270 lines
6.7 KiB
C++
270 lines
6.7 KiB
C++
#include <iostream>
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#include <fstream>
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#include <sstream>
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#include <string>
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#include <vector>
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#include <algorithm>
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using namespace std;
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int intype=0, outype=0;
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char *fn;
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char *otn;
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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):
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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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// ~Sample(){
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// delete[] taxas;
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// delete[] chars;
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// }
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};
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void show_help(int help_num);
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Sample read_input();
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Sample readFas();
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Sample readPhy();
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void write_output(class Sample sam);
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void writeFas(class Sample sam);
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void writePhy(class Sample sam);
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void writeTnt(class Sample sam);
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void writeNexus(class Sample sam);
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Sample readPhy(){
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// unsigned ntax, nchar;
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// string *taxas, *chars;
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// Sample sam(ntax, nchar);
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int num=0;
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//read file
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ifstream seqfile;
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seqfile.open(fn);
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//read number of taxa and charcter
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string sntax, snseq, snall;
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cout << "Reading from the file" << endl;
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getline(seqfile,snall);
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istringstream istr(snall);
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istr >> sntax; istr >> snseq;
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int ntax, nchar;
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ntax = stoi (sntax); nchar = stoi (snseq); // string to int
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cout << "ntax=" << ntax << " nseq=" << nchar << endl;
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Sample sam(ntax, nchar);
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//read sequence
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int lennum;
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for(lennum=0;lennum<sam.ntax;lennum++){
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getline(seqfile,snall);
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istringstream istr(snall);
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istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
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cout << "tax" << lennum << " is " << sam.taxas[lennum] << "; seq" << lennum << " is " << sam.chars[lennum] << endl;
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}
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seqfile.close();
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// return to class
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return sam;
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}
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Sample readFas(){
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int ntax, nchar, lnum;
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ifstream seqfile;
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seqfile.open(fn);
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ntax = 0;
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string temln;
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for(lnum=0;getline(seqfile,temln);lnum++){
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if(temln[0]=='>'){
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ntax++;
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}
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}
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cout << "lnum= " << lnum << ", ntax= " << ntax << endl;
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seqfile.clear();
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seqfile.seekg(0);
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string *str_a = new string;
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string *str_b = new string;
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int r = lnum/ntax;
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for (int i=0; i<r;i++){
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getline(seqfile, *str_a);
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if(i>0){
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*str_b = *str_b + *str_a;
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}
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}
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nchar = (*str_b).length();
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delete str_a;
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str_a = nullptr;
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delete str_b;
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str_b = nullptr;
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cout << "ntax= " << ntax << ", nchar= " << nchar << endl;
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seqfile.clear();
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seqfile.seekg(0);
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Sample sam(ntax, nchar);
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string *str_c = new string;
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for (int a=1, b=0;a<=lnum;a++){
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if(a%r==1){
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getline(seqfile,sam.taxas[b]);
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sam.taxas[b].erase(0,1);
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}
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if(a%r>1){
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getline(seqfile,*str_c);
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sam.chars[b] = sam.chars[b] + *str_c;
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}
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if(a%r==0){
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getline(seqfile,*str_c);
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sam.chars[b] = sam.chars[b] + *str_c;
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b++;
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}
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}
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delete str_c;
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str_c = nullptr;
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seqfile.close();
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int lennum;
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for(lennum=0;lennum<sam.ntax;lennum++){
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cout << "tax" << lennum << " is " << sam.taxas[lennum] << "; seq" << lennum << " is " << sam.chars[lennum] << endl;
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}
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return sam;
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}
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Sample readTnt(){
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int ntax, nchar;
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Sample sam(ntax,nchar);
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return sam;
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}
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void writeFas(class Sample sam){
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ofstream outputFile(otn);
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if (outputFile.is_open()) {
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for(int i=0;i<sam.ntax;i++){
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outputFile << ">" << sam.taxas[i] << endl;
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outputFile << sam.chars[i] << endl;
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}
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} else {
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cout << "File can't be written" << endl;
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}
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outputFile.close();
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}
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void writePhy(class Sample sam){
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ofstream outputFile(otn);
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if (outputFile.is_open()) {
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outputFile << sam.ntax << " " << sam.nchar << endl;
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for(int i=0;i<sam.ntax;i++){
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outputFile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
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}
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} else {
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cout << "File can't be written" << endl;
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}
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outputFile.close();
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}
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void writeNexus(class Sample sam){
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ofstream outputFile(otn);
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if (outputFile.is_open()) {
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outputFile << "#NEXUS" << endl << "Begin TAXA;" << endl << "\tDimensions ntax=" << sam.ntax << ";" << endl << "\tTaxLabels";
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for(int i1=0;i1<sam.ntax;i1++){
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outputFile << " " << sam.taxas[i1] << endl;
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}
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outputFile << ";" << endl << "End;" << endl << endl << "Begin data;" << endl << "\tDimensions nchar=" << sam.nchar << ";" << endl << "\tFormat datatype=dna missing=? gap=-;" << endl << "\tMatrix" << endl;
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for(int i2=0;i2<sam.ntax;i2++){
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outputFile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
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}
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outputFile << "\t;" << endl << "End;" << endl;
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} else {
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cout << "File can't be written" << endl;
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}
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outputFile.close();
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}
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void writeTnt(class Sample sam){
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ofstream outputFile(otn);
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if (outputFile.is_open()) {
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outputFile << sam.nchar << " " << sam.ntax << endl;
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outputFile << "\' \'" << endl;
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for(int i=0;i<sam.ntax;i++){
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outputFile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
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}
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outputFile << "proc / ;" << endl;
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} else {
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cout << "File can't be written" << endl;
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}
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outputFile.close();
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}
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void procargs (int nargs, char ** arg){ //*arg 视为整体，是字符串指针
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int i;
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char * cp;//cp 字符指针 *p 第一个char
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//string ext1, ext2;
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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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}
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//recognize arg
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for (i=1;i<nargs;i++){
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cp = *(arg+i);
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//error arg
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if (*cp != '-'){
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cout << "Unknown arguments, please use -h to check" << endl;
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exit(0);
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}
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//check arg
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switch (*++cp){//先++
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case 'f':
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cp++;
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if (*cp=='f') {intype=1; cout << "intype is fasta, " << intype << endl;}
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if (*cp=='n') intype=2;
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if (*cp=='p') {intype=3; cout << "intype is phylip, " << intype << endl;}
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break;
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case 'h': show_help(1); break;
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case 'i': cp++; fn = cp; break;
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case 'o': cp++; otn = cp; break;
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case 't':
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cp++;
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if (*cp=='f') outype=1;
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if (*cp=='n') outype=2;
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if (*cp=='p') {outype=3; cout << "outype is phylip, " << intype << endl;}
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if (*cp=='t') outype=4;
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break;
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default: cout << "Unrecognized agruments " << *(arg+i) << endl; exit(0);
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}
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}
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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 << "SeqConvert GPL, please use -h to see more help" << endl;
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} else {
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cout << "-f from: -ff fasta; -fn nexus; -fp phylip;\n-h help;\n-i input: -i${filename};" << endl;
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}
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}
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Sample read_input (void){
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int ntax, nchar;
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Sample sam(ntax,nchar);
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if (intype==1) sam = readFas();
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if (intype==3) sam = readPhy();
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return sam;
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}
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void write_output (class Sample sam){
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if (outype==1) writeFas(sam);
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if (outype==2) writeNexus(sam);
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if (outype==3) writePhy(sam);
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if (outype==4) writeTnt(sam);
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}
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int main(int argc, char **argv){
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procargs (argc, argv);
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if(intype!=0&&outype!=0){
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Sample sam = read_input();
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write_output(sam);
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}
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int i;
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for (i = 0; i < argc; i++) cout << "argument "<< i << " is " << *(argv+i) << endl;
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return 1;
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}
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