void gffIntoDatabase(char *database, char *fileName, char *table, int offset)
/* Load a gff file into database. */
{
struct gffFile *gff = gffFileNew("");
struct gffGroup *group;
struct genePred *gpList = NULL, *gp;
FILE *f;
char *tabName = "genePred.tab";
/* Load fixed gff and convert it to genePred. */
gffFileAdd(gff, fileName, 0);
gffGroupLines(gff);
for (group = gff->groupList; group != NULL; group = group->next)
{
gp = genePredFromGroupedGff(gff, group, group->name, "exon",
genePredCdsStatFld|genePredExonFramesFld,
genePredGxfDefaults);
if (gp != NULL)
{
slAddHead(&gpList, gp);
genePredOffset(gp, offset);
}
}
slSort(&gpList, genePredCmp);
/* Create tab-delimited file. */
f = mustOpen(tabName, "w");
for (gp = gpList; gp != NULL; gp = gp->next)
genePredTabOut(gp, f);
carefulClose(&f);
/* Load into database. */
loadIntoDatabase(database, createGenePred, "sanger22", tabName);
}
void hgSanger20(char *database, char *gffFile, char *infoFile)
/* Process chromosome 20 gff file. */
{
struct hash *infoHash = readInfoFile(infoFile);
struct sanger22extra *sxList = processGff(gffFile, infoHash), *sx;
char *tabName = "extra.tab";
FILE *f = mustOpen(tabName, "w");
for (sx = sxList; sx != NULL; sx = sx->next)
sanger22extraTabOut(sx, f);
carefulClose(&f);
loadIntoDatabase(database, sanger22extraCreate, "sanger20extra", tabName);
}
void hgSanger22(char *database, char *txGff, char *cdsGff, char *mrnaFa, char *aaFa,
int shortArmSize)
/* hgSanger22 - Load up database with Sanger 22 annotations. */
{
char *fixedGff = "fixed.gff";
char *extraBed = "extras.bed";
struct hash *extraHash = newHash(0);
struct sanger22extra *extraList;
extraList = makeFixedGffAndReadExtra(txGff, cdsGff, fixedGff, extraHash);
saveExtras(extraBed, extraList);
loadIntoDatabase(database, sanger22extraCreate, "sanger22extra", extraBed);
gffIntoDatabase(database, fixedGff, "sanger22", shortArmSize);
}