static MOTIF_T* post_process_motif(MREAD_T *mread, MOTIF_T *motif) {
ARRAY_T *bg;
int site_count;
if (motif == NULL) return NULL;
assert(motif->alph != INVALID_ALPH);
if (motif->freqs) normalize_motif(motif, 0.00001);
site_count = (motif->num_sites > 0 ? motif->num_sites : DEFAULT_SITES);
if (motif->freqs != NULL && motif->scores != NULL) {
// validate? May not be possible for protein motifs as MEME tweaks the PSSM
} else if (motif->scores != NULL) {
// calculate the freqs
motif->freqs = convert_scores_into_freqs(motif->alph, motif->scores,
mread->motif_bg, site_count, PSEUDO);
} else if (motif->freqs != NULL) {
// calculate the scores
motif->scores = convert_freqs_into_scores(motif->alph, motif->freqs,
mread->motif_bg, site_count, PSEUDO);
} else {
die("Motif with no PSPM or PSSM should not get here!\n");
}
apply_pseudocount_to_motif(motif, mread->pseudo_bg, mread->pseudo_total);
motif->complexity = compute_motif_complexity(motif);
if (mread->options & CALC_AMBIGS) calc_motif_ambigs(motif);
if (mread->trim) trim_motif_by_bit_threshold(motif, mread->trim_bits);
return motif;
}
/***********************************************************************
* Converts a TRANSFAC motif to a MEME motif.
* Caller is responsible for freeing the returned MOTIF_T.
***********************************************************************/
MOTIF_T *convert_transfac_motif_to_meme_motif(
char *id,
int pseudocount,
ARRAY_T *bg,
TRANSFAC_MOTIF_T *motif
) {
MATRIX_T *counts = get_transfac_counts(motif);
if (counts == NULL) {
die(
"Unable to convert TRANSFAC motif %s to MEME motif: "
"missing counts matrix.",
id
);
};
// Convert the motif counts to frequencies.
int num_bases = get_num_cols(counts);
int motif_width = get_num_rows(counts);
int motif_position = 0;
MATRIX_T *freqs = allocate_matrix(motif_width, num_bases);
for (motif_position = 0; motif_position < motif_width; ++motif_position) {
int i_base = 0;
int num_seqs = 0; // motif columns may have different counts
for (i_base = 0; i_base < num_bases; i_base++) {
num_seqs += get_matrix_cell(motif_position, i_base, counts);
}
for (i_base = 0; i_base < num_bases; i_base++) {
double freq =
(get_matrix_cell(motif_position, i_base, counts)
+ (pseudocount * get_array_item(i_base, bg))) / (num_seqs + pseudocount);
set_matrix_cell(motif_position, i_base, freq, freqs);
}
}
MOTIF_T *meme_motif = allocate_motif(id, DNA_ALPH, NULL, freqs);
calc_motif_ambigs(meme_motif);
return meme_motif;
}
