/*************************************************************************
* Output JSON data for a motif
*************************************************************************/
static void output_motif_json(JSONWR_T* json, MOTIF_STATS_T* stats,
SITE_COUNTS_T* counts) {
//vars
MOTIF_T *motif;
MATRIX_T *freqs;
int i, j, mlen, asize, end;
motif = stats->motif;
freqs = get_motif_freqs(motif);
asize = alph_size(get_motif_alph(motif), ALPH_SIZE);
jsonwr_start_object_value(json);
jsonwr_lng_prop(json, "db", stats->db->id);
jsonwr_str_prop(json, "id", get_motif_id(motif));
if (*(get_motif_id2(motif))) {
jsonwr_str_prop(json, "alt", get_motif_id2(motif));
}
mlen = get_motif_length(motif);
jsonwr_lng_prop(json, "len", mlen);
jsonwr_dbl_prop(json, "motif_evalue", get_motif_evalue(motif));
jsonwr_dbl_prop(json, "motif_nsites", get_motif_nsites(motif));
if (get_motif_url(motif) && *get_motif_url(motif)) {
jsonwr_str_prop(json, "url", get_motif_url(motif));
}
jsonwr_property(json, "pwm");
jsonwr_start_array_value(json);
for (i = 0; i < mlen; i++) {
jsonwr_start_array_value(json);
for (j = 0; j < asize; j++) {
jsonwr_dbl_value(json, get_matrix_cell(i, j, freqs));
}
jsonwr_end_array_value(json);
}
jsonwr_end_array_value(json);
jsonwr_lng_prop(json, "bin_width", stats->central_window+1);
jsonwr_dbl_prop(json, "bin_sites", stats->central_sites);
jsonwr_lng_prop(json, "total_sites", counts->total_sites);
jsonwr_dbl_prop(json, "log_pvalue", stats->log_adj_pvalue);
jsonwr_dbl_prop(json, "max_prob", stats->max_prob);
jsonwr_property(json, "sites");
jsonwr_start_array_value(json);
end = counts->allocated - (mlen - 1);
for (i = (mlen - 1); i < end; i += 2) {
jsonwr_dbl_value(json, counts->sites[i]);
}
jsonwr_end_array_value(json);
jsonwr_end_object_value(json);
}
/*************************************************************************
* Output motif site counts
*************************************************************************/
static void output_site_counts(FILE* fh, int sequence_length,
MOTIF_DB_T* db, MOTIF_T* motif, SITE_COUNTS_T* counts) {
// vars
int i, w, end;
char *alt;
fprintf(fh, "DB %d MOTIF\t%s", db->id, get_motif_id(motif));
alt = get_motif_id2(motif);
if (alt[0]) fprintf(fh, "\t%s", alt);
fprintf(fh, "\n");
w = get_motif_length(motif);
end = counts->allocated - (w - 1);
for (i = (w - 1); i < end; i += 2) {
fprintf(fh, "% 6.1f\t%g\n",
((double)(i - sequence_length + 1)) / 2.0,
counts->sites[i]);
}
}
/**************************************************************************
* Outputs txt for the spacings
**************************************************************************/
void output_secondary_motif_txt(FILE *txt_output,
MOTIF_DB_T *primary_db, MOTIF_T *primary_motif,
SECONDARY_MOTIF_T *parent, SECONDARY_MOTIF_T *smotif,
int n_secondary_motifs, LINKLST_T *rmotifs) {
LINK_T *node;
SIGSPACE_T sig;
int i, quad;
char* orient_names[NORIENTS];
// this maintains the previous definition of orientation but actual names would be better
orient_names[LEFT | SAME] = "0";
orient_names[LEFT | OPPO] = "1";
orient_names[RIGHT | SAME] = "2";
orient_names[RIGHT | OPPO] = "3";
orient_names[UP_SEC_PAL] = "4";
orient_names[UP_PRI_PAL] = "5";
orient_names[DOWN_PRI_PAL] = "6";
orient_names[DOWN_SEC_PAL] = "7";
orient_names[BOTH_PAL] = "8";
for (i = 0; i < smotif->sig_count; ++i) {
sig = smotif->sigs[i];
// Output txt line.
fprintf(txt_output, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%.2e\t%d\t%s\t%d\t%d\t%.2e\t%.2e\n",
primary_db->name,
get_motif_id(primary_motif),
strcmp(get_motif_id2(primary_motif), "") ? get_motif_id2(primary_motif) : ".",
get_motif_consensus(primary_motif),
smotif->db->name,
get_motif_id(smotif->motif),
strcmp(get_motif_id2(smotif->motif), "") ? get_motif_id2(smotif->motif) : ".",
get_motif_consensus(smotif->motif),
get_motif_trim_left(smotif->motif),
get_motif_trim_right(smotif->motif),
parent ? smotif->db->name : ".",
parent ? get_motif_id(parent->motif) : ".",
parent && strcmp(get_motif_id2(parent->motif), "") ? get_motif_id2(parent->motif) : ".",
smotif->min_pvalue * n_secondary_motifs, // E-value
sig.bin, // gap
orient_names[sig.orient], // orientation
smotif->spacings[sig.orient].count[sig.bin], // count
smotif->total_spacings, // total occurrences of secondary in margins
sig.pvalue < 1e-10 ? sig.pvalue/NORIENTS : 1-pow((1-sig.pvalue),1.0/NORIENTS),
sig.pvalue
);
}
if (rmotifs != NULL && linklst_size(rmotifs) > 0) {
for (node = linklst_first(rmotifs); node != NULL; node = linklst_next(node)) {
SECONDARY_MOTIF_T *rmotif = linklst_get(node);
output_secondary_motif_txt(txt_output, primary_db, primary_motif, smotif, rmotif, n_secondary_motifs, NULL);
}
}
}
/*************************************************************************
* Output CentriMo text output
*************************************************************************/
static void output_centrimo_text(CENTRIMO_OPTIONS_T *options, int motifN,
ARRAYLST_T *stats_list) {
MOTIF_STATS_T *stats;
char *file_path;
int i, pad;
double log_motifN;
FILE *text_file;
MOTIF_T *motif;
// find the evalue conversion factor
log_motifN = log(motifN);
// Sort and write centrimo.txt
arraylst_qsort(motif_stats_compar, stats_list);
// open centrimo text file
file_path = make_path_to_file(options->output_dirname, TEXT_FILENAME);
text_file = fopen(file_path, "w");
free(file_path);
fputs("# motif \tE-value\tadj_p-value\tlog_adj_p-value\t"
"bin_width\ttotal_width\tsites_in_bin\ttotal_sites\tp_success\t"
"p-value\tmult_tests\n", text_file);
fprintf(text_file, "# Found %d motifs with E-values <= %g\n",
arraylst_size(stats_list), options->evalue_thresh);
// write centrimo text output
for (i = 0; i < arraylst_size(stats_list); i++) {
stats = arraylst_get(i, stats_list);
motif = stats->motif;
pad = 19 - strlen(get_motif_id(motif));
fprintf(text_file, "%s %-*s\t", get_motif_id(motif),
pad, get_motif_id2(motif));
print_log_value(text_file, stats->log_adj_pvalue + log_motifN, 1);
fputs("\t", text_file);
print_log_value(text_file, stats->log_adj_pvalue, 1);
fprintf(text_file, "\t%.2f\t%d\t%d\t%.0f\t%ld\t%.5f\t",
stats->log_adj_pvalue, stats->central_window+1, stats->all_window,
stats->central_sites, stats->total_sites,
stats->central_prob);
print_log_value(text_file, stats->log_pvalue, 1);
fprintf(text_file, "\t%d\n", stats->n_win_tested);
}
fclose(text_file);
}
