static void processBed6(char *database, char *track, FILE *f, struct bed *bed,
struct slName *orgList)
/* generate MAF alignment for a bed6 */
{
struct mafAli *maf;
char *useName = refCoords ? NULL : bed->name;
if (txStarts)
{
maf = hgMafFrag(database, track,
bed->chrom, bed->chromStart, bed->chromEnd, bed->strand[0],
useName, orgList);
maf->regDef = mafRegDefNew(mafRegDefTxUpstream,
bed->chromEnd-bed->chromStart,
bed->name);
if (meFirst)
moveMeToFirst(maf, database);
}
else
{
maf = hgMafFrag(database, track,
bed->chrom, bed->chromStart, bed->chromEnd, bed->strand[0],
useName, orgList);
if (meFirst)
moveMeToFirst(maf, bed->name);
}
mafWrite(f, maf);
mafAliFree(&maf);
}
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 mafFrags(char *database, char *track, char *bedFile, char *mafFile)
/* mafFrags - Collect MAFs from regions specified in a 6 column bed file. */
{
struct slName *orgList = NULL;
struct lineFile *lf = lineFileOpen(bedFile, TRUE);
FILE *f = mustOpen(mafFile, "w");
if (optionExists("orgs"))
{
char *orgFile = optionVal("orgs", NULL);
char *buf;
readInGulp(orgFile, &buf, NULL);
orgList = stringToSlNames(buf);
/* Ensure that org list starts with database. */
struct slName *me = slNameFind(orgList, database);
if (me == NULL)
errAbort("Need to have reference database '%s' in %s", database, orgFile);
if (me != orgList)
{
slRemoveEl(&orgList, me);
slAddHead(&orgList, me);
}
}
mafWriteStart(f, "zero");
if (bed12)
{
char *row[12];
while (lineFileRow(lf, row))
{
struct bed *bed = bedLoadN(row, ArraySize(row));
struct mafAli *maf = mafFromBed12(database, track, bed, orgList);
if (meFirst)
moveMeToFirst(maf, bed->name);
mafWrite(f, maf);
mafAliFree(&maf);
bedFree(&bed);
}
}
else
{
char *row[6];
while (lineFileRow(lf, row))
{
struct bed *bed = bedLoadN(row, ArraySize(row));
processBed6(database, track, f, bed, orgList);
bedFree(&bed);
}
}
mafWriteEnd(f);
carefulClose(&f);
}
