void mapPSLs(struct psl *psl, FILE *fileHandle, char *query, char *target) { /* *Map coordinates of all the psls in the list psl to the query and target reference genomes */ int32_t qrefsize = 0; int32_t qstart = 0; int32_t qlen = 0; int32_t trefsize = 0; int32_t tstart = 0; int32_t tlen = 0; char sep = '\t'; char lastStep = '\n'; if( sscanf(query, "%d.%d.%d", &qrefsize, &qstart, &qlen) != 3){ fprintf(stderr, "Wrong query format\n"); usage(); return; } if( sscanf(target, "%d.%d.%d", &trefsize, &tstart, &tlen) != 3){ fprintf(stderr, "Wrong target format\n"); usage(); return; } while(psl != NULL){ mapPslCoor(psl, qrefsize, qstart, qlen, trefsize, tstart, tlen); pslOutput(psl, fileHandle, sep, lastStep); psl = psl->next; } return; }
static void writePslx(FILE *pslOutFh, struct seqReader *qSeqReader, struct seqReader *tSeqReader, struct psl *psl) /* output a pslx, cheating in not creating the whole pslx to avoid more sequence * manipulation */ { if (pslIsProtein(psl)) errAbort("doesn't support protein PSLs: qName: %s", psl->qName); pslOutput(psl, pslOutFh, '\t', '\t'); outputBlocks(pslOutFh, qSeqReader, psl->qName, psl->strand[0], psl->qStart, psl->qEnd, psl->blockCount, psl->qStarts, psl->blockSizes); fputc('\t', pslOutFh); outputBlocks(pslOutFh, tSeqReader, psl->tName, psl->strand[1], psl->tStart, psl->tEnd, psl->blockCount, psl->tStarts, psl->blockSizes); fputc('\n', pslOutFh); }
static void processMatchLine(FILE *pslF, struct gff3Ann *node, struct hash *chromHash) { struct gff3Attr *attr = gff3AnnFindAttr(node, "Gap"); char *cigar = NULL; if (!((attr == NULL) || (attr->vals == NULL) || (attr->vals->name == NULL))) cigar = attr->vals->name; struct nameAndSize *nsT = getNameAndSize(chromHash, node->targetId); struct nameAndSize *nsQ = getNameAndSize(chromHash, node->seqid); struct psl *psl = pslFromGff3Cigar(node->seqid, nsQ->size, node->start, node->end, nsT->name, nsT->size, node->targetStart, node->targetEnd, node->targetStrand, cigar); pslOutput(psl, pslF, '\t' , '\n'); pslFree(&psl); }
void checkExp(char *bedFileName, char *tNibDir, char *nibList) { struct lineFile *bf = lineFileOpen(bedFileName , TRUE), *af = NULL; char *row[PSEUDOGENELINK_NUM_COLS] ; struct pseudoGeneLink *ps; char *tmpName[512], cmd[512]; struct axt *axtList = NULL, *axt, *mAxt = NULL; struct dnaSeq *qSeq = NULL, *tSeq = NULL, *seqList = NULL; struct nibInfo *qNib = NULL, *tNib = NULL; FILE *op; int ret; if (nibHash == NULL) nibHash = hashNew(0); while (lineFileNextRow(bf, row, ArraySize(row))) { struct misMatch *misMatchList = NULL; struct binKeeper *bk = NULL; struct binElement *el, *elist = NULL; struct psl *mPsl = NULL, *rPsl = NULL, *pPsl = NULL, *psl ; struct misMatch *mf = NULL; ps = pseudoGeneLinkLoad(row); tmpName[0] = cloneString(ps->name); chopByChar(tmpName[0], '.', tmpName, sizeof(tmpName)); verbose(2,"name %s %s:%d-%d\n", ps->name, ps->chrom, ps->chromStart,ps->chromEnd); /* get expressed retro from hash */ bk = hashFindVal(mrnaHash, ps->chrom); elist = binKeeperFindSorted(bk, ps->chromStart, ps->chromEnd ) ; for (el = elist; el != NULL ; el = el->next) { rPsl = el->val; verbose(2,"retroGene %s %s:%d-%d\n",rPsl->qName, ps->chrom, ps->chromStart,ps->chromEnd); } /* find mrnas that overlap parent gene */ bk = hashFindVal(mrnaHash, ps->gChrom); elist = binKeeperFindSorted(bk, ps->gStart , ps->gEnd ) ; for (el = elist; el != NULL ; el = el->next) { pPsl = el->val; verbose(2,"parent %s %s:%d %d,%d\n", pPsl->qName, pPsl->tName,pPsl->tStart, pPsl->match, pPsl->misMatch); } /* find self chain */ bk = hashFindVal(chainHash, ps->chrom); elist = binKeeperFind(bk, ps->chromStart , ps->chromEnd ) ; slSort(&elist, chainCmpScoreDesc); for (el = elist; el != NULL ; el = el->next) { struct chain *chain = el->val, *subChain, *retChainToFree, *retChainToFree2; int qs = chain->qStart; int qe = chain->qEnd; int id = chain->id; if (chain->qStrand == '-') { qs = chain->qSize - chain->qEnd; qe = chain->qSize - chain->qStart; } if (!sameString(chain->qName , ps->gChrom) || !positiveRangeIntersection(qs, qe, ps->gStart, ps->gEnd)) { verbose(2," wrong chain %s:%d-%d %s:%d-%d parent %s:%d-%d\n", chain->qName, qs, qe, chain->tName,chain->tStart,chain->tEnd, ps->gChrom,ps->gStart,ps->gEnd); continue; } verbose(2,"chain id %d %4.0f",chain->id, chain->score); chainSubsetOnT(chain, ps->chromStart+7, ps->chromEnd-7, &subChain, &retChainToFree); if (subChain != NULL) chain = subChain; chainSubsetOnQ(chain, ps->gStart, ps->gEnd, &subChain, &retChainToFree2); if (subChain != NULL) chain = subChain; if (chain->qStrand == '-') { qs = chain->qSize - chain->qEnd; qe = chain->qSize - chain->qStart; } verbose(2," %s:%d-%d %s:%d-%d ", chain->qName, qs, qe, chain->tName,chain->tStart,chain->tEnd); if (subChain != NULL) verbose(2,"subChain %s:%d-%d %s:%d-%d\n", subChain->qName, subChain->qStart, subChain->qEnd, subChain->tName,subChain->tStart,subChain->tEnd); qNib = nibInfoFromCache(nibHash, tNibDir, chain->qName); tNib = nibInfoFromCache(nibHash, tNibDir, chain->tName); tSeq = nibInfoLoadStrand(tNib, chain->tStart, chain->tEnd, '+'); qSeq = nibInfoLoadStrand(qNib, chain->qStart, chain->qEnd, chain->qStrand); axtList = chainToAxt(chain, qSeq, chain->qStart, tSeq, chain->tStart, maxGap, BIGNUM); verbose(2,"axt count %d misMatch cnt %d\n",slCount(axtList), slCount(misMatchList)); for (axt = axtList; axt != NULL ; axt = axt->next) { addMisMatch(&misMatchList, axt, chain->qSize); } verbose(2,"%d in mismatch list %s id %d \n",slCount(misMatchList), chain->qName, id); chainFree(&retChainToFree); chainFree(&retChainToFree2); break; } /* create axt of each expressed retroGene to parent gene */ /* get alignment for each mrna overlapping retroGene */ bk = hashFindVal(mrnaHash, ps->chrom); elist = binKeeperFindSorted(bk, ps->chromStart , ps->chromEnd ) ; { char queryName[512]; char axtName[512]; char pslName[512]; safef(queryName, sizeof(queryName), "/tmp/query.%s.fa", ps->chrom); safef(axtName, sizeof(axtName), "/tmp/tmp.%s.axt", ps->chrom); safef(pslName, sizeof(pslName), "/tmp/tmp.%s.psl", ps->chrom); op = fopen(pslName,"w"); for (el = elist ; el != NULL ; el = el->next) { psl = el->val; pslOutput(psl, op, '\t','\n'); qSeq = twoBitReadSeqFrag(twoBitFile, psl->qName, 0, 0); if (qSeq != NULL) slAddHead(&seqList, qSeq); else errAbort("seq %s not found \n", psl->qName); } fclose(op); faWriteAll(queryName, seqList); safef(cmd,sizeof(cmd),"pslPretty -long -axt %s %s %s %s",pslName , nibList, queryName, axtName); ret = system(cmd); if (ret != 0) errAbort("ret is %d %s\n",ret,cmd); verbose(2, "ret is %d %s\n",ret,cmd); af = lineFileOpen(axtName, TRUE); while ((axt = axtRead(af)) != NULL) slAddHead(&mAxt, axt); lineFileClose(&af); } slReverse(&mAxt); /* for each parent/retro pair, count bases matching retro and parent better */ for (el = elist; el != NULL ; el = el->next) { int i, scoreRetro=0, scoreParent=0, scoreNeither=0; struct dyString *parentMatch = newDyString(16*1024); struct dyString *retroMatch = newDyString(16*1024); mPsl = el->val; if (mAxt != NULL) { verbose(2,"mrna %s %s:%d %d,%d axt %s\n", mPsl->qName, mPsl->tName,mPsl->tStart, mPsl->match, mPsl->misMatch, mAxt->qName); assert(sameString(mPsl->qName, mAxt->qName)); for (i = 0 ; i< (mPsl->tEnd-mPsl->tStart) ; i++) { int j = mAxt->tStart - mPsl->tStart; verbose(5, "listLen = %d\n",slCount(&misMatchList)); if ((mf = matchFound(&misMatchList, (mPsl->tStart)+i)) != NULL) { if (toupper(mf->retroBase) == toupper(mAxt->qSym[j+i])) { verbose (3,"match retro[%d] %d %c == %c parent %c %d\n", i,mf->retroLoc, mf->retroBase, mAxt->qSym[j+i], mf->parentBase, mf->parentLoc); dyStringPrintf(retroMatch, "%d,", mf->retroLoc); scoreRetro++; } else if (toupper(mf->parentBase) == toupper(mAxt->qSym[j+i])) { verbose (3,"match parent[%d] %d %c == %c retro %c %d\n", i,mf->parentLoc, mf->parentBase, mAxt->qSym[j+i], mf->retroBase, mf->retroLoc); dyStringPrintf(parentMatch, "%d,", mf->parentLoc); scoreParent++; } else { verbose (3,"match neither[%d] %d %c != %c retro %c %d\n", i,mf->parentLoc, mf->parentBase, mAxt->tSym[j+i], mf->retroBase, mf->retroLoc); scoreNeither++; } } } verbose(2,"final score %s parent %d retro %d neither %d\n", mPsl->qName, scoreParent, scoreRetro, scoreNeither); fprintf(outFile,"%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%d\t%d\t%s\t%s\n", ps->chrom, ps->chromStart, ps->chromEnd, ps->name, ps->score, mPsl->tName, mPsl->tStart, mPsl->tEnd, mPsl->qName, scoreParent, scoreRetro, scoreNeither, parentMatch->string, retroMatch->string); mAxt = mAxt->next; } dyStringFree(&parentMatch); dyStringFree(&retroMatch); } } }