116 lines
2.6 KiB
C++
116 lines
2.6 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, ntax, nseq;
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char * fn;
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void show_help(int help_num);
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void read_input(void);
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void readPhy(){
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int num=0;
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cout << "readphy is working, filename is " << fn << endl;
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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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ntax = stoi (sntax); nseq = stoi (snseq); // string to int
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cout << "ntax=" << ntax << " nseq=" << nseq << endl;
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//read sequence
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string taxa[ntax], sequ[ntax];
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//taxa[ntax] = new string*[];
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int lennum;
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for(lennum=0;lennum<ntax;lennum++){
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getline(seqfile,snall);
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istringstream istr(snall);
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istr >> taxa[lennum]; istr >> sequ[lennum];
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cout << "tax" << lennum << " is " << taxa << "; seq" << lennum << " is " << sequ << endl;
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}
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seqfile.close();
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// return taxa;
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// return sequ;
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}
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void writeFas(){
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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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//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;
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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 '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 << "intype is phylip, " << intype << endl;}
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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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void read_input (void){
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if (intype==3) readPhy();
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}
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void write_output (void){
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switch(outype){
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case '1': ; break;
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case '2': ; break;
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case '3': ; break;
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}
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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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read_input();
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write_output();
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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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