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;
}
char *
msa2tree (char **mfa, unsigned int num) {
// fprintf(stderr, "TREELIB: Starting msa2tree [%d]\n", num);
struct DistanceMatrix *mat = NULL;
struct Alignment *aln = NULL;
struct ClusterGroup *group = NULL;
struct Tree *njTree = NULL;
char *treestring = NULL;
assert(num >= 0);
if (num == 0) {
return NULL;
} else if (num == 1) {
if(asprintf(&treestring, "%d;", 0) == -1)
fatal_util("asprintf failed");
return treestring;
} else if (num == 2) {
float dist = jcdist(mfa[0], mfa[1]);
dist *= 0.5;
if(asprintf(&treestring, "(%d:%g, %d:%g)", 0, dist, 1, dist) == -1)
fatal_util("asprintf failed");
return treestring;
}
// fprintf(stderr, "TREELIB: Here is the msa\n");
// unsigned int i = 0;
// for (i=0; i<num; i++) {
// fprintf(stderr, "TREELIB:\t[%s]\n", mfa[i]);
// }
// fprintf(stderr, "TREELIB: Building the distance matrix\n");
mat = mfa2dist(mfa, num);
aln_init(&aln, num);
group = alignment_to_ClusterGroup(aln, 0);
group->matrix = mat;
// print_DistanceMatrix(stderr, mat);
fprintf(stderr, "TREELIB: Building the NJ tree\n");
njTree = neighbour_joining_buildtree(group, 0);
struct Tnode *tmpNode = NULL;
tmpNode = njTree->child[2];
njTree->child[2] = NULL;
// fprintf(stderr, "TREELIB: Rooting the tree\n");
struct Tnode *leftNode = NULL;
leftNode = (struct Tnode *) malloc_util(sizeof(struct Tnode));
leftNode->left = njTree->child[0];
leftNode->right = njTree->child[1];
leftNode->distance = 0.0;
struct Tnode *rootNode = NULL;
rootNode = (struct Tnode *) malloc_util(sizeof(struct Tnode));
rootNode->left = leftNode;
rootNode->right = tmpNode;
njTree->child[0] = rootNode;
njTree->child[1] = NULL;
fprintf(stderr, "TREELIB: Converting tree to string\n");
treestring = tree2string(njTree);
// fprintf(stderr, "TREELIB: [[%s]]\n", treestring);
// fprintf(stderr, "TREELIB: free aln\n");
aln = free_Alignment(aln);
// fprintf(stderr, "TREELIB: free group\n");
group = free_ClusterGroup(group);
// fprintf(stderr, "TREELIB: free njTree\n");
// njTree = free_Tree(njTree);
// fprintf(stderr, "TREELIB: Ending msa2tree\n");
return treestring;
}
