struct genePred *loadGenes(int numGenePreds, char **genePredFiles)
/* load and sort genes */
{
int i;
struct genePred *genes = NULL;
for (i = 0; i < numGenePreds; i++)
genes = slCat(genes, genePredReaderLoadFile(genePredFiles[i], NULL));
slSort(&genes, genePredCmp);
return genes;
}
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);
}
void mafGene(char *dbName, char *mafTable, char *geneTable,
char *speciesList, char *outName)
/* mafGene - output protein alignments using maf and genePred. */
{
struct slName *speciesNames = readList(speciesList);
FILE *f = mustOpen(outName, "w");
struct genePred *list = NULL;
if (geneList != NULL)
{
struct slName *geneNames = readList(geneList);
for(; geneNames; geneNames = geneNames->next)
{
struct genePred *pred =
getPredsForName(geneNames->name, geneTable, dbName);
if (pred != NULL)
slCat(&list, pred);
}
}
else if (useFile)
/* Read genePreds from a file passed instead of a table */
list = genePredReaderLoadFile(geneTable, NULL);
else if (geneName != NULL)
list = getPredsForName(geneName, geneTable, dbName);
else if (geneBeds != NULL)
list = getPredsFromBeds(geneBeds, geneTable, dbName);
else
list = queryPreds(dbName, geneTable);
for(; list; list = list->next)
{
verbose(2, "outting gene %s \n",list->name);
outGenePred(f, list, dbName, mafTable, geneTable, speciesNames);
if (delay)
{
verbose(2, "delaying %d seconds\n",delay);
sleep(delay);
}
}
}
