/*
* Output font area and font name strings as a literal string
*/
static void
nameout(char *area, char *name)
{
char buf[500];
char *s;
if (*area==0 && okascmd(name)) {
snprintf(buf, sizeof(buf), "/%s", name);
cmdout(name);
} else {
for (s=area; *s; s++)
scout(*s);
for (s=name; *s; s++)
scout(*s);
stringend();
cmdout("cvn");
}
}
int test_search() {
Board b;
int status, depth, val;
status = WIN;
setup(&b);
depth = 4;
val = scout(&b, -20000, 20000, depth);
printf("negascout after depth %d came out as %d\n", depth, val);
return WIN;
}
void Operation::proceedTurn()
{
startMission(_nextMission); //startujemy misje, nextMission roœnie o jeden
scout(); //przeprowadzamy zwiad
}
int main(int argc, const char* argv[]) {
if(argc != 6) {
cerr << "Usage:\n";
cerr << "scanmot <ace_file> <motif_number> <sequence_file> <output_file> <max_sites>\n";
exit(0);
}
string ace_file(argv[1]);
string motnum(argv[2]);
string seq_file(argv[3]);
string out_file(argv[4]);
unsigned int ms = atoi(argv[5]);
// Read sequences and create background model
vector<string> seqs, nameset;
get_fasta_fast(seq_file.c_str(), seqs, nameset, 12);
Seqset scan_sseq(seqs);
BGModel bgm(scan_sseq, 0.5);
// Read motif from ACE file
vector<string> hits;
string line;
ifstream acein(ace_file.c_str());
bool found = false;
while(acein.good()) {
getline(acein, line);
istringstream iss(line);
vector<string> fields;
copy(istream_iterator<string>(iss),
istream_iterator<string>(),
back_inserter<vector<string> >(fields));
if(found) {
if(line[0] != '*') {
hits.push_back(fields[0]);
} else {
break;
}
} else {
if(fields.size() > 0
&& (fields[0].compare("Motif") == 0)
&& (fields[1].compare(motnum) == 0)) {
found = true;
}
}
}
if(! found) {
cerr << "Motif number " << motnum << " not found in ACE file '" << ace_file << "'\n";
exit(1);
}
Seqset ace_sseq(hits);
Motif mot(ace_sseq, 12, bgm.gcgenome());
mot.clear_cols();
for(unsigned int i = 0; i < line.length(); i++) {
if(line[i] == '*') mot.add_col(i);
}
for(unsigned int i = 0; i < hits.size(); i++) {
mot.add_site(i, 0, 1);
}
acein.close();
// Scan sequences
SiteHeap sh(ms);
double* sm = new double[mot.ncols() * 4];
double* am = new double[mot.ncols()];
mot.calc_score_matrix(sm, am);
int width = mot.get_width();
int n = 0;
double msc, bsc, scw, scc;
for(int c = 0; c < scan_sseq.num_seqs(); c++) {
for(int p = 0; p < scan_sseq.len_seq(c) - width; p++) {
msc = mot.score_site(scan_sseq, sm, am, c, p, 1);
bsc = bgm.score_site(mot, c, p, 1);
scw = msc - bsc;
// cerr << c << '\t' << p << '\t' << seqs[c].substr(p, width) << '\t' << 1 << '\t' << setprecision(4) << msc << '\t' << bsc << '\t' << scw << '\n';
ScoredSite ssw(scw, c, p, 1);
sh.add(ssw);
msc = mot.score_site(scan_sseq, sm, am, c, p, 0);
bsc = bgm.score_site(mot, c, p, 0);
scc = msc - bsc;
// cerr << c << '\t' << p << '\t' << seqs[c].substr(p, width) << '\t' << 0 << '\t' << setprecision(4) << msc << '\t' << bsc << '\t' << scc << '\n';
ScoredSite ssc(scc, c, p, 0);
sh.add(ssc);
n += 2;
}
}
delete [] sm;
// Print out the sites
ofstream scout(out_file.c_str());
for(int i = 0; i < sh.sitecount(); i++) {
ScoredSite bestss = sh.get_site(i);
scout << nameset[bestss.site.chrom()] << '\t';
scout << bestss.site.posit() << '\t';
scout << bestss.site.posit() + width - 1 << '\t';
scout << bestss.site.strand() << "\t";
if(bestss.site.strand())
scout << seqs[bestss.site.chrom()].substr(bestss.site.posit(), width) << '\t';
else
scout << reverse_comp(seqs[bestss.site.chrom()].substr(bestss.site.posit(), width)) << '\t';
scout << bestss.score << '\n';
}
scout.close();
}