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;
}
void read_regexp_file(
char* filename, // Name of MEME file IN
int* num_motifs, // Number of motifs retrieved OUT
MOTIF_T* motifs // The retrieved motifs - NOT ALLOCATED!
) {
FILE* motif_file; // MEME file containing the motifs.
char motif_name[MAX_MOTIF_ID_LENGTH+1];
char motif_regexp[MAX_MOTIF_WIDTH];
ARRAY_T* these_freqs;
MOTIF_T* m;
int i;
//Set things to the defaults.
*num_motifs = 0;
// Open the given MEME file.
if (open_file(filename, "r", TRUE, "motif", "motifs", &motif_file) == 0)
exit(1);
//Set alphabet - ONLY supports dna.
set_alphabet(verbosity, "ACGT");
while (fscanf(motif_file, "%s\t%s", motif_name, motif_regexp) == 2) {
/*
* Now we:
* 1. Fill in new motif (preallocated)
* 2. Assign name
* 3. Convert regexp into frequency table.
*/
m = &(motifs[*num_motifs]);
set_motif_id(motif_name, m);
m->length = strlen(motif_regexp);
/* Store the alphabet size in the motif. */
m->alph_size = get_alph_size(ALPH_SIZE);
m->ambigs = get_alph_size(AMBIG_SIZE);
/* Allocate memory for the matrix. */
m->freqs = allocate_matrix(m->length, get_alph_size(ALL_SIZE));
//Set motif frequencies here.
for (i=0;i<strlen(motif_regexp);i++) {
switch(toupper(motif_regexp[i])) {
case 'A':
set_matrix_cell(i,alphabet_index('A',get_alphabet(TRUE)),1,m->freqs);
break;
case 'C':
set_matrix_cell(i,alphabet_index('C',get_alphabet(TRUE)),1,m->freqs);
break;
case 'G':
set_matrix_cell(i,alphabet_index('G',get_alphabet(TRUE)),1,m->freqs);
break;
case 'T':
set_matrix_cell(i,alphabet_index('T',get_alphabet(TRUE)),1,m->freqs);
break;
case 'U':
set_matrix_cell(i,alphabet_index('U',get_alphabet(TRUE)),1,m->freqs);
break;
case 'R': //purines
set_matrix_cell(i,alphabet_index('G',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('A',get_alphabet(TRUE)),1,m->freqs);
break;
case 'Y': //pyramidines
set_matrix_cell(i,alphabet_index('T',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('C',get_alphabet(TRUE)),1,m->freqs);
break;
case 'K': //keto
set_matrix_cell(i,alphabet_index('G',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('T',get_alphabet(TRUE)),1,m->freqs);
break;
case 'M': //amino
set_matrix_cell(i,alphabet_index('A',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('C',get_alphabet(TRUE)),1,m->freqs);
break;
case 'S': //strong
set_matrix_cell(i,alphabet_index('G',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('C',get_alphabet(TRUE)),1,m->freqs);
break;
case 'W': //weak
set_matrix_cell(i,alphabet_index('A',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('T',get_alphabet(TRUE)),1,m->freqs);
break;
case 'B':
set_matrix_cell(i,alphabet_index('G',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('T',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('C',get_alphabet(TRUE)),1,m->freqs);
break;
case 'D':
set_matrix_cell(i,alphabet_index('G',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('A',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('T',get_alphabet(TRUE)),1,m->freqs);
break;
case 'H':
set_matrix_cell(i,alphabet_index('A',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('C',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('T',get_alphabet(TRUE)),1,m->freqs);
break;
case 'V':
set_matrix_cell(i,alphabet_index('G',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('C',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('A',get_alphabet(TRUE)),1,m->freqs);
break;
case 'N':
set_matrix_cell(i,alphabet_index('A',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('C',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('G',get_alphabet(TRUE)),1,m->freqs);
set_matrix_cell(i,alphabet_index('T',get_alphabet(TRUE)),1,m->freqs);
break;
}
}
/* Compute values for ambiguous characters. */
for (i = 0; i < m->length; i++) {
these_freqs = get_matrix_row(i, m->freqs);
fill_in_ambiguous_chars(FALSE, these_freqs);
}
/* Compute and store the motif complexity. */
m->complexity = compute_motif_complexity(m);
//Move our pointer along to do the next motif.
(*num_motifs)++;
}
}
