/**************************************************************************
* Generate logos for a motif
* Warning, this may modify the path and motif arguments.
**************************************************************************/
static void generate_motif_logos(OPTIONS_T *options, STR_T *path, MOTIF_T *motif) {
int path_len;
char name[MAX_MOTIF_ID_LENGTH + 1];
copy_and_sanatise_name(name, get_motif_id(motif), MAX_MOTIF_ID_LENGTH);
name[MAX_MOTIF_ID_LENGTH] = '\0';
path_len = str_len(path);
str_appendf(path, "logo%s", name);
CL_create1(motif, FALSE, FALSE, "MEME (no SSC)", str_internal(path),
options->eps, options->png);
if (options->rc) {
str_truncate(path, path_len);
str_appendf(path, "logo_rc%s", name);
reverse_complement_motif(motif);
CL_create1(motif, FALSE, FALSE, "MEME (no SSC)", str_internal(path),
options->eps, options->png);
}
str_truncate(path, path_len);
}
void generate_ceq_logos(char *meme_path, char *output_dir) {
int i, dir_len, prefix_len, path_len;
ARRAY_T *background;
BOOLEAN_T has_reverse_strand;
char *path, *alphabet;
double logo_height, logo_width;
ARRAYLST_T *motifs;
MOTIF_T *motif;
motifs = arraylst_create();
logo_height = LOGOHEIGHT;
//make the path
dir_len = strlen(output_dir);
prefix_len = strlen(LOGO_PREFIX);
path_len = dir_len + 1 + prefix_len + MAX_MOTIF_ID_LENGTH + 1;
path = malloc(sizeof(char)*path_len);
strncpy(path, output_dir, path_len);
if (path[dir_len-1] != '/') {
path[dir_len] = '/';
path[++dir_len] = '\0';
}
strncpy(path+dir_len, LOGO_PREFIX, path_len - dir_len);
// Read all motifs into an array.
read_meme_file2(meme_path,
NULL, // bg file name
DEFAULT_PSEUDOCOUNTS,
REQUIRE_PSPM,
motifs,
NULL,//motif occurrences
&has_reverse_strand,
&background);
// global alphabet is set by read_meme_file
alphabet = get_alphabet(FALSE);
if (create_output_directory(output_dir, TRUE, (verbosity >= NORMAL_VERBOSE))) {
// Failed to create output directory.
exit(1);
}
for(i = 0; i < arraylst_size(motifs); i++) {
motif = (MOTIF_T*)arraylst_get(i, motifs);
logo_width = get_motif_length(motif);
if (logo_width > MAXLOGOWIDTH) logo_width = MAXLOGOWIDTH;
copy_and_sanatise_name(path+(dir_len+prefix_len), get_motif_id(motif), path_len - (dir_len + prefix_len));
CL_create2(
motif, // motif
"", // no title
NULL, // no second motif
"", // no x-axis label
FALSE, // no error bars
FALSE, // ssc
logo_height, // logo height (cm)
logo_width, // logo width (cm)
alphabet, // alphabet
0, // no offset to second motif
path, // output file path
"MEME (no SSC)" // program name
);
}
free_motifs(motifs);
free_array(background); // not used
free(path);
}
