static double motifScoreHere(char *chrom, int start, int end,
char *motifName, char *motifTable)
/* Return score of motif at given position. */
{
double score;
struct dnaSeq *seq = hDnaFromSeq(database, chrom, start, end, dnaLower);
struct dnaMotif *motif = loadDnaMotif(motifName, motifTable);
char strand = dnaMotifBestStrand(motif, seq->dna);
if (strand == '-')
reverseComplement(seq->dna, seq->size);
score = dnaMotifBitScore(motif, seq->dna);
dnaMotifFree(&motif);
dnaSeqFree(&seq);
return score;
}
void emblMatrixToMotif(char *inName, char *outName)
/* emblMatrixToMotif - Convert transfac matrix in EMBL format to dnaMotif. */
{
struct hash *hash = NULL;
struct lineFile *lf = emblOpen(inName, NULL);
FILE *f = mustOpen(outName, "w");
struct dnaMotif *motif;
while ((hash = emblRecord(lf)) != NULL)
{
char *ac = hashFindVal(hash, "AC");
char *po = hashFindVal(hash, "P0");
if (ac != NULL && po != NULL && orgFits(hash))
{
motif = emblToMotif(ac, hash);
dnaMotifTabOut(motif, f);
dnaMotifFree(&motif);
}
}
}
