char *PredictionTranscript_getcDNA(PredictionTranscript *trans) {
Vector *exons = PredictionTranscript_getAllExons(trans,0);
char *cdna = StrUtil_copyString(&cdna, "", 0);
//int lastPhase = 0;
int i;
int first = 1;
int cdnaStart;
int pepStart;
cdnaStart = 1;
pepStart = 1;
for (i=0; i<Vector_getNumElement(exons); i++) {
PredictionExon *exon = Vector_getElementAt(exons, i);
int phase;
if (!exon) {
if (cdna[0] == '\0') {
continue;
} else {
break;
}
}
phase = 0;
// NIY if (defined($exon->phase)) {
phase = PredictionExon_getPhase(exon);
// }
//fprintf(stderr, " phase for exon %d is %d\n", i, phase);
if (first) {
cdna = SeqUtil_addNs(cdna,phase);
first = 0;
}
/*
// Hack for now - should never happen
if (phase != lastPhase ) {
if (lastPhase == 1) {
cdna = StrUtil_appendString(cdna,"NN");
} else if (lastPhase == 2) {
cdna = StrUtil_appendString(cdna,"N");
}
// startpadding for this exon
cdna = SeqUtil_addNs(cdna,phase);
}
*/
cdna = StrUtil_appendString(cdna, PredictionExon_getSeqString(exon));
//lastPhase = PredictionExon_getEndPhase(exon);
//lastPhase = phase;
}
// NIY Freeing exons vector?
return cdna;
}
void GenomicAlignAdaptor_addDerivedAlignments(GenomicAlignAdaptor *gaa,
Vector *mergedAligns, GenomicAlign *alignA, GenomicAlign *alignB) {
// variable name explanation
// q - query c - consensus s - start e - end l - last
// o, ov overlap j - jump_in_
// r - result
int qs, qe, lqs, lqe, cs, ce, lce,
ocs, oce, oqs, oqe, jc, jq, ovs, ove,
rcs, rce, rqs, rqe;
int currentMatch = 0;
int newMatch;
int cigAPos = 0, cigBPos = 0;
char *resultCig;
char tmpStr[128];
// initialization phase
Vector *cigA = CigarStrUtil_getPieces(GenomicAlign_getCigarString(alignA));
Vector *cigB = CigarStrUtil_getPieces(GenomicAlign_getCigarString(alignB));
if (GenomicAlign_getQueryStrand(alignA) == -1 ) {
Vector_reverse(cigB);
}
// need a 'normalized' start for qs, qe, oxs so I dont
// have to check strandedness all the time
// consensus is strand 1 and is not compared to anything,
// can keep its original coordinate system
lce = GenomicAlign_getConsensusStart(alignA) - 1;
ce = lce;
cs = ce + 1;
// alignBs query can be + or - just keep relative coords for now
lqe = 0; lqs = 1;
qe = 0; qs = 1;
// ocs will be found relative to oce and has to be comparable
// to oqs. But it could be that we have to move downwards if we
// are not - strand. thats why coordinates are transformed here
if (GenomicAlign_getQueryStrand(alignA) == -1 ) {
// query_end is first basepair of alignment
if (GenomicAlign_getQueryEnd(alignA) < GenomicAlign_getConsensusEnd(alignB)) {
oce = 0; ocs = 1;
oqe = GenomicAlign_getConsensusEnd(alignB) - GenomicAlign_getQueryEnd(alignA);
oqs = oqe + 1;
} else {
oqe = 0; oqs = 1;
oce = GenomicAlign_getQueryEnd(alignA) - GenomicAlign_getConsensusEnd(alignB);
ocs = oce + 1;
}
} else {
// in theory no coordinate magic necessary :-)
oqs = GenomicAlign_getQueryStart(alignA);
oqe = oqs - 1;
ocs = GenomicAlign_getConsensusStart(alignB);
oce = ocs - 1;
}
// initializing result
rcs = rce = rqs = rqe = 0;
resultCig= StrUtil_copyString(&resultCig,"",0);
while (1) {
int newGa;
// exit if you request a new piece of alignment and the cig list is
// empty
if (oce < ocs || oce < oqs) {
// next M area in cigB
if (cigBPos == Vector_getNumElement(cigB)) break;
GenomicAlignAdaptor_nextCig(gaa, cigB, &cigBPos, &ocs, &oce, &qs, &qe );
continue;
}
if (oqe < oqs || oqe < ocs) {
// next M area in cigA
if (cigAPos == Vector_getNumElement(cigA)) break;
GenomicAlignAdaptor_nextCig(gaa, cigA, &cigAPos, &cs, &ce, &oqs, &oqe );
continue;
}
// now matching region overlap in reference genome
ovs = ocs < oqs ? oqs : ocs;
ove = oce < oqe ? oce : oqe;
if (currentMatch) {
jc = cs + (ovs - oqs) - lce - 1;
jq = qs + (ovs - ocs) - lqe - 1;
} else {
jc = jq = 0;
}
newMatch = ove - ovs + 1;
newGa = 0;
if (jc==0) {
if (jq==0) {
currentMatch += newMatch;
} else {
// store current match;
sprintf(tmpStr,"%dM",currentMatch);
resultCig = StrUtil_appendString(resultCig,tmpStr);
// jq deletions;
if (jq == 1) {
resultCig = StrUtil_appendString(resultCig,"D");
} else {
sprintf(tmpStr,"%dD",jq);
resultCig = StrUtil_appendString(resultCig,tmpStr);
}
currentMatch = newMatch;
}
} else {
if (jq==0) {
// store current match;
sprintf(tmpStr,"%dM",currentMatch);
resultCig = StrUtil_appendString(resultCig,tmpStr);
// jc insertions;
if (jc==1) {
resultCig = StrUtil_appendString(resultCig,"I");
} else {
sprintf(tmpStr,"%dI",jc);
resultCig = StrUtil_appendString(resultCig,tmpStr);
}
currentMatch = newMatch;
} else {
double percId;
double score;
GenomicAlign *ga;
sprintf(tmpStr,"%dM",currentMatch);
resultCig = StrUtil_appendString(resultCig,tmpStr);
// new GA
int queryStrand = GenomicAlign_getQueryStrand(alignA) * GenomicAlign_getQueryStrand(alignB);
int queryStart, queryEnd;
if (queryStrand == 1) {
queryStart = rqs + GenomicAlign_getQueryStart(alignB) - 1;
queryEnd = rqe + GenomicAlign_getQueryStart(alignB) - 1;
} else {
queryEnd = GenomicAlign_getQueryEnd(alignB) - rqs + 1;
queryStart = GenomicAlign_getQueryEnd(alignB) - rqe + 1;
}
score = (GenomicAlign_getScore(alignA) < GenomicAlign_getScore(alignB)) ?
GenomicAlign_getScore(alignA) : GenomicAlign_getScore(alignB);
percId = (int)(GenomicAlign_getPercentId(alignA)*GenomicAlign_getPercentId(alignB)/100.0);
ga = GenomicAlign_new();
GenomicAlign_setConsensusDNAFrag(ga, GenomicAlign_getConsensusDNAFrag(alignA));
GenomicAlign_setQueryDNAFrag(ga, GenomicAlign_getQueryDNAFrag(alignB));
GenomicAlign_setCigarString(ga, resultCig);
GenomicAlign_setConsensusStart(ga, rcs);
GenomicAlign_setConsensusEnd(ga, rce);
GenomicAlign_setQueryStrand(ga, queryStrand);
GenomicAlign_setQueryStart(ga, queryStart);
GenomicAlign_setQueryEnd(ga, queryEnd);
GenomicAlign_setAdaptor(ga, (BaseAdaptor *)gaa);
GenomicAlign_setPercentId(ga, percId);
GenomicAlign_setScore(ga, score);
Vector_addElement(mergedAligns, ga);
rcs = rce = rqs = rqe = 0;
resultCig[0] = '\0';
currentMatch = newMatch;
}
}
if (!rcs) rcs = cs+(ovs-oqs);
rce = cs+(ove-oqs);
if (!rqs) rqs = qs+(ovs-ocs);
rqe = qs+(ove-ocs);
// update the last positions
lce = rce;
lqe = rqe;
// next piece on the one that end earlier
if (oce <= oqe) {
// next M area in cigB
if (cigBPos == Vector_getNumElement(cigB)) break;
GenomicAlignAdaptor_nextCig(gaa, cigB, &cigBPos, &ocs, &oce, &qs, &qe );
}
if (oce >= oqe) {
// next M area in cigA
if (cigAPos == Vector_getNumElement(cigA)) break;
GenomicAlignAdaptor_nextCig(gaa, cigA, &cigAPos, &cs, &ce, &oqs, &oqe );
}
} // end of while loop
// if there is a last floating current match
if (currentMatch) {
// new GA
int queryStrand = GenomicAlign_getQueryStrand(alignA) * GenomicAlign_getQueryStrand(alignB);
int queryStart, queryEnd;
double percId;
double score;
GenomicAlign *ga;
sprintf(tmpStr,"%dM",currentMatch);
resultCig = StrUtil_appendString(resultCig, tmpStr);
if (queryStrand == 1) {
queryStart = rqs + GenomicAlign_getQueryStart(alignB) - 1;
queryEnd = rqe + GenomicAlign_getQueryStart(alignB) - 1;
} else {
queryEnd = GenomicAlign_getQueryEnd(alignB) - rqs + 1;
queryStart = GenomicAlign_getQueryEnd(alignB) - rqe + 1;
}
score = (GenomicAlign_getScore(alignA) < GenomicAlign_getScore(alignB)) ?
GenomicAlign_getScore(alignA) : GenomicAlign_getScore(alignB);
percId = (int)(GenomicAlign_getPercentId(alignA)*GenomicAlign_getPercentId(alignB)/100.0);
ga = GenomicAlign_new();
GenomicAlign_setConsensusDNAFrag(ga, GenomicAlign_getConsensusDNAFrag(alignA));
GenomicAlign_setQueryDNAFrag(ga, GenomicAlign_getQueryDNAFrag(alignB));
GenomicAlign_setCigarString(ga, resultCig);
GenomicAlign_setConsensusStart(ga, rcs);
GenomicAlign_setConsensusEnd(ga, rce);
GenomicAlign_setQueryStrand(ga, queryStrand);
GenomicAlign_setQueryStart(ga, queryStart);
GenomicAlign_setQueryEnd(ga, queryEnd);
GenomicAlign_setAdaptor(ga, (BaseAdaptor *)gaa);
GenomicAlign_setPercentId(ga, percId);
GenomicAlign_setScore(ga, score);
Vector_addElement(mergedAligns, ga);
}
free(resultCig);
Vector_free(cigA);
Vector_free(cigB);
// nothing to return all in merged_aligns
}
void GenomicAlignAdaptor_store(GenomicAlignAdaptor *gaa, Vector *genomicAligns) {
int ok = 1;
char *qStr = NULL;
StatementHandle *sth;
char commaStr[2] = {'\0','\0'};
int i;
char *tmpStr = NULL;
if ((tmpStr = (char *)calloc(65556,sizeof(char))) == NULL) {
fprintf(stderr,"Failed allocating tmpStr\n");
ok = 0;
}
if (ok) {
StrUtil_copyString(&qStr, "INSERT INTO genomic_align_block"
" (consensus_dnafrag_id, consensus_start, consensus_end,"
" query_dnafrag_id, query_start, query_end, query_strand, method_link_id,"
" score, perc_id, cigar_line) VALUES ",0);
for (i=0; i<Vector_getNumElement(genomicAligns); i++) {
GenomicAlign *ga = Vector_getElementAt(genomicAligns,i);
DNAFrag *consDNAFrag = GenomicAlign_getConsensusDNAFrag(ga);
DNAFrag *queryDNAFrag = GenomicAlign_getQueryDNAFrag(ga);
// check that everything has dbIDs
if (!DNAFrag_getDbID(consDNAFrag) || !DNAFrag_getDbID(queryDNAFrag)) {
fprintf(stderr, "Error: dna_fragment in GenomicAlign is not in DB\n");
ok = 0;
break;
}
}
}
GenomicAlign *ga = NULL;
DNAFrag *consDNAFrag = NULL;
DNAFrag *queryDNAFrag = NULL;
IDType methodLinkId = 0;
if (ok) {
// all clear for storing
for (i=0; i<Vector_getNumElement(genomicAligns); i++) {
ga = Vector_getElementAt(genomicAligns,i);
consDNAFrag = GenomicAlign_getConsensusDNAFrag(ga);
queryDNAFrag = GenomicAlign_getQueryDNAFrag(ga);
methodLinkId = GenomicAlignAdaptor_methodLinkIdByAlignmentType(gaa, GenomicAlign_getAlignmentType(ga));
if (!methodLinkId) {
fprintf(stderr, "Error: There is no method_link with this type [%s] in the DB.\n",
GenomicAlign_getAlignmentType(ga));
ok = 0;
break;
}
}
if (ok) {
sprintf(tmpStr," %s(" IDFMTSTR ", %d, %d, " IDFMTSTR ", %d, %d, %d, " IDFMTSTR ", %f, %f, '%s')",
commaStr,
DNAFrag_getDbID(consDNAFrag),
GenomicAlign_getConsensusStart(ga),
GenomicAlign_getConsensusEnd(ga),
DNAFrag_getDbID(queryDNAFrag),
GenomicAlign_getQueryStart(ga),
GenomicAlign_getQueryEnd(ga),
GenomicAlign_getQueryStrand(ga),
methodLinkId,
GenomicAlign_getScore(ga),
GenomicAlign_getPercentId(ga),
GenomicAlign_getCigarString(ga));
qStr = StrUtil_appendString(qStr, tmpStr);
commaStr[0] = ',';
}
sth = gaa->prepare((BaseAdaptor *)gaa, qStr, strlen(qStr));
sth->execute(sth);
sth->finish(sth);
}
if (qStr)
free(qStr);
if (tmpStr)
free(tmpStr);
}
Vector *GenomicAlignAdaptor_fetchAllByDNAFragGenomeDBDirect( GenomicAlignAdaptor *gaa,
DNAFrag *dnaFrag, GenomeDB *targetGenome, int *startP, int *endP, IDType methodLinkId) {
IDType dnaFragId;
GenomeDB *genomeDB;
char *qStr = NULL;
char tmpStr[512];
Vector *results;
StatementHandle *sth;
int ok = 0;
if (!dnaFrag) {
fprintf(stderr, "Error: Input dnafrag must not be NULL\n");
ok = 0;
}
if (ok) {
// formatting the dnafrag
dnaFragId = DNAFrag_getDbID(dnaFrag);
genomeDB = DNAFrag_getGenomeDB(dnaFrag);
StrUtil_copyString(&qStr,
"SELECT gab.consensus_dnafrag_id,"
" gab.consensus_start,"
" gab.consensus_end,"
" gab.query_dnafrag_id,"
" gab.query_start,"
" gab.query_end,"
" gab.query_strand,"
" gab.method_link_id,"
" gab.score,"
" gab.perc_id,"
" gab.cigar_line"
" FROM genomic_align_block gab ",0);
if (targetGenome) {
qStr = StrUtil_appendString(qStr,", dnafrag d");
}
sprintf(tmpStr," WHERE gab.method_link_id = " IDFMTSTR, methodLinkId);
qStr = StrUtil_appendString(qStr,tmpStr);
results = Vector_new();
if (!targetGenome ||
GenomeDB_hasQuery(genomeDB, targetGenome, methodLinkId)) {
Vector *qres;
sprintf(tmpStr," AND gab.consensus_dnafrag_id = " IDFMTSTR, dnaFragId);
qStr = StrUtil_appendString(qStr, tmpStr);
if (startP && endP) {
int lowerBound = *startP - gaa->maxAlignmentLength;
sprintf(tmpStr,
" AND gab.consensus_start <= %d"
" AND gab.consensus_start >= %d"
" AND gab.consensus_end >= %d", *endP, lowerBound, *startP ) ;
qStr = StrUtil_appendString(qStr, tmpStr);
}
if (targetGenome) {
sprintf(tmpStr,
" AND gab.query_dnafrag_id = d.dnafrag_id"
" AND d.genome_db_id = " IDFMTSTR, GenomeDB_getDbID(targetGenome));
qStr = StrUtil_appendString(qStr, tmpStr);
}
sth = gaa->prepare((BaseAdaptor *)gaa, qStr, strlen(qStr));
sth->execute(sth);
qres = GenomicAlignAdaptor_objectsFromStatementHandle(gaa, sth, 0);
Vector_append(results,qres);
Vector_free(qres);
sth->finish(sth);
}
if (!targetGenome ||
GenomeDB_hasConsensus(genomeDB, targetGenome, methodLinkId)) {
Vector *cres;
sprintf(tmpStr," AND gab.query_dnafrag_id = " IDFMTSTR, dnaFragId);
qStr = StrUtil_appendString(qStr, tmpStr);
if (startP && endP) {
int lowerBound = *startP - gaa->maxAlignmentLength;
sprintf(tmpStr,
" AND gab.query_start <= %d"
" AND gab.query_start >= %d"
" AND gab.query_end >= %d", *endP, lowerBound, *startP ) ;
qStr = StrUtil_appendString(qStr, tmpStr);
}
if (targetGenome) {
sprintf(tmpStr,
" AND gab.consensus_dnafrag_id = d.dnafrag_id"
" AND d.genome_db_id = " IDFMTSTR, GenomeDB_getDbID(targetGenome));
qStr = StrUtil_appendString(qStr, tmpStr);
}
sth = gaa->prepare((BaseAdaptor *)gaa, qStr, strlen(qStr));
sth->execute(sth);
cres = GenomicAlignAdaptor_objectsFromStatementHandle(gaa, sth, 1);
Vector_append(results,cres);
Vector_free(cres);
sth->finish(sth);
}
}
if (qStr)
free(qStr);
return results;
}
