void mafOrtholog(char *database, char *track, char *genePredFile, char *outFile)
/* mafOrtholog - find orthlogs in other species based on maf alignment and reference genePred */
{
struct slName *orgList = NULL;
FILE *f = mustOpen(outFile, "w");
struct genePredReader *gpr = genePredReaderFile(genePredFile, NULL);
struct genePred *gpList = genePredReaderAll(gpr), *gp = NULL;
struct sqlConnection *conn = hAllocConn();
if (optionExists("nibDir"))
nibDir = optionVal("nibDir", NULL);
if (optionExists("orgs"))
{
char *orgFile = optionVal("orgs", NULL);
char *buf;
readInGulp(orgFile, &buf, NULL);
orgList = stringToSlNames(buf);
}
for (gp = gpList ; gp != NULL ; gp=gp->next)
{
struct mafAli *maf = NULL;
if (thickOnly)
maf = mafLoadInRegion(conn, track,
gp->chrom, gp->cdsStart, gp->cdsEnd);
else
maf = mafLoadInRegion(conn, track,
gp->chrom, gp->txStart, gp->txEnd);
if (meFirst)
moveMeToFirst(maf, database);
printOrthologs(f, maf, gp);
mafAliFree(&maf);
}
carefulClose(&f);
}
struct genePred *genePredReaderLoadFile(char* gpFile, char* chrom)
/* Function that encapsulates reading a genePred file */
{
struct genePredReader *gpr = genePredReaderFile(gpFile, chrom);
struct genePred *gpList = genePredReaderAll(gpr);
genePredReaderFree(&gpr);
return gpList;
}
struct genePred *genePredReaderLoadQuery(struct sqlConnection* conn,
char* table, char* where)
/* Function that encapsulates doing a query and loading the results */
{
struct genePredReader *gpr = genePredReaderQuery(conn, table, where);
struct genePred *gpList = genePredReaderAll(gpr);
genePredReaderFree(&gpr);
return gpList;
}
struct genePred *genePredReaderLoadRangeQuery(struct sqlConnection* conn,
char* table, char* chrom,
int start, int end,
char* extraWhere)
/* Function that encapsulates doing a range query and loading the results */
{
struct genePredReader *gpr = genePredReaderRangeQuery(conn, table, chrom,
start, end, extraWhere);
struct genePred *gpList = genePredReaderAll(gpr);
genePredReaderFree(&gpr);
return gpList;
}
static void printCcdsHgGeneUrl(struct sqlConnection *conn, char *ccdsId, char* kgId)
/* output a URL to hgGene for a ccds */
{
char where[128];
struct genePredReader *gpr;
struct genePred *ccdsGene = NULL, *kgGene = NULL;
/* get ccds genePred to get location */
sqlSafefFrag(where, sizeof(where), "chrom = '%s' and name = '%s'", seqName, ccdsId);
gpr = genePredReaderQuery(conn, "ccdsGene", where);
ccdsGene = genePredReaderAll(gpr);
genePredReaderFree(&gpr);
if (ccdsGene == NULL)
errAbort("%s not found in ccdsGene table for chrom %s", ccdsId, seqName);
else if (ccdsGene->next != NULL)
errAbort("multiple %s rows found in ccdsGene table for chrom %s", ccdsId, seqName);
/* get KG genePred, as need exact location for link */
sqlSafefFrag(where, sizeof(where), "name = '%s' and strand = '%s'", kgId,
ccdsGene->strand);
gpr = genePredReaderRangeQuery(conn, "knownGene", seqName,
ccdsGene->txStart, ccdsGene->txEnd, where);
kgGene = genePredReaderAll(gpr);
genePredReaderFree(&gpr);
if (kgGene == NULL)
errAbort("%s not found in knownGene table for chrom %s", kgId, seqName);
else if (kgGene->next != NULL)
errAbort("multiple %s rows found in knownGene table for chrom %s", kgId, seqName);
printf("../cgi-bin/hgGene?%s&%s=%s&%s=%s&%s=%s&%s=%d&%s=%d",
cartSidUrlString(cart),
"db", database,
"hgg_gene", kgId,
"hgg_chrom", seqName,
"hgg_start", kgGene->txStart,
"hgg_end", kgGene->txEnd);
genePredFree(&ccdsGene);
genePredFree(&kgGene);
}
/* query the list of gene names from the frames table */
static struct genePred *queryPreds(char *dbName, char *geneTable)
{
struct sqlConnection *conn = hAllocConn(dbName);
struct genePred *list = NULL;
char buf[2048];
char *extra = NULL;
struct genePredReader *reader;
if (onlyChrom != NULL)
{
safef(buf, sizeof buf, "chrom='%s'", onlyChrom);
extra = buf;
}
reader = genePredReaderQuery( conn, geneTable, extra);
list = genePredReaderAll(reader);
hFreeConn(&conn);
return list;
}
struct genePred *getOverlappingGeneDb(struct genePred **list, char *table, char *chrom, int cStart, int cEnd, char *name, int *retOverlap, char *db)
{
/* read all genes from a table find the gene with the biggest overlap.
Cache the list of genes to so we only read it once */
struct genePred *el = NULL, *bestMatch = NULL, *gp = NULL;
int overlap = 0 , bestOverlap = 0, i;
int *eFrames;
if (list == NULL)
return NULL;
if (*list == NULL)
{
struct genePred *gpList = NULL;
struct sqlConnection *conn = sqlConnect(db);
struct genePredReader *gpr = NULL;
if (!hTableExistsDb(db,table))
table = altTable;
if (!hTableExistsDb(db,table))
{
verbose(2,"no table %s in %s\n",table, db);
return NULL;
}
gpr = genePredReaderQuery(conn, table, NULL);
verbose(1,"Loading Predictions from %s in %s\n",table, db);
gpList = genePredReaderAll(gpr);
if (gpList != NULL)
{
hashAdd(geneListHash, db, gpList);
*list = gpList;
}
sqlDisconnect(&conn);
}
for (el = *list; el != NULL; el = el->next)
{
if (chrom != NULL && el->chrom != NULL)
{
overlap = 0;
if ( sameString(chrom, el->chrom))
{
for (i = 0 ; i<(el->exonCount); i++)
{
overlap += positiveRangeIntersection(cStart,cEnd, el->exonStarts[i], el->exonEnds[i]) ;
}
if (overlap > 20 && sameString(name, el->name))
{
bestMatch = el;
bestOverlap = overlap;
*retOverlap = bestOverlap;
}
if (overlap > bestOverlap)
{
bestMatch = el;
bestOverlap = overlap;
*retOverlap = bestOverlap;
}
}
}
}
if (bestMatch != NULL)
{
/* Allocate genePred and fill in values. */
AllocVar(gp);
gp->name = cloneString(bestMatch->name);
gp->chrom = cloneString(bestMatch->chrom);
gp->strand[1] = bestMatch->strand[1];
gp->strand[0] = bestMatch->strand[0];
gp->txStart = bestMatch->txStart;
gp->txEnd = bestMatch->txEnd;
gp->cdsStart = bestMatch->cdsStart;
gp->cdsEnd = bestMatch->cdsEnd;
gp->exonCount = bestMatch->exonCount;
AllocArray(gp->exonStarts, bestMatch->exonCount);
AllocArray(gp->exonEnds, bestMatch->exonCount);
for (i=0; i<bestMatch->exonCount; ++i)
{
gp->exonStarts[i] = bestMatch->exonStarts[i] ;
gp->exonEnds[i] = bestMatch->exonEnds[i] ;
}
gp->optFields = bestMatch->optFields;
gp->id = bestMatch->id;
if (bestMatch->optFields & genePredName2Fld)
gp->name2 = cloneString(bestMatch->name2);
else
gp->name2 = NULL;
if (bestMatch->optFields & genePredCdsStatFld)
{
gp->cdsStartStat = bestMatch->cdsStartStat;
gp->cdsEndStat = bestMatch->cdsEndStat;
}
if (bestMatch->optFields & genePredExonFramesFld)
{
gp->exonFrames = AllocArray(eFrames, bestMatch->exonCount);
for (i = 0; i < bestMatch->exonCount; i++)
gp->exonFrames[i] = bestMatch->exonFrames[i];
}
eFrames = gp->exonFrames;
}
return gp;
}
