#include using namespace std; using ll = long long; string P[3] = { "ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCA", "TTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTC", "TCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCT" }; double score[3][7] = {{449.7,449.7,449.7,449.7,437.7,161,147.35}, {450,435,450,449.7,444,180,139.8}, {449.4,449.1,404.7,450,449.7,147,148} }; vector vrt[7]; ll levenshtein(string &s, string &t){ int n = s.size(), m = t.size(); ll dp[n + 1][m + 1]; //goal to be low as possible for(int i = 0; i <= n; i++) for(int j = 0; j <= m; j++){ ll &dpc = dp[i][j] = (i || j) * n * m; if(i) dpc = min(dpc, dp[i - 1][j] + 1); //add char s if(j) dpc = min(dpc, dp[i][j - 1] + 1); //add char t if(i && j) dpc = min(dpc, dp[i - 1][j - 1] + (s[i - 1] != t[j - 1])); //replace or equal } return dp[n][m]; } ll smithWaterman(string &s, string &t){ int n = s.size(), m = t.size(), x = 0, y = 0; ll dp[n + 1][m + 1]; //goal to be high as possible for(int i = 0; i <= n; i++) for(int j = 0; j <= m; j++){ ll &dpc = dp[i][j] = 0; if(i) dpc = max(dpc, dp[i - 1][j] - 2); //add char s if(j) dpc = max(dpc, dp[i][j - 1] - 2); //add char t if(i && j) dpc = max(dpc, dp[i - 1][j - 1] + 3 * (2 * (s[i - 1] == t[j - 1]) - 1)); //test equality if(dpc > dp[x][y]) x = i, y = j; } return dp[x][y]; } //change return to switch out objective ll sequenceCmp(string s, string t){ return smithWaterman(s, t); } const int k = 21; bitset test(string & probe) { bitset bs; double avg[7]; for (int i = 0; i < 7; ++i) { avg[i] = 0; for (int j = 0; j < 20; ++j) { avg[i] += sequenceCmp(probe, vrt[i][j]); } avg[i] /= 20; cout << avg[i] << ' '; } cout << '\n'; int cnt = 0; for (int i = 0; i < 7; ++i) { for (int j = i+1; j < 7; ++j) { if (abs(avg[i]-avg[j]) > 10) bs[cnt] = 1; cnt++; cout << avg[i] << ' ' << avg[j] << ' ' << bs[cnt-1] << '\n'; } } cout << bs << '\n'; return bs; } vector dp[4][1 << k]; void analyze_spike_sequences(){ int cnt = 0; for (int i = 0; i < 7; ++i) { for (int j = 0; j <= vrt[i][0].size()-150; ++j) { string probe(begin(vrt[i][0])+j, begin(vrt[i][0])+j+150); bitset bs = test(probe); cout << probe << ' ' << cnt++ << endl; int bsint = 0; //change to int for(int i = 0; i < k; i++) bsint |= bs[i] << i; //add to dp knapack fashion for(int i = 2; ~i; i--) for(int j = 0; j < (1 << k); j++){ if(dp[i][j].size() == i && (i || !j)){ int x = i + 1, y = j | bsint; if(dp[x][y].empty()){ dp[x][y] = dp[i][j]; dp[x][y].push_back(probe); } } } } } int retx = 0, rety = 0; //find best dp coverage for(int i = 3; i <= 3; i++) for(int j = 0; j < (1 << k); j++){ if(!dp[i][j].empty() && __builtin_popcount(j) > __builtin_popcount(rety)){ retx = i, rety = j; } } cout << retx << " " << rety << endl; for(string probe : dp[retx][rety]){ bitset bs = test(probe); for(int i = 0; i < k; i++) cout << bs[i]; cout << endl; cout << probe << endl; } } void mkscores() { cout << '{'; for (int i = 0; i < 3; ++i) { cout << "{"; for (int j = 0; j < 7; ++j) { score[i][j] = 0; for (int k = 0; k < 20; ++k) score[i][j] += sequenceCmp(P[i], vrt[j][k]); score[i][j] /= 20; cout << score[i][j]; if (j < 6) cout << ","; } cout <<"}"; if (i < 2) cout << ","; cout << '\n'; } cout << '}'; } // classify a string int solve(string & s) { double val[3]; for (int i = 0; i < 3; ++i) val[i] = sequenceCmp(P[i], s); double diff[7]; for (int i = 0; i < 7; ++i) { diff[i] = 0; for (int j = 0; j < 3; ++j) diff[i] += pow(val[j]-score[j][i], 2); } return min_element(diff, diff+7)-diff; } string types[7] = {"original", "B.1.1.7", "B.1.351", "B.1.427", "P.1", "not_sars_cov2", "not_sars_cov2" }; void answer(){ for(int i = 0; i < 100;i++){ string inp; cin >> inp; cout << types[solve(inp)] << '\n'; } } int main(){ ios::sync_with_stdio(0); cin.tie(0); srand(time(0)); /*if (fopen("input.txt", "r")) { freopen("input.txt", "r", stdin); answer(); return 0; }*/ if (fopen("spikesequences.txt", "r")) { freopen("spikesequences.txt", "r", stdin); for (int i = 0; i < 7; ++i) { // 7 vrts for (int j = 0; j < 20; ++j) { string s, t; cin >> s >> t; vrt[i].push_back(t); } } // if (P[0] != "") mkscores(); // else analyze_spike_sequences(); return 0; } answer(); return 0; }