int main(int argc, char* argv[])
{
// Read parameters from console.
CCmdLine cmdLine;
if(cmdLine.SplitLine(argc, argv) < 5)
{
cerr << "Usage: ./bbnet -s score_file -n node -b bkg -f func_depth -o output" << endl;
cerr << endl << "Additional parameter:" << endl;
cerr << "-k\tPenalty parameter(logK, Default = 5.0)" << endl;
cerr << "-c\tnumber of candidate motifs (Default=50)" << endl;
cerr << "-d\tpositive negative (for prediction using BN)" << endl;
cerr << "-l\toutput of all training samples' information." << endl;
cerr << "-t\ttranslational(transcriptional) start sites.(Default = right end)" << endl;
cerr << "-rb\tbit-string to determine which rules to include.(Default = 111110)" << endl;
cerr << "-i\tUse mutual information instead of Bayesian score" << endl;
cerr << endl << "Contact: \"Li Shen\"<*****@*****.**>" << endl;
return 1;
}
string s, n, b, f, o;
try
{
s = cmdLine.GetArgument("-s", 0); // score file.
n = cmdLine.GetArgument("-n", 0); // node gene list file.
b = cmdLine.GetArgument("-b", 0); // bkg gene list file.
f = cmdLine.GetArgument("-f", 0); // func depth folder.
o = cmdLine.GetArgument("-o", 0); // results output file.
}
catch(int)
{
cerr << "Wrong arguments!" << endl;
return 1;
}
if(cmdLine.HasSwitch("-i"))
itag = true;
//itag = true;
//string s = "../gbnet/data/Beer/scor_test.list";
//string n = "../gbnet/data/Beer/node.list";
//string b = "../gbnet/data/Beer/bkg.list";
//string f = "../gbnet/data/Beer/func";
//string k = "0.015";
//logK = atof(k.data());
//string o = "../gbnet/data/Beer/bb_res_test2.txt";
string k; // Penalty parameter; logK value.
if(!itag)
k = cmdLine.GetSafeArgument("-k", 0, "5.0");
else
k = cmdLine.GetSafeArgument("-k", 0, "0.015");
logK = atof(k.data());
string c = cmdLine.GetSafeArgument("-c", 0, "50"); // number of candidate motifs. default = 50.
motifcand = atoi(c.data());
// Use prior counts for some motifs if specified.
string p = cmdLine.GetSafeArgument("-p", 0, "0"); // prior counts.
pricnt = atoi(p.data());
if(pricnt > 0) // read preferred motifs list from file.
{
prior = 1;
string fPrim = cmdLine.GetSafeArgument("-p", 1, "primot.txt");
vector<string> primv;
if(get1stcol(fPrim, primv) < 0)
return 1;
for(size_t i = 0; i < primv.size(); i++)
primo.insert(primv[i]);
}
// File names for positive, negative and left-out testing lists.
string pos = cmdLine.GetSafeArgument("-d", 0, ""); // positive testing cases.
string neg = cmdLine.GetSafeArgument("-d", 1, ""); // negative testing cases.
string res = cmdLine.GetSafeArgument("-d", 2, ""); // left-out testing cases.
vector<string> plst, nlst, rlst; // positive, negative and left-out lists.
if(pos != "" && neg != "")
{
if(get1stcol(pos, plst) < 0)
return 1;
if(get1stcol(neg, nlst) < 0)
return 1;
}
if(res != "")
{
if(get1stcol(res, rlst) < 0)
return 1;
}
// File for output of all training samples' information.
string finfo = cmdLine.GetSafeArgument("-l", 0, "");
// File to store all genes' translational/transcriptional start sites.
string ftss = cmdLine.GetSafeArgument("-t", 0, "");
if(ftss != "")
loadtss(ftss, mtss);
// A bit-string to determine which rules to include.
rb = cmdLine.GetSafeArgument("-rb", 0, "111110");
string bp = cmdLine.GetSafeArgument("-bp", 0, ""); // Output each gene's probability like in Beer's prediction.
// Load motif Bayesian score file.
if(loadscor(mscor, s) != 0)
{
cerr << "Load motif scores eror!" << endl;
return 1;
}
else
{
#ifdef VERBOSE
cout << "Display candidate motifs that are loaded:" << endl;
dispscor(mscor);
#endif
}
vector<MotifScore> oscor = mscor; // Save an original copy of motif scores.
// Load gene list.
vector<Case> tlst, blst, genlst;
set<string> genset;
if(loadgene(tlst, blst, n, b) != 0)
{
cerr << "Load gene lists error!" << endl;
return 1;
}
else
{
genlst.insert(genlst.end(), tlst.begin(), tlst.end());
genlst.insert(genlst.end(), blst.begin(), blst.end());
#ifdef VERBOSE
cout << "Load gene list completed!" << endl;
#endif
// All training and testing gene names are put into genmap.
for(size_t i = 0; i < genlst.size(); i++)
genset.insert(genlst[i].name);
for(size_t i = 0; i < plst.size(); i++)
genset.insert(plst[i]);
for(size_t i = 0; i < nlst.size(); i++)
genset.insert(nlst[i]);
for(size_t i = 0; i < rlst.size(); i++)
genset.insert(rlst[i]);
}
// Load motif binding information of genes in genmap.
if(loadbind(allbind, mscor, genset, f) != 0)
{
cerr << "Load binding information error!" << endl;
return 1;
}
else
{
#ifdef VERBOSE
cout << "Load binding information completed!" << endl;
#endif
}
// File for output.
ofstream hOut(o.data());
if(!hOut)
{
cerr << "Can't open " << o << endl;
return 1;
}
hOut << "Number of genes in category 1: " << tlst.size() << endl;
hOut << "Number of genes in category 0: " << blst.size() << endl << endl;
#ifdef VERBOSE
cout << endl << "Running on original data." << endl;
#endif
vector<Constraint> cons;
vector<CPTRow> cpt;
clock_t start = clock();
double scor = bbnet(cons, cpt, genlst);
clock_t finish = clock();
if(outbayes(hOut, scor, cons, cpt, oscor, tlst.size(), blst.size()) != 0)
{
cerr << "Output Bayesian network results error!" << endl;
return 1;
}
if(finfo != "")
{
if(outgene(finfo, tlst, blst, cons) != 0)
cerr << "Output training samples' information error!" << endl;
return 1;
}
if(pos != "" && neg != "")
{
Pred d = predict(cons, cpt, plst, nlst);
outpred(hOut, d, n, b, pos, neg);
if(bp != "") // output each gene's probability being in this cluster if output file is specified.
{
ofstream hbp(bp.data());
if(!hbp)
{
cerr << "Can't open " << bp << endl;
return 1;
}
vector<BPred> trnbp = predict(cons, cpt, genlst, 0); // probabilities for training genes.
outpred(hbp, trnbp);
vector<string> tstlst; // probabilities for testing genes.
tstlst.insert(tstlst.end(), plst.begin(), plst.end()); // positive testings.
tstlst.insert(tstlst.end(), nlst.begin(), nlst.end()); // negative testings.
vector<BPred> tstbp = predict(cons, cpt, tstlst, 1);
outpred(hbp, tstbp);
if(res != "") // probabilities for left-out genes if the left-out file is specified.
{
vector<BPred> lefbp = predict(cons, cpt, rlst, -1);
outpred(hbp, lefbp);
}
hbp.close();
}
}
hOut << endl << "Bayesian network occupied CPU " << (double)(finish-start)/CLOCKS_PER_SEC << " seconds." << endl;
hOut.close();
return 0;
}
void *
dlopen(const char *path, int mode)
{
ModulePtr mp;
static void *mainModule;
/*
* Upon the first call register a terminate handler that will close all
* libraries. Also get a reference to the main module for use with
* loadbind.
*/
if (!mainModule)
{
if ((mainModule = findMain()) == NULL)
return NULL;
atexit(terminate);
}
/*
* Scan the list of modules if we have the module already loaded.
*/
for (mp = modList; mp; mp = mp->next)
if (strcmp(mp->name, path) == 0)
{
mp->refCnt++;
return mp;
}
if ((mp = (ModulePtr) calloc(1, sizeof(*mp))) == NULL)
{
errvalid++;
strcpy(errbuf, "calloc: ");
strcat(errbuf, strerror(errno));
return NULL;
}
if ((mp->name = strdup(path)) == NULL)
{
errvalid++;
strcpy(errbuf, "strdup: ");
strcat(errbuf, strerror(errno));
free(mp);
return NULL;
}
/*
* load should be declared load(const char *...). Thus we cast the path to
* a normal char *. Ugly.
*/
if ((mp->entry = (void *) load((char *) path, L_NOAUTODEFER, NULL)) == NULL)
{
free(mp->name);
free(mp);
errvalid++;
strcpy(errbuf, "dlopen: ");
strcat(errbuf, path);
strcat(errbuf, ": ");
/*
* If AIX says the file is not executable, the error can be further
* described by querying the loader about the last error.
*/
if (errno == ENOEXEC)
{
char *tmp[BUFSIZ / sizeof(char *)];
if (loadquery(L_GETMESSAGES, tmp, sizeof(tmp)) == -1)
strcpy(errbuf, strerror(errno));
else
{
char **p;
for (p = tmp; *p; p++)
caterr(*p);
}
}
else
strcat(errbuf, strerror(errno));
return NULL;
}
mp->refCnt = 1;
mp->next = modList;
modList = mp;
if (loadbind(0, mainModule, mp->entry) == -1)
{
dlclose(mp);
errvalid++;
strcpy(errbuf, "loadbind: ");
strcat(errbuf, strerror(errno));
return NULL;
}
/*
* If the user wants global binding, loadbind against all other loaded
* modules.
*/
if (mode & RTLD_GLOBAL)
{
ModulePtr mp1;
for (mp1 = mp->next; mp1; mp1 = mp1->next)
if (loadbind(0, mp1->entry, mp->entry) == -1)
{
dlclose(mp);
errvalid++;
strcpy(errbuf, "loadbind: ");
strcat(errbuf, strerror(errno));
return NULL;
}
}
if (readExports(mp) == -1)
{
dlclose(mp);
return NULL;
}
/*
* If there is a dl_info structure, call the init function.
*/
if (mp->info = (struct dl_info *) dlsym(mp, "dl_info"))
{
if (mp->info->init)
(*mp->info->init) ();
}
else
errvalid = 0;
/*
* If the shared object was compiled using xlC we will need to call static
* constructors (and later on dlclose destructors).
*/
if (mp->cdtors = (CdtorPtr) dlsym(mp, "__cdtors"))
{
while (mp->cdtors->init)
{
(*mp->cdtors->init) ();
mp->cdtors++;
}
}
else
errvalid = 0;
return mp;
}
/* ARGSUSED */
void *dlopen(const char *path, int mode)
{
register ModulePtr mp;
static void *mainModule;
/*
* Upon the first call register a terminate handler that will
* close all libraries. Also get a reference to the main module
* for use with loadbind.
*/
if (!mainModule) {
if ((mainModule = findMain()) == NULL)
return NULL;
atexit(terminate);
}
/*
* Scan the list of modules if have the module already loaded.
*/
for (mp = modList; mp; mp = mp->next)
if (strcmp(mp->name, path) == 0) {
mp->refCnt++;
return mp;
}
if ((mp = (ModulePtr)calloc(1, sizeof(*mp))) == NULL) {
errvalid++;
strcpy(errbuf, "calloc: ");
strcat(errbuf, strerror(errno));
return NULL;
}
if ((mp->name = strdup(path)) == NULL) {
errvalid++;
strcpy(errbuf, "strdup: ");
strcat(errbuf, strerror(errno));
free(mp);
return NULL;
}
/*
* load should be declared load(const char *...). Thus we
* cast the path to a normal char *. Ugly.
*/
if ((mp->entry = (void *)load((char *)path, L_NOAUTODEFER, NULL)) == NULL) {
free(mp->name);
free(mp);
errvalid++;
strcpy(errbuf, "dlopen: ");
strcat(errbuf, path);
strcat(errbuf, ": ");
/*
* If AIX says the file is not executable, the error
* can be further described by querying the loader about
* the last error.
*/
if (errno == ENOEXEC) {
char *tmp[BUFSIZ/sizeof(char *)];
if (loadquery(L_GETMESSAGES, tmp, sizeof(tmp)) == -1)
strcpy(errbuf, strerror(errno));
else {
char **p;
for (p = tmp; *p; p++)
caterr(*p);
}
} else
strcat(errbuf, strerror(errno));
return NULL;
}
mp->refCnt = 1;
mp->next = modList;
modList = mp;
if (loadbind(0, mainModule, mp->entry) == -1) {
dlclose(mp);
errvalid++;
strcpy(errbuf, "loadbind: ");
strcat(errbuf, strerror(errno));
return NULL;
}
if (readExports(mp) == -1) {
dlclose(mp);
return NULL;
}
/*
* If there is a dl_info structure, call the init function.
*/
if (mp->info = (struct dl_info *)dlsym(mp, "dl_info")) {
if (mp->info->init)
(*mp->info->init)();
} else
errvalid = 0;
return mp;
}
