static void fakePslFromGenePred(char *db, char *fileTbl, char *pslOut, char *cdsOut)
/* check a genePred */
{
struct genePredReader *gpr;
struct genePred *gp;
FILE *pslFh = mustOpen(pslOut, "w");
FILE *cdsFh = mustOpen(cdsOut, "w");
struct hash *chromHash = getChromHash(db);
if (fileExists(fileTbl))
{
gpr = genePredReaderFile(fileTbl, NULL);
}
else
{
struct sqlConnection *conn = hAllocConn(db);
gpr = genePredReaderQuery(conn, fileTbl, NULL);
hFreeConn(&conn);
}
while ((gp = genePredReaderNext(gpr)) != NULL)
{
cnvGenePred(chromHash, gp, pslFh, cdsFh);
}
genePredReaderFree(&gpr);
carefulClose(&pslFh);
carefulClose(&cdsFh);
}
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);
}
static void checkGenePred(char *fileTbl)
/* check a genePred file or table */
{
struct sqlConnection *conn = NULL;
struct genePredReader *gpr;
struct genePred *gp;
int iRec = 0;
if (fileExists(fileTbl))
{
gpr = genePredReaderFile(fileTbl, NULL);
}
else if (gDb != NULL)
{
conn = hAllocConn(gDb);
gpr = genePredReaderQuery(conn, fileTbl, NULL);
}
else
{
errAbort("file %s doesn't exist, must specify -db=db if this is a table", fileTbl);
}
while ((gp = genePredReaderNext(gpr)) != NULL)
{
checkAGenePred(fileTbl, ++iRec, gp);
genePredFree(&gp);
}
genePredReaderFree(&gpr);
hFreeConn(&conn);
}
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;
}
static void loadGenes(struct orgGenes *genes, char *genePredFile)
/* load genePred file into object */
{
struct genePredReader *gpr = genePredReaderFile(genePredFile, NULL);
struct genePred *gp;
while ((gp = genePredReaderNext(gpr)) != NULL)
{
if ((gp->optFields & genePredExonFramesFld) == 0)
genePredAddExonFrames(gp);
loadGene(genes, gp);
}
genePredReaderFree(&gpr);
}
static void genePredHisto(char *what, char *gpFile, char *outFile)
/* get data for generating histograms from a genePred file. */
{
struct genePredReader *gpr = genePredReaderFile(gpFile, NULL);
histoFuncType histoFunc = getHistoFunc(what);
struct genePred *gp;
FILE *outFh = mustOpen(outFile, "w");
while ((gp = genePredReaderNext(gpr)) != NULL)
{
histoFunc(gp, outFh);
genePredFree(&gp);
}
carefulClose(&outFh);
genePredReaderFree(&gpr);
}
