/******************************************************************************
* This function scores a sequence database using mhmmscan
*****************************************************************************/
void run_mhmmscan(
MCAST_OPTIONS_T *options,
char *hmm_filename,
char *seq_filename,
char *scores_filename
) {
if (verbosity >= NORMAL_VERBOSE) {
fprintf(stderr, "%s", "Creating HMM from motif file.\n");
}
// Build the command line for mhmmscan
const char *bin_dir = get_meme_bin_dir();
char *cmd;
cmd = build_cmd(
"mhmmscan",
"%s/mhmmscan %s %s %s --fancy --allow-weak-motifs %s --p-thresh %s "
"--max-gap %s --e-thresh %s --eg-cost 1 --pseudo-weight %s %s "
"%s %s > %s",
bin_dir,
options->bg_filename != NULL ? "--bg-file" : "",
options->bg_filename != NULL ? options->bg_filename : "",
options->text_only ? "--text" : "",
options->use_synth ? "--synth" : "",
options->p_thresh,
options->max_gap,
options->e_thresh,
options->pseudo_weight,
options->quiet ? "--quiet" : "",
hmm_filename,
seq_filename,
scores_filename
);
// Execute mhmmscan
if (verbosity >= NORMAL_VERBOSE) {
fprintf(stderr, "Executing %s\n", cmd);
}
int status = system(cmd);
// Check for interrupts
if (WIFSIGNALED(status) &&
(WTERMSIG(status) == SIGINT || WTERMSIG(status) == SIGQUIT)) {
die("Interrupted while running mhmmscan");
}
if (status == -1) {
// Unable to start mhmmscan
perror("Error starting mhmmscan command");
die("Unable to start mhmmscan command (%s)", cmd);
}
// Check result of running mhmmscan
int result = WEXITSTATUS(status);
if (result != 0) {
die("mhmmscan failed with exit status %d, command run was: %s", result, cmd);
}
free(cmd);
}
/******************************************************************************
* This function builds a star topology HMM from a MEME format motif file.
* The HMM is stored in a text file in the output directory.
*****************************************************************************/
void run_mhmm(
char *motif_filename,
char *hmm_filename
) {
if (verbosity >= NORMAL_VERBOSE) {
fprintf(stderr, "%s", "Creating HMM from motif file.\n");
}
// Build the command line for mhmm
const char *bin_dir = get_meme_bin_dir();
char *cmd;
cmd = build_cmd(
"mhmm",
"%s/mhmm --type star --keep-unused --verbosity %d %s > %s",
bin_dir,
verbosity,
motif_filename,
hmm_filename
);
// Execute mhmm
if (verbosity >= NORMAL_VERBOSE) {
fprintf(stderr, "Executing %s\n", cmd);
}
int status = system(cmd);
// Check for interrupts
if (WIFSIGNALED(status) &&
(WTERMSIG(status) == SIGINT || WTERMSIG(status) == SIGQUIT)) {
die("Interrupted while running mhmm");
}
if (status == -1) {
// Unable to start mhmm
perror("Error starting mhmm command");
die("Unable to start mhmm command (%s)", cmd);
}
// Check result of running mhmm
int result = WEXITSTATUS(status);
if (result != 0) {
die("mhmm failed with exit status %d, command run was: %s", result, cmd);
}
free(cmd);
}
int main(int argc, char **argv) {
data d;
glam2_aln *alns;
int r;
prog_name = "glam2"; /* for error messages */
getargs(&d.a, argc, argv);
init(&d);
fputs("GLAM2: Gapped Local Alignment of Motifs\nVersion "
#include "glam2_version.h"
"\n\n", d.out);
printargs(d.out, argc, argv);
print_misc_info(d.out, &d);
putc('\n', d.out);
XMALLOC(alns, d.a.runs);
for (r = 0; r < d.a.runs; ++r) {
glam2_aln *aln = &alns[r];
if (!d.a.quiet) {
fprintf(stderr, "Run %d... ", r+1);
fflush(stderr);
}
aln_init(aln, d.seqs.seqnum, d.a.max_width, d.alph.size);
d.sm.underflow_flag = 1; /* do we care about underflow in start_aln? */
start_aln(aln, &d);
optimise_aln(aln, &d);
if (d.sm.underflow_flag < (d.a.algorithm == 2 ? DBL_EPSILON : DBL_MIN))
fprintf(stderr, "%s: accuracy loss due to numeric underflow (%g)\nIf the alignment looks suspect, try rerunning with higher -u, or maybe lower -b\n", prog_name, d.sm.underflow_flag);
if (d.a.profile)
print_aln_info(d.out, aln, &d);
}
if (!d.a.quiet) putc('\n', stderr);
SORT(alns, d.a.runs, aln_cmp);
if (!d.a.profile)
print_alns(d.out, alns, &d);
xfclose(d.out); // close text output file
// Create the HTML output and MEME format output
char *glam2html, *glam2psfm, *command;
int command_length, command_ret;
// create the paths to the programs
glam2html = make_path_to_file(get_meme_bin_dir(), "glam2html");
glam2psfm = make_path_to_file(get_meme_bin_dir(), "glam2psfm");
// allocate memory for the command
command_length = strlen(glam2html) + strlen(d.txt_filename) + strlen(d.html_filename) + 50;
command = xmalloc(command_length);
// run glam2html
sprintf(command, "%s < %s > %s", glam2html, d.txt_filename, d.html_filename);
if ((command_ret = system(command)) != 0) {
report_external_failure("glam2html", command_ret);
fprintf(stderr, "Warning: failed to convert output to HTML!\n");
}
// run glam2psfm
sprintf(command, "%s < %s > %s", glam2psfm, d.txt_filename, d.psfm_filename);
if ((command_ret = system(command)) != 0) {
report_external_failure("glam2psfm", command_ret);
fprintf(stderr, "Warning: failed to convert output to MEME format motif!\n");
}
free(command);
free(glam2psfm);
free(glam2html);
return 0;
}
