gene span associated to chr|gene_id (mostly for Ensembl conversion)
bool debugMode=false;
bool verbose=false;
void loadSeqInfo(FILE* f, GHash<SeqInfo> &si) {
GLineReader fr(f);
while (!fr.isEof()) {
char* line=fr.getLine();
if (line==NULL) break;
char* id=line;
char* lenstr=NULL;
char* text=NULL;
char* p=line;
while (*p!=0 && !isspace(*p)) p++;
if (*p==0) continue;
*p=0;p++;
while (*p==' ' || *p=='\t') p++;
if (*p==0) continue;
lenstr=p;
while (*p!=0 && !isspace(*p)) p++;
if (*p!=0) { *p=0;p++; }
while (*p==' ' || *p=='\t') p++;
if (*p!=0) text=p; //else text remains NULL
int len=0;
if (!parseInt(lenstr,len)) {
GMessage("Warning: could not parse sequence length: %s %s\n",
id, lenstr);
continue;
}
// --- here we have finished parsing the line
si.Add(id, new SeqInfo(len,text));
} //while lines
}
void loadRefTable(FILE* f, GHash<RefTran>& rt) {
GLineReader fr(f);
char* line=NULL;
while ((line=fr.getLine())) {
char* orig_id=line;
char* p=line;
while (*p!=0 && !isspace(*p)) p++;
if (*p==0) continue;
*p=0;p++;//split the line here
while (*p==' ' || *p=='\t') p++;
if (*p==0) continue;
rt.Add(orig_id, new RefTran(p));
} //while lines
}
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;
}
GFaSeqGet* fastaSeqGet(GFastaDb& gfasta, GffObj& gffrec) {
if (gfasta.fastaPath==NULL) return NULL;
return gfasta.fetch(gffrec.gseq_id);
}
int adjust_stopcodon(GffObj& gffrec, int adj, GList<GSeg>* seglst=NULL) {
//adj>0 => extedn CDS, adj<0 => shrink CDS
//when CDS is expanded, exons have to be checked too and
// expanded accordingly if they had the same boundary
int realadj=0;
if (gffrec.strand=='-') {
if ((int)gffrec.CDstart>adj) {
gffrec.CDstart-=adj;
realadj=adj;
if (adj<0) { //restore
if (gffrec.exons.First()->start==gffrec.CDstart+adj) {
gffrec.exons.First()->start-=adj;
gffrec.start=gffrec.exons.First()->start;
gffrec.covlen+=adj;
}
}
else if (gffrec.exons.First()->start>=gffrec.CDstart) {
gffrec.exons.First()->start-=adj;
gffrec.start=gffrec.exons.First()->start;
gffrec.covlen+=adj;
}
}
}
else {
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.exons.Last()->end+=adj;
gffrec.end=gffrec.exons.Last()->end;
gffrec.covlen+=adj;
}
}
if (seglst!=NULL) seglst->Last()->end+=adj;
return realadj;
}
bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {
//returns true if the transcript passed the filter
char* gname=gffrec.getGeneName();
if (gname==NULL) gname=gffrec.getGeneID();
GStr defline(gffrec.getID());
if (f_out && !fmtGTF) {
const char* tname=NULL;
if ((tname=gffrec.getAttr("transcript_name"))!=NULL) {
gffrec.addAttr("Name", tname);
gffrec.removeAttr("transcript_name");
}
}
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,isonum);
}
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 (ilen>4000000)
GMessage("Warning: very large intron (%d) for transcript %s\n",
ilen, gffrec.getID());
if (ilen>maxintron) {
return false;
}
}
GList<GSeg> seglst(false,true);
GFaSeqGet* faseq=fastaSeqGet(gfasta, gffrec);
if (spliceCheck && gffrec.exons.Count()>1) {
//check introns for splice site consensi ( GT-AG, GC-AG or AT-AC )
if (faseq==NULL) GError("Error: no genomic sequence available!\n");
int glen=gffrec.end-gffrec.start+1;
const char* gseq=faseq->subseq(gffrec.start, glen);
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") { //
if (donorSite!="AT") { ssValid=false; break; }
}
else { ssValid=false; break; }
}
//GFREE(gseq);
if (!ssValid) {
if (verbose)
GMessage("Invalid splice sites found for '%s'\n",gffrec.getID());
return false; //don't print this one!
}
}
bool trprint=true;
int stopCodonAdjust=0;
int mCDphase=0;
bool hasStop=false;
if (gffrec.CDphase=='1' || gffrec.CDphase=='2')
mCDphase = gffrec.CDphase-'0';
if (f_y!=NULL || f_x!=NULL || validCDSonly) {
if (faseq==NULL) GError("Error: no genomic sequence provided!\n");
//if (protmap && fullCDSonly) {
//if (protmap && (fullCDSonly || (gffrec.qlen>0 && gffrec.qend==gffrec.qlen))) {
if (validCDSonly) { //make sure the stop codon is always included
//adjust_stopcodon(gffrec,3);
stopCodonAdjust=adjust_stopcodon(gffrec,3);
}
int strandNum=0;
int phaseNum=0;
CDS_CHECK:
cdsnt=gffrec.getSpliced(faseq, true, &seqlen, NULL, NULL, &seglst);
if (cdsnt==NULL) trprint=false;
else { //has CDS
if (validCDSonly) {
cdsaa=translateDNA(cdsnt, aalen, seqlen);
char* p=strchr(cdsaa,'.');
hasStop=false;
if (p!=NULL) {
if (p-cdsaa>=aalen-2) { //stop found as the last codon
*p='0';//remove it
hasStop=true;
if (aalen-2==p-cdsaa) {
//previous to last codon is the stop codon
//so correct the CDS stop accordingly
adjust_stopcodon(gffrec,-3, &seglst);
stopCodonAdjust=0; //clear artificial stop adjustment
seqlen-=3;
cdsnt[seqlen]=0;
}
aalen=p-cdsaa;
}
else {//stop found before the last codon
trprint=false;
}
}//stop codon found
if (trprint==false) { //failed CDS validity check
//in-frame stop codon found
if (altPhases && phaseNum<3) {
phaseNum++;
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("In-frame STOP found for '%s'\n",gffrec.getID());
} //has in-frame STOP
if (fullCDSonly) {
if (!hasStop || cdsaa[0]!='M') trprint=false;
}
} // CDS check requested
} //has CDS
} //translation or codon check/output was requested
if (!trprint) {
GFREE(cdsnt);
GFREE(cdsaa);
return false;
}
if (stopCodonAdjust>0 && !hasStop) {
//restore stop codon location
adjust_stopcodon(gffrec, -stopCodonAdjust, &seglst);
if (cdsnt!=NULL && seqlen>0) {
seqlen-=stopCodonAdjust;
cdsnt[seqlen]=0;
}
if (cdsaa!=NULL) aalen--;
}
if (f_y!=NULL) { //CDS translation fasta output requested
//char*
if (cdsaa==NULL) { //translate now if not done before
cdsaa=translateDNA(cdsnt, aalen, seqlen);
}
if (fullattr && gffrec.attrs!=NULL) {
//append all attributes found for each transcripts
for (int i=0;i<gffrec.attrs->Count();i++) {
defline.append(" ");
defline.append(gffrec.getAttrName(i));
defline.append("=");
defline.append(gffrec.getAttrValue(i));
}
}
printFasta(f_y, defline, cdsaa, aalen);
}
if (f_x!=NULL) { //CDS only
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 (fullattr && gffrec.attrs!=NULL) {
//append all attributes found for each transcript
for (int i=0;i<gffrec.attrs->Count();i++) {
defline.append(" ");
defline.append(gffrec.getAttrName(i));
defline.append("=");
defline.append(gffrec.getAttrValue(i));
}
}
printFasta(f_x, defline, cdsnt, seqlen);
}
GFREE(cdsnt);
GFREE(cdsaa);
if (f_w!=NULL) { //write spliced exons
uint cds_start=0;
uint cds_end=0;
seglst.Clear();
char* exont=gffrec.getSpliced(faseq, false, &seqlen, &cds_start, &cds_end, &seglst);
if (exont!=NULL) {
if (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;
}
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 (fullattr && gffrec.attrs!=NULL) {
//append all attributes found for each transcripts
for (int i=0;i<gffrec.attrs->Count();i++) {
defline.append(" ");
defline.append(gffrec.getAttrName(i));
defline.append("=");
defline.append(gffrec.getAttrValue(i));
}
}
printFasta(f_w, defline, exont, seqlen);
GFREE(exont);
}
} //writing f_w (spliced exons)
return true;
}
void openfw(FILE* &f, GArgs& args, char opt) {
GStr s=args.getOpt(opt);
if (!s.is_empty()) {
if (s=='-')
f=stdout;
else {
f=fopen(s,"w");
if (f==NULL) GError("Error creating file: %s\n", s.chars());
}
}
}
#define FWCLOSE(fh) if (fh!=NULL && fh!=stdout) fclose(fh)
#define FRCLOSE(fh) if (fh!=NULL && fh!=stdin) fclose(fh)
void printGff3Header(FILE* f, GArgs& args) {
fprintf(f, "# ");
args.printCmdLine(f);
fprintf(f, "##gff-version 3\n");
//for (int i=0;i<gseqdata.Count();i++) {
//
//}
}
bool validateGffRec(GffObj* gffrec, GList<GffObj>* gfnew) {
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);
}
else return false; //discard, ref seq not in the given translation table
}
if (mRNAOnly && 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 (rfltGSeq!=NULL) { //filter by gseqName
if (strcmp(gffrec->getGSeqName(),rfltGSeq)!=0) {
return false;
}
}
if (rfltStrand>0 && gffrec->strand !=rfltStrand) {
return false;
}
//check coordinates
if (rfltStart!=0 || rfltEnd!=MAX_UINT) {
if (rfltWithin) {
if (gffrec->start<rfltStart || gffrec->end>rfltEnd) {
return false; //not within query range
}
}
else {
if (gffrec->start>rfltEnd || gffrec->end<rfltStart) {
return false;
}
}
}
if (multiExon && gffrec->exons.Count()<=1) {
return false;
}
if (wCDSonly && gffrec->CDstart==0) {
return false;
}
if (ensembl_convert && startsWith(gffrec->getID(), "ENS")) {
//keep track of chr|gene_id data -- coordinate range
char* geneid=gffrec->getGeneID();
if (geneid!=NULL) {
GeneInfo* ginfo=gene_ids.Find(geneid);
if (ginfo==NULL) {//first time seeing this gene ID
GeneInfo* geneinfo=new GeneInfo(gffrec, ensembl_convert);
gene_ids.Add(geneid, geneinfo);
if (gfnew!=NULL)
gfnew->Add(geneinfo->gf); //FIXME: do I really need this?
}
else ginfo->update(gffrec);
}
}
return true;
}
int main(int argc, char * const argv[]) {
GArgs args(argc, argv,
"debug;merge;cluster-only;help;force-exons;no-pseudo;MINCOV=MINPID=hvOUNHWCVJMKQNSXTDAPRZFGLEm:g:i:r:s:t:a:b:o:w:x:y:d:");
args.printError(USAGE, true);
if (args.getOpt('h') || args.getOpt("help")) {
GMessage("%s",USAGE);
exit(1);
}
debugMode=(args.getOpt("debug")!=NULL);
decodeChars=(args.getOpt('D')!=NULL);
forceExons=(args.getOpt("force-exons")!=NULL);
NoPseudo=(args.getOpt("no-pseudo")!=NULL);
mRNAOnly=(args.getOpt('O')==NULL);
//sortByLoc=(args.getOpt('S')!=NULL);
addDescr=(args.getOpt('A')!=NULL);
verbose=(args.getOpt('v')!=NULL);
wCDSonly=(args.getOpt('C')!=NULL);
validCDSonly=(args.getOpt('V')!=NULL);
altPhases=(args.getOpt('H')!=NULL);
fmtGTF=(args.getOpt('T')!=NULL); //switch output format to GTF
bothStrands=(args.getOpt('B')!=NULL);
fullCDSonly=(args.getOpt('J')!=NULL);
spliceCheck=(args.getOpt('N')!=NULL);
bool matchAllIntrons=(args.getOpt('K')==NULL);
bool fuzzSpan=(args.getOpt('Q')!=NULL);
if (args.getOpt('M') || args.getOpt("merge")) {
doCluster=true;
doCollapseRedundant=true;
}
else {
if (!matchAllIntrons || fuzzSpan) {
GMessage("%s",USAGE);
GMessage("Error: -K or -Q options require -M/--merge option!\n");
exit(1);
}
}
if (args.getOpt("cluster-only")) {
doCluster=true;
doCollapseRedundant=false;
if (!matchAllIntrons || fuzzSpan) {
GMessage("%s",USAGE);
GMessage("Error: -K or -Q options have no effect with --cluster-only.\n");
exit(1);
}
}
if (fullCDSonly) validCDSonly=true;
if (verbose) {
fprintf(stderr, "Command line was:\n");
args.printCmdLine(stderr);
}
fullattr=(args.getOpt('F')!=NULL);
if (args.getOpt('G')==NULL)
noExonAttr=!fullattr;
else {
noExonAttr=true;
fullattr=true;
}
if (NoPseudo && !fullattr) {
noExonAttr=true;
fullattr=true;
}
ensembl_convert=(args.getOpt('L')!=NULL);
if (ensembl_convert) {
fullattr=true;
noExonAttr=false;
//sortByLoc=true;
}
mergeCloseExons=(args.getOpt('Z')!=NULL);
multiExon=(args.getOpt('U')!=NULL);
writeExonSegs=(args.getOpt('W')!=NULL);
tracklabel=args.getOpt('t');
GFastaDb gfasta(args.getOpt('g'));
//if (gfasta.fastaPath!=NULL)
// sortByLoc=true; //enforce sorting by chromosome/contig
GStr s=args.getOpt('i');
if (!s.is_empty()) maxintron=s.asInt();
FILE* f_repl=NULL;
s=args.getOpt('d');
if (!s.is_empty()) {
if (s=="-") f_repl=stdout;
else {
f_repl=fopen(s.chars(), "w");
if (f_repl==NULL) GError("Error creating file %s\n", s.chars());
}
}
rfltWithin=(args.getOpt('R')!=NULL);
s=args.getOpt('r');
if (!s.is_empty()) {
s.trim();
if (s[0]=='+' || s[0]=='-') {
rfltStrand=s[0];
s.cut(0,1);
}
int isep=s.index(':');
if (isep>0) { //gseq name given
if (rfltStrand==0 && (s[isep-1]=='+' || s[isep-1]=='-')) {
isep--;
rfltStrand=s[isep];
s.cut(isep,1);
}
if (isep>0)
rfltGSeq=Gstrdup((s.substr(0,isep)).chars());
s.cut(0,isep+1);
}
GStr gsend;
char slast=s[s.length()-1];
if (rfltStrand==0 && (slast=='+' || slast=='-')) {
s.chomp(slast);
rfltStrand=slast;
}
if (s.index("..")>=0) gsend=s.split("..");
else gsend=s.split('-');
if (!s.is_empty()) rfltStart=(uint)s.asInt();
if (!gsend.is_empty()) {
rfltEnd=(uint)gsend.asInt();
if (rfltEnd==0) rfltEnd=MAX_UINT;
}
} //gseq/range filtering
else {
if (rfltWithin)
GError("Error: option -R requires -r!\n");
//if (rfltWholeTranscript)
// GError("Error: option -P requires -r!\n");
}
s=args.getOpt('m');
if (!s.is_empty()) {
FILE* ft=fopen(s,"r");
if (ft==NULL) GError("Error opening reference table: %s\n",s.chars());
loadRefTable(ft, reftbl);
fclose(ft);
}
s=args.getOpt('s');
if (!s.is_empty()) {
FILE* fsize=fopen(s,"r");
if (fsize==NULL) GError("Error opening info file: %s\n",s.chars());
loadSeqInfo(fsize, seqinfo);
fclose(fsize);
}
openfw(f_out, args, 'o');
//if (f_out==NULL) f_out=stdout;
if (gfasta.fastaPath==NULL && (validCDSonly || spliceCheck || args.getOpt('w')!=NULL || args.getOpt('x')!=NULL || args.getOpt('y')!=NULL))
GError("Error: -g option is required for options -w, -x, -y, -V, -N, -M !\n");
openfw(f_w, args, 'w');
openfw(f_x, args, 'x');
openfw(f_y, args, 'y');
if (f_y!=NULL || f_x!=NULL) wCDSonly=true;
//useBadCDS=useBadCDS || (fgtfok==NULL && fgtfbad==NULL && f_y==NULL && f_x==NULL);
int numfiles = args.startNonOpt();
//GList<GffObj> gfkept(false,true); //unsorted, free items on delete
int out_counter=0; //number of records printed
while (true) {
GStr infile;
if (numfiles) {
infile=args.nextNonOpt();
if (infile.is_empty()) break;
if (infile=="-") { f_in=stdin; infile="stdin"; }
else
if ((f_in=fopen(infile, "r"))==NULL)
GError("Error: cannot open input file %s!\n",infile.chars());
}
else
infile="-";
GffLoader gffloader(infile.chars());
gffloader.transcriptsOnly=mRNAOnly;
gffloader.fullAttributes=fullattr;
gffloader.noExonAttrs=noExonAttr;
gffloader.mergeCloseExons=mergeCloseExons;
gffloader.showWarnings=(args.getOpt('E')!=NULL);
gffloader.noPseudo=NoPseudo;
gffloader.load(g_data, &validateGffRec, doCluster, doCollapseRedundant,
matchAllIntrons, fuzzSpan, forceExons);
if (doCluster)
collectLocusData(g_data);
if (numfiles==0) break;
}
GStr loctrack("gffcl");
if (tracklabel) loctrack=tracklabel;
g_data.setSorted(&gseqCmpName);
GffPrintMode exonPrinting;
if (fmtGTF) {
exonPrinting = pgtfAny;
} else {
exonPrinting = forceExons ? pgffBoth : pgffAny;
}
bool firstGff3Print=!fmtGTF;
if (doCluster) {
//grouped in loci
for (int g=0;g<g_data.Count();g++) {
GenomicSeqData* gdata=g_data[g];
int gfs_i=0;
for (int l=0;l<gdata->loci.Count();l++) {
GffLocus& loc=*(gdata->loci[l]);
//check all non-replaced transcripts in this locus:
int numvalid=0;
int idxfirstvalid=-1;
for (int i=0;i<loc.rnas.Count();i++) {
GffObj& t=*(loc.rnas[i]);
if (f_out) {
while (gfs_i<gdata->gfs.Count() && gdata->gfs[gfs_i]->start<=t.start) {
GffObj& gfst=*(gdata->gfs[gfs_i]);
if ((gfst.udata&4)==0) { //never printed
gfst.udata|=4;
if (firstGff3Print) { printGff3Header(f_out, args);firstGff3Print=false; }
if (gfst.exons.Count()==0 && gfst.children.Count()==0 && forceExons)
gfst.addExon(gfst.start,gfst.end);
gfst.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
}
++gfs_i;
}
}
GTData* tdata=(GTData*)(t.uptr);
if (tdata->replaced_by!=NULL) {
if (f_repl && (t.udata & 8)==0) {
//t.udata|=8;
fprintf(f_repl, "%s", t.getID());
GTData* rby=tdata;
while (rby->replaced_by!=NULL) {
fprintf(f_repl," => %s", rby->replaced_by->getID());
rby->rna->udata|=8;
rby=(GTData*)(rby->replaced_by->uptr);
}
fprintf(f_repl, "\n");
}
continue;
}
if (process_transcript(gfasta, t)) {
t.udata|=4; //tag it as valid
numvalid++;
if (idxfirstvalid<0) idxfirstvalid=i;
}
}
if (f_out && numvalid>0) {
GStr locname("RLOC_");
locname.appendfmt("%08d",loc.locus_num);
if (!fmtGTF) {
if (firstGff3Print) { printGff3Header(f_out, args);firstGff3Print=false; }
fprintf(f_out,"%s\t%s\tlocus\t%d\t%d\t.\t%c\t.\tID=%s;locus=%s",
loc.rnas[0]->getGSeqName(), loctrack.chars(), loc.start, loc.end, loc.strand,
locname.chars(), locname.chars());
//const char* loc_gname=loc.getGeneName();
if (loc.gene_names.Count()>0) { //print all gene names associated to this locus
fprintf(f_out, ";genes=%s",loc.gene_names.First()->name.chars());
for (int i=1;i<loc.gene_names.Count();i++) {
fprintf(f_out, ",%s",loc.gene_names[i]->name.chars());
}
}
if (loc.gene_ids.Count()>0) { //print all GeneIDs names associated to this locus
fprintf(f_out, ";geneIDs=%s",loc.gene_ids.First()->name.chars());
for (int i=1;i<loc.gene_ids.Count();i++) {
fprintf(f_out, ",%s",loc.gene_ids[i]->name.chars());
}
}
fprintf(f_out, ";transcripts=%s",loc.rnas[idxfirstvalid]->getID());
for (int i=idxfirstvalid+1;i<loc.rnas.Count();i++) {
fprintf(f_out, ",%s",loc.rnas[i]->getID());
}
fprintf(f_out, "\n");
}
//now print all valid, non-replaced transcripts in this locus:
for (int i=0;i<loc.rnas.Count();i++) {
GffObj& t=*(loc.rnas[i]);
GTData* tdata=(GTData*)(t.uptr);
if (tdata->replaced_by!=NULL || ((t.udata & 4)==0)) continue;
t.addAttr("locus", locname.chars());
out_counter++;
if (fmtGTF) t.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
else {
if (firstGff3Print) { printGff3Header(f_out, args);firstGff3Print=false; }
//print the parent first, if any
if (t.parent!=NULL && ((t.parent->udata & 4)==0)) {
GTData* pdata=(GTData*)(t.parent->uptr);
if (pdata && pdata->geneinfo!=NULL)
pdata->geneinfo->finalize();
t.parent->addAttr("locus", locname.chars());
t.parent->printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
t.parent->udata|=4;
}
t.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
}
}
} //have valid transcripts to print
}//for each locus
//print the rest of the isolated pseudo/gene/region features not printed yet
if (f_out) {
while (gfs_i<gdata->gfs.Count()) {
GffObj& gfst=*(gdata->gfs[gfs_i]);
if ((gfst.udata&4)==0) { //never printed
gfst.udata|=4;
if (firstGff3Print) { printGff3Header(f_out, args);firstGff3Print=false; }
if (gfst.exons.Count()==0 && gfst.children.Count()==0 && forceExons)
gfst.addExon(gfst.start,gfst.end);
gfst.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);
}
++gfs_i;
}
}
} //for each genomic sequence
}
else {
//not grouped into loci, print the rnas with their parents, if any
int numvalid=0;
for (int g=0;g<g_data.Count();g++) {
GenomicSeqData* gdata=g_data[g];
int gfs_i=0;
for (int m=0;m<gdata->rnas.Count();m++) {
GffObj& t=*(gdata->rnas[m]);
if (f_out) {
while (gfs_i<gdata->gfs.Count() && gdata->gfs[gfs_i]->start<=t.start) {
GffObj& gfst=*(gdata->gfs[gfs_i]);
if ((gfst.udata&4)==0) { //never printed
gfst.udata|=4;
if (firstGff3Print) { printGff3Header(f_out, args);firstGff3Print=false; }
if (gfst.exons.Count()==0 && gfst.children.Count()==0 && forceExons)
gfst.addExon(gfst.start,gfst.end);