505 lines
13 KiB
C++
505 lines
13 KiB
C++
#include <algorithm>
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#include <fstream>
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#include <iostream>
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#include <sstream>
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#include <string>
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#include <vector>
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using namespace std;
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class Basic_arg {
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public:
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int intype = 0, outype = 0;
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char *itn, *otn;
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Basic_arg(int intype, int outype, char* itn, char* otn)
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: intype(intype), outype(outype), itn(itn), otn(otn){};
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};
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class Sample {
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public:
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unsigned ntax, nchar;
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string *taxas, *chars;
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Sample(unsigned ntax, unsigned nchar) : ntax(ntax), nchar(nchar) {
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taxas = new string[ntax];
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chars = new string[ntax];
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};
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};
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Basic_arg procargs(int nargs, char** arg);
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Sample read_input(char* itn, int intype);
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void show_help(int help_num);
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Sample readFas(char* itn);
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Sample readPhy(char* itn);
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Sample readTnt(char* itn);
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Sample readNex(char* itn);
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void write_output(class Sample sam, char* otn, int outype);
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void writeFas(class Sample sam, char* otn);
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void writePhy(class Sample sam, char* otn);
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void writeTnt(class Sample sam, char* otn);
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void writeNex(class Sample sam, char* otn);
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bool isNum(string strnum);
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bool checkalign(class Sample sam);
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string to_lower(string stri);
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string add_space(char x, string str_old);
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string rep_space(string str_old);
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string del_space(string str_old);
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string checktype(string str);
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int countfre(string str, char c);
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int checkextension(string str);
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Sample readPhy(char* itn) {
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// read file
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ifstream matrixfile;
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matrixfile.open(itn);
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// read number of taxa and charcter
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string sntax, snseq, snall;
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getline(matrixfile, snall);
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istringstream istr(snall);
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istr >> sntax;
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istr >> snseq;
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int ntax, nchar;
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ntax = stoi(sntax);
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nchar = stoi(snseq); // string to int
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Sample sam(ntax, nchar);
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// read sequence
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unsigned int lennum;
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for (lennum = 0; lennum < sam.ntax; lennum++) {
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getline(matrixfile, snall);
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istringstream istr(snall);
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istr >> sam.taxas[lennum];
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istr >> sam.chars[lennum];
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}
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matrixfile.close();
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// return to class
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return sam;
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}
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Sample readFas(char* itn) {
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int ntax, nchar, lnum;
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ifstream matrixfile;
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matrixfile.open(itn);
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// use vector to read once use serveral times
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vector<string> file_content;
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// check line number and taxa number
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ntax = 0;
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string temln;
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for (lnum = 0; getline(matrixfile, temln); lnum++) {
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file_content.push_back(temln);
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if (temln[0] == '>') {
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ntax++;
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}
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}
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matrixfile.close();
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// check the nchar
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string str_i;
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int r;
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if (file_content.size() != 0) {
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r = file_content.size() / ntax;
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} else {
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cout << "MiMi:\tInput file contains 0 line" << endl;
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exit(0);
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}
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for (int i = 0; i < r; i++) {
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if (i > 0) {
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file_content[i] = del_space(file_content[i]);
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str_i = str_i + file_content[i];
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}
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}
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nchar = str_i.length();
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// create class
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Sample sam(ntax, nchar);
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// get class
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for (int a = 0, b = 0; a < (int)file_content.size(); a++) {
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if ((a + 1) % r == 1) {
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sam.taxas[b] = file_content[a];
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sam.taxas[b].erase(0, 1);
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sam.taxas[b] = rep_space(sam.taxas[b]);
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}
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if ((a + 1) % r > 1) {
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file_content[a] = del_space(file_content[a]);
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sam.chars[b] = sam.chars[b] + file_content[a];
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}
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if ((a + 1) % r == 0) {
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file_content[a] = del_space(file_content[a]);
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sam.chars[b] = sam.chars[b] + file_content[a];
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b++;
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}
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}
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return sam;
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}
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Sample readTnt(char* itn) {
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int ntax, nchar;
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ifstream matrixfile;
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matrixfile.open(itn);
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// get nchar and ntax
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string stri, sntax, snchar;
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for (int i = 0; i < 1;) {
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getline(matrixfile, stri);
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istringstream istr(stri);
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istr >> snchar;
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istr >> sntax;
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if (isNum(sntax) && isNum(snchar)) {
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ntax = stoi(sntax);
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nchar = stoi(snchar);
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i++;
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}
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}
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// create class
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Sample sam(ntax, nchar);
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// get class
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unsigned int lennum;
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for (lennum = 0; lennum < sam.ntax; lennum++) {
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getline(matrixfile, stri);
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istringstream istr(stri);
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istr >> sam.taxas[lennum];
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istr >> sam.chars[lennum];
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}
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matrixfile.close();
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return sam;
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}
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bool isNum(string strnum) {
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char* p;
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strtol(strnum.c_str(), &p, 10);
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return *p == 0;
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}
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Sample readNex(char* itn) {
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int ntax, nchar;
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// open file
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ifstream matrixfile;
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matrixfile.open(itn);
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// some var
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string snall, stri, str_a, str_b;
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bool found_ntax = false, found_nchar = false, found_equal = false;
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char x = '=';
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// get line number and read line to vector
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int lnum;
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unsigned int eulnum;
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vector<string> file_content;
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while (getline(matrixfile, snall)) {
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file_content.push_back(snall);
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}
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matrixfile.close();
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// getline line by line
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for (lnum = 0; lnum < (int)file_content.size(); lnum++) {
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str_a = to_lower(file_content[lnum]);
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str_b = add_space(x, str_a);
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istringstream istr(str_b);
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// convert to words
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while (istr >> stri) {
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if (stri == "ntax") {
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found_ntax = true;
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} else if (stri == "nchar") {
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found_nchar = true;
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} else if (stri == "=") {
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found_equal = true;
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} else if (found_ntax && found_equal) {
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if (stri.back() == ';') {
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stri.pop_back();
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}
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ntax = stoi(stri);
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found_equal = false;
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found_ntax = false;
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} else if (found_nchar && found_equal) {
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if (stri.back() == ';') {
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stri.pop_back();
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}
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nchar = stoi(stri);
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found_equal = false;
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found_nchar = false;
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} else if (stri == "matrix") {
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eulnum = lnum + 1;
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}
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}
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}
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// create class
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Sample sam(ntax, nchar);
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// read line by line, limit line number
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int l = 0;
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for (unsigned int z = eulnum; z < (eulnum + sam.ntax); z++) {
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// convert to word
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istringstream istr(file_content[z]);
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istr >> sam.taxas[l];
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istr >> sam.chars[l];
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l++;
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}
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return sam;
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}
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string add_space(char x, string str_old) {
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int i;
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string str_new;
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for (i = 0; i < (int)str_old.length(); i++) {
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if (str_old[i] != x) {
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str_new = str_new + str_old[i];
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} else {
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str_new = str_new + " " + str_old[i] + " ";
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}
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}
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return str_new;
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}
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string del_space(string str_old) {
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int i;
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string str_new;
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char x = ' ';
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for (i = 0; i < (int)str_old.length(); i++) {
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if (str_old[i] != x) {
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str_new = str_new + str_old[i];
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}
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}
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return str_new;
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}
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string rep_space(string str_old) {
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int i;
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string str_new;
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char x = ' ', c = '_';
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for (i = 0; i < (int)str_old.length(); i++) {
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if (str_old[i] != x) {
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str_new = str_new + str_old[i];
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} else {
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str_new = str_new + c;
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}
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}
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return str_new;
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}
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string to_lower(string stri) {
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transform(stri.begin(), stri.end(), stri.begin(), ::tolower);
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return stri;
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}
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void writeFas(class Sample sam, char* otn) {
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ofstream matrixfile(otn);
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for (unsigned int i = 0; i < sam.ntax; i++) {
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matrixfile << ">" << sam.taxas[i] << endl;
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matrixfile << sam.chars[i] << endl;
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}
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matrixfile.close();
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}
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void writePhy(class Sample sam, char* otn) {
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ofstream matrixfile(otn);
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matrixfile << sam.ntax << " " << sam.nchar << endl;
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for (unsigned int i = 0; i < sam.ntax; i++) {
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matrixfile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
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}
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matrixfile.close();
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}
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void writeNex(class Sample sam, char* otn) {
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ofstream matrixfile(otn);
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string datatype;
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datatype = checktype(sam.chars[0]);
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matrixfile << "#NEXUS\nBegin data;\n\tDimensions nchar=" << sam.nchar
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<< " ntax=" << sam.ntax << ";\n\tFormat datatype=" << datatype
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<< " missing=? gap=-;\n\tMatrix" << endl;
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for (unsigned int i2 = 0; i2 < sam.ntax; i2++) {
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matrixfile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
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}
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matrixfile << "\t;\nEnd;" << endl;
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matrixfile.close();
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}
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string checktype(string str) {
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// some var
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float a, c, t, g, zero, one, two, dna, standard;
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char ca = 'a', cc = 'c', ct = 't', cg = 'g', czero = '0', cone = '1',
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ctwo = '2';
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string datatype;
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// count fre
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a = countfre(str, ca);
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c = countfre(str, cc);
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t = countfre(str, ct);
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g = countfre(str, cg);
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zero = countfre(str, czero);
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one = countfre(str, cone);
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two = countfre(str, ctwo);
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// summary dna or morphology
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dna = a + c + t + g;
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standard = zero + one + two;
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// use percentage to test
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if ((dna / str.length()) > 0.7) {
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datatype = "dna";
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} else if ((standard / str.length()) > 0.7) {
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datatype = "standard";
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} else {
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datatype = "protein";
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}
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return datatype;
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}
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int countfre(string str, char c) {
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int num;
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str = to_lower(str);
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num = count(str.begin(), str.end(), c);
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return num;
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}
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void writeTnt(class Sample sam, char* otn) {
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ofstream matrixfile(otn);
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matrixfile << "xread\n\' \'\n" << sam.nchar << " " << sam.ntax << endl;
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for (unsigned int i = 0; i < sam.ntax; i++) {
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matrixfile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
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}
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matrixfile << "\n;\nproc / ;" << endl;
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matrixfile.close();
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}
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Basic_arg procargs(int nargs, char** arg) {
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int i, sta = 0, intype = 0, outype = 0;
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string para, inputfile, outputfile;
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char *itn, *otn;
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// no arg, show help
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if (nargs == 1) {
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show_help(0);
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exit(0);
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sta = 2;
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}
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// recognize arg
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for (i = 1; i < nargs; i++) {
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// to string
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string para(arg[i]);
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if ((para == "-h") || (para == "--help")) {
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show_help(1);
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sta = 2;
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} else if ((para == "-i") || (para == "--input")) {
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if ((i + 1) < nargs) {
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i++;
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itn = arg[i];
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string inputfile(arg[i]);
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intype = checkextension(inputfile);
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sta++;
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} else {
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cout << "MiMi:\tOInput file name must be defined" << endl;
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}
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} else if (((para == "-o") || (para == "--output"))) {
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if ((i + 1) < nargs) {
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i++;
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otn = arg[i];
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string outputfile(arg[i]);
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outype = checkextension(outputfile);
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sta++;
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} else {
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cout << "MiMi:\tOutput file name must be defined" << endl;
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}
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} else {
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cout << "MiMi:\tUnknown arguments, please use -h to check" << endl;
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exit(0);
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}
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}
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if (sta != 2) {
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cout << "MiMi:\tInput and Output can't be empty" << endl;
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exit(0);
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}
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Basic_arg arguvar(intype, outype, itn, otn);
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return arguvar;
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}
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int checkextension(string str) {
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int loc, type;
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string extension;
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loc = str.rfind('.');
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if (loc) {
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extension = str.substr(loc + 1);
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} else {
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cout << "MiMi:\tPlease sepecifc the extension name" << endl;
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exit(0);
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}
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extension = to_lower(extension);
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if ((extension == "fas") || (extension == "fasta")) {
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type = 1;
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} else if ((extension == "nex") || (extension == "nexus")) {
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type = 2;
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} else if ((extension == "phy") || (extension == "phylip")) {
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type = 3;
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} else if ((extension == "tnt") || (extension == "ss")) {
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type = 4;
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} else {
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cout << "MiMi:\tUnknown format" << endl;
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exit(0);
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}
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return type;
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}
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void show_help(int help_num) {
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if (help_num == 0) {
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cout << "MiMi, GPL, Guoyi Zhang, 2023.\nPlease use -h to see more help"
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<< endl;
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} else {
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cout << "\n ／l、 \t. . . .\n（ﾟ､ ｡ ７ \t|\\/|*|\\/|*\n l ~ヽ "
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" \t| ||| ||\n じしf_,)ノ\t| ||| ||\n\nMorphology into "
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"Molecules into\nGPL;\tGuoyi "
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"Zhang;\t2023\n\nArguments:\n-h\t--help;\n-i\t--input\t\t${"
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"filename};\n-o\t--output\t${filename};\n\nAccepted "
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"formats:\nfas\tfasta;\nnex\tnexus;\nphy\tphylip;\ntnt\tss;"
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<< endl;
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}
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}
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Sample read_input(char* itn, int intype) {
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int ntax = 0, nchar = 0;
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Sample sam(ntax, nchar);
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ifstream matrixfile;
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matrixfile.open(itn);
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if (matrixfile.is_open()) {
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if (intype == 1) sam = readFas(itn);
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if (intype == 2) sam = readNex(itn);
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if (intype == 3) sam = readPhy(itn);
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if (intype == 4) sam = readTnt(itn);
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} else {
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cout << "MiMi:\tInput file can't be open" << endl;
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exit(0);
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}
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return sam;
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}
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void write_output(class Sample sam, char* otn, int outype) {
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ofstream matrixfile(otn);
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if (matrixfile.is_open()) {
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if (outype == 1) writeFas(sam, otn);
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if (outype == 2) writeNex(sam, otn);
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if (outype == 3) writePhy(sam, otn);
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if (outype == 4) writeTnt(sam, otn);
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} else {
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cout << "MiMi:\tOutput file can't be open" << endl;
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exit(0);
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}
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}
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bool checkalign(class Sample sam) {
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int a = 0, b = 0;
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unsigned int x = 0;
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a = sam.nchar;
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bool aligned = true;
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for (unsigned int i = 0; i < sam.ntax; i++) {
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b = sam.chars[i].length();
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if (a == b) {
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x++;
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}
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}
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if (x != sam.ntax) {
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aligned = false;
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}
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return aligned;
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}
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int main(int argc, char** argv) {
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Basic_arg arguvar = procargs(argc, argv);
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if (arguvar.intype != 0 && arguvar.outype != 0) {
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Sample sam = read_input(arguvar.itn, arguvar.intype);
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cout << "MiMi:\tInput\tfinished" << endl;
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if (!checkalign(sam)) {
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cout << "MiMi:\tInput file should be aligned" << endl;
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exit(0);
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}
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write_output(sam, arguvar.otn, arguvar.outype);
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cout << "MiMi:\tOutput\tfinished" << endl;
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}
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return 0;
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}
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