static void getGeneAnns(struct sqlConnection *conn, struct hash *refSeqVerInfoTbl, char *outFile)
/* get request genePred annotations from database */
{
struct genePred *gps = genePredReaderLoadQuery(conn, "refGene", NULL);
slSort(&gps, genePredNameCmp);
FILE *fh = mustOpen(outFile, "w");
struct genePred *gp;
for (gp = gps; gp != NULL; gp = gp->next)
processGenePred(fh, refSeqVerInfoTbl, gp);
carefulClose(&fh);
genePredFreeList(&gps);
}
void genePredToGtf(char *database, char *table, char *gtfOut)
/* genePredToGtf - Convert genePredName table or file to gtf.. */
{
FILE *f = mustOpen(gtfOut, "w");
struct hash *dupeHash = newHash(16);
struct genePred *gpList = NULL, *gp = NULL;
if (sameString(database, "file"))
{
gpList = genePredReaderLoadFile(table, NULL);
}
else
{
struct sqlConnection *conn = sqlConnect(database);
gpList = genePredReaderLoadQuery(conn, table, NULL);
sqlDisconnect(&conn);
}
for (gp = gpList; gp != NULL; gp = gp->next)
genePredWriteToGtf(gp, source, dupeHash, f);
carefulClose(&f);
}
static boolean allelesExists(struct section *section,
struct sqlConnection *conn, char *geneId)
// Return TRUE if common haplotype alleles exist.
{
// If there was a reset then clear out settings
if (cartUsualBoolean(cart, HAPLO_RESET_ALL, FALSE))
cartRemovePrefix(cart,HAPLO_TABLE "_" );
// Start with the default variables for haplotype retrieval
struct haploExtras *he = haplotypeExtrasDefault(database, 0);
section->extras = he;
// Need to get genePred struct from geneId
char where[128];
safef(where,sizeof(where),"name = '%s'",geneId);
struct genePred *gp = genePredReaderLoadQuery(conn,he->geneTable, where);
if (gp == NULL || gp->cdsStart == gp->cdsEnd) // Ain't interested in non-protein coding genes
{
haplotypeExtrasFree(&he);
return FALSE;
}
he->chrom = gp->chrom; // Probably not needed
he->justModel = lmCloneString(he->lm,geneId);
//he->growTree = FALSE; // Tree growing not needed here
// Need to determine the correct vcf file and open it
if (haplotypesDiscoverVcfFile(he, gp->chrom) == NULL)
{
haplotypeExtrasFree(&he);
return FALSE;
}
struct vcfFile *vcff = vcfTabixFileMayOpen(he->inFile, NULL, 0, 0,VCF_IGNORE_ERRS, 0);
if (vcff == NULL)
{
haplotypeExtrasFree(&he);
return FALSE;
}
vcfFileMakeReusePool(vcff,1024 * 1024);
// All or Limit to the 99%
boolean rareVars = cartUsualBoolean(cart, HAPLO_RARE_VAR, FALSE);
if (rareVars)
he->synonymous = TRUE;
else
he->variantMinPct = HAPLO_COMMON_VARIANT_MIN_PCT;
// Lets show the population distribution
he->populationsToo = cartUsualBoolean(cart, HAPLO_MAJOR_DIST, FALSE);
he->populationsMinor = cartUsualBoolean(cart, HAPLO_MINOR_DIST, FALSE);
if (he->populationsToo)
he->populationMinPct = 5;
else if (he->populationsMinor)
{
he->populationsMinor = FALSE;
cartRemove(cart, HAPLO_MINOR_DIST );
}
// Need to generate haplotypes
section->items = geneHapSetForOneModel(he,vcff,gp,TRUE);
return TRUE;// (section->items != NULL);
}
