add: function checkaligned, format the arg, clean code
This commit is contained in:
parent
5a337fd47a
commit
b038025948
2 changed files with 329 additions and 271 deletions
47
README.md
Normal file
47
README.md
Normal file
|
|
@ -0,0 +1,47 @@
|
|||
# MiMi
|
||||
|
||||
```
|
||||
／l、 . . . .
|
||||
（ﾟ､ ｡ ７ |\/|*|\/|*
|
||||
l ~ヽ | ||| ||
|
||||
じしf_,)ノ | ||| ||
|
||||
|
||||
Morphology into Molecules into
|
||||
GPL Guoyi Zhang, 2023
|
||||
```
|
||||
|
||||
## Functions
|
||||
|
||||
Convert any formats listed in `Accepted formats` to each other.
|
||||
|
||||
## Arguments
|
||||
|
||||
- -h --help;
|
||||
|
||||
- -i --input ${filename};
|
||||
|
||||
- -o --output ${filename};
|
||||
|
||||
## Accepted formats
|
||||
|
||||
- fas fasta
|
||||
|
||||
- nex nexus
|
||||
|
||||
- phy phylip
|
||||
|
||||
- tnt ss
|
||||
|
||||
## Compile
|
||||
|
||||
```
|
||||
g++ main.cpp -o mimi
|
||||
```
|
||||
|
||||
## License
|
||||
|
||||
You should note that the license is (GPL)[https://www.gnu.org/licenses/gpl-3.0.html].
|
||||
|
||||
## Acknowledgements
|
||||
|
||||
Thanks to my beloved daughter MiMi (Ragdoll cat) for accompanying me in my life, mom loves you forever.
|
||||
531
main.cpp
531
main.cpp
|
|
@ -1,33 +1,30 @@
|
|||
#include <iostream>
|
||||
#include <algorithm>
|
||||
#include <fstream>
|
||||
#include <iostream>
|
||||
#include <sstream>
|
||||
#include <string>
|
||||
#include <algorithm>
|
||||
|
||||
using namespace std;
|
||||
|
||||
class Basic_arg{
|
||||
public:
|
||||
int intype=0, outype=0;
|
||||
char *itn, *otn;
|
||||
Basic_arg(int intype, int outype, char* itn, char *otn):
|
||||
intype(intype), outype(outype),
|
||||
itn(itn), otn(otn)
|
||||
{};
|
||||
class Basic_arg {
|
||||
public:
|
||||
int intype = 0, outype = 0;
|
||||
char *itn, *otn;
|
||||
Basic_arg(int intype, int outype, char* itn, char* otn)
|
||||
: intype(intype), outype(outype), itn(itn), otn(otn){};
|
||||
};
|
||||
|
||||
class Sample {
|
||||
public:
|
||||
unsigned ntax, nchar;
|
||||
string *taxas, *chars;
|
||||
Sample(unsigned ntax, unsigned nchar):
|
||||
ntax(ntax), nchar(nchar) {
|
||||
taxas = new string[ntax];
|
||||
chars = new string[ntax];
|
||||
};
|
||||
public:
|
||||
unsigned ntax, nchar;
|
||||
string *taxas, *chars;
|
||||
Sample(unsigned ntax, unsigned nchar) : ntax(ntax), nchar(nchar) {
|
||||
taxas = new string[ntax];
|
||||
chars = new string[ntax];
|
||||
};
|
||||
};
|
||||
|
||||
Basic_arg procargs (int nargs, char ** arg, char* itn, char* otn);
|
||||
Basic_arg procargs(int nargs, char** arg, char* itn, char* otn);
|
||||
Sample read_input(char* itn, int intype);
|
||||
void show_help(int help_num);
|
||||
Sample readFas(char* itn);
|
||||
|
|
@ -47,52 +44,55 @@ string checktype(string str);
|
|||
int countfre(string str, char c);
|
||||
int checkextension(string str);
|
||||
|
||||
Sample readPhy(char* itn){
|
||||
//read file
|
||||
Sample readPhy(char* itn) {
|
||||
// read file
|
||||
ifstream matrixfile;
|
||||
matrixfile.open(itn);
|
||||
//read number of taxa and charcter
|
||||
// read number of taxa and charcter
|
||||
string sntax, snseq, snall;
|
||||
getline(matrixfile,snall);
|
||||
getline(matrixfile, snall);
|
||||
istringstream istr(snall);
|
||||
istr >> sntax; istr >> snseq;
|
||||
istr >> sntax;
|
||||
istr >> snseq;
|
||||
int ntax, nchar;
|
||||
ntax = stoi (sntax); nchar = stoi (snseq); // string to int
|
||||
ntax = stoi(sntax);
|
||||
nchar = stoi(snseq); // string to int
|
||||
Sample sam(ntax, nchar);
|
||||
//read sequence
|
||||
// read sequence
|
||||
int lennum;
|
||||
for(lennum=0;lennum<sam.ntax;lennum++){
|
||||
getline(matrixfile,snall);
|
||||
for (lennum = 0; lennum < sam.ntax; lennum++) {
|
||||
getline(matrixfile, snall);
|
||||
istringstream istr(snall);
|
||||
istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
|
||||
istr >> sam.taxas[lennum];
|
||||
istr >> sam.chars[lennum];
|
||||
}
|
||||
matrixfile.close();
|
||||
// return to class
|
||||
return sam;
|
||||
}
|
||||
|
||||
Sample readFas(char* itn){
|
||||
Sample readFas(char* itn) {
|
||||
int ntax, nchar, lnum;
|
||||
ifstream matrixfile;
|
||||
matrixfile.open(itn);
|
||||
// check line number and taxa number
|
||||
ntax = 0;
|
||||
string temln;
|
||||
for(lnum=0;getline(matrixfile,temln);lnum++){
|
||||
if(temln[0]=='>'){
|
||||
for (lnum = 0; getline(matrixfile, temln); lnum++) {
|
||||
if (temln[0] == '>') {
|
||||
ntax++;
|
||||
}
|
||||
}
|
||||
matrixfile.clear();
|
||||
matrixfile.seekg(0);
|
||||
// check the nchar
|
||||
string *str_a = new string;
|
||||
string *str_b = new string;
|
||||
int r = lnum/ntax;
|
||||
for (int i=0; i<r;i++){
|
||||
string* str_a = new string;
|
||||
string* str_b = new string;
|
||||
int r = lnum / ntax;
|
||||
for (int i = 0; i < r; i++) {
|
||||
getline(matrixfile, *str_a);
|
||||
if(i>0){
|
||||
*str_b = *str_b + *str_a;
|
||||
if (i > 0) {
|
||||
*str_b = *str_b + *str_a;
|
||||
}
|
||||
}
|
||||
nchar = (*str_b).length();
|
||||
|
|
@ -105,18 +105,18 @@ Sample readFas(char* itn){
|
|||
// create class
|
||||
Sample sam(ntax, nchar);
|
||||
// get class
|
||||
string *str_c = new string;
|
||||
for (int a=1, b=0;a<=lnum;a++){
|
||||
if(a%r==1){
|
||||
getline(matrixfile,sam.taxas[b]);
|
||||
sam.taxas[b].erase(0,1);
|
||||
string* str_c = new string;
|
||||
for (int a = 1, b = 0; a <= lnum; a++) {
|
||||
if (a % r == 1) {
|
||||
getline(matrixfile, sam.taxas[b]);
|
||||
sam.taxas[b].erase(0, 1);
|
||||
}
|
||||
if(a%r>1){
|
||||
getline(matrixfile,*str_c);
|
||||
if (a % r > 1) {
|
||||
getline(matrixfile, *str_c);
|
||||
sam.chars[b] = sam.chars[b] + *str_c;
|
||||
}
|
||||
if(a%r==0){
|
||||
getline(matrixfile,*str_c);
|
||||
if (a % r == 0) {
|
||||
getline(matrixfile, *str_c);
|
||||
sam.chars[b] = sam.chars[b] + *str_c;
|
||||
b++;
|
||||
}
|
||||
|
|
@ -127,161 +127,170 @@ Sample readFas(char* itn){
|
|||
return sam;
|
||||
}
|
||||
|
||||
Sample readTnt(char* itn){
|
||||
Sample readTnt(char* itn) {
|
||||
int ntax, nchar;
|
||||
ifstream matrixfile;
|
||||
matrixfile.open(itn);
|
||||
// get nchar and ntax
|
||||
string stri, sntax, snchar;
|
||||
for(int i=0;i<1;){
|
||||
getline(matrixfile,stri);
|
||||
istringstream istr(stri);
|
||||
istr >> snchar; istr >> sntax;
|
||||
if(isNum(sntax) && isNum(snchar)){
|
||||
ntax=stoi(sntax);
|
||||
nchar=stoi(snchar);
|
||||
i++;
|
||||
}
|
||||
for (int i = 0; i < 1;) {
|
||||
getline(matrixfile, stri);
|
||||
istringstream istr(stri);
|
||||
istr >> snchar;
|
||||
istr >> sntax;
|
||||
if (isNum(sntax) && isNum(snchar)) {
|
||||
ntax = stoi(sntax);
|
||||
nchar = stoi(snchar);
|
||||
i++;
|
||||
}
|
||||
}
|
||||
// create class
|
||||
Sample sam(ntax,nchar);
|
||||
Sample sam(ntax, nchar);
|
||||
// get class
|
||||
int lennum;
|
||||
for(lennum=0;lennum<sam.ntax;lennum++){
|
||||
getline(matrixfile,stri);
|
||||
for (lennum = 0; lennum < sam.ntax; lennum++) {
|
||||
getline(matrixfile, stri);
|
||||
istringstream istr(stri);
|
||||
istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
|
||||
istr >> sam.taxas[lennum];
|
||||
istr >> sam.chars[lennum];
|
||||
}
|
||||
matrixfile.close();
|
||||
return sam;
|
||||
}
|
||||
|
||||
bool isNum(string strnum) {
|
||||
char* p;
|
||||
strtol(strnum.c_str(), &p, 10);
|
||||
return *p == 0;
|
||||
char* p;
|
||||
strtol(strnum.c_str(), &p, 10);
|
||||
return *p == 0;
|
||||
}
|
||||
|
||||
Sample readNex(char* itn){
|
||||
Sample readNex(char* itn) {
|
||||
int ntax, nchar;
|
||||
// open file
|
||||
ifstream matrixfile;
|
||||
matrixfile.open(itn);
|
||||
// some tem
|
||||
string snall, stri, str_a, str_b;
|
||||
bool found = false, found_ntax = false, found_nchar = false, found_equal = false;
|
||||
bool found = false, found_ntax = false, found_nchar = false,
|
||||
found_equal = false;
|
||||
char x = '=';
|
||||
int lnum, eulnum;
|
||||
// getline line by line
|
||||
for(lnum=0;getline(matrixfile,snall);lnum++){
|
||||
str_a = to_lower(snall);
|
||||
str_b = add_space(x,str_a);
|
||||
istringstream istr(str_b);
|
||||
// convert to words
|
||||
while(istr>> stri){
|
||||
if(stri=="dimensions"){
|
||||
found = true;
|
||||
} else if(stri=="ntax"){
|
||||
found_ntax = true;
|
||||
} else if(stri=="nchar"){
|
||||
found_nchar = true;
|
||||
} else if(stri=="="){
|
||||
found_equal = true;
|
||||
} else if (found_ntax&&found_equal){
|
||||
if(stri.back()==';'){
|
||||
stri.pop_back();
|
||||
found = false;
|
||||
}
|
||||
ntax = stoi(stri);
|
||||
found_equal = false;
|
||||
found_ntax = false;
|
||||
} else if (found_nchar&&found_equal){
|
||||
if(stri.back()==';'){
|
||||
stri.pop_back();
|
||||
found = false;
|
||||
}
|
||||
nchar = stoi(stri);
|
||||
found_equal = false;
|
||||
found_nchar = false;
|
||||
} else if (stri=="matrix"){
|
||||
eulnum = lnum+1;
|
||||
}
|
||||
for (lnum = 0; getline(matrixfile, snall); lnum++) {
|
||||
str_a = to_lower(snall);
|
||||
str_b = add_space(x, str_a);
|
||||
istringstream istr(str_b);
|
||||
// convert to words
|
||||
while (istr >> stri) {
|
||||
if (stri == "dimensions") {
|
||||
found = true;
|
||||
} else if (stri == "ntax") {
|
||||
found_ntax = true;
|
||||
} else if (stri == "nchar") {
|
||||
found_nchar = true;
|
||||
} else if (stri == "=") {
|
||||
found_equal = true;
|
||||
} else if (found_ntax && found_equal) {
|
||||
if (stri.back() == ';') {
|
||||
stri.pop_back();
|
||||
found = false;
|
||||
}
|
||||
ntax = stoi(stri);
|
||||
found_equal = false;
|
||||
found_ntax = false;
|
||||
} else if (found_nchar && found_equal) {
|
||||
if (stri.back() == ';') {
|
||||
stri.pop_back();
|
||||
found = false;
|
||||
}
|
||||
nchar = stoi(stri);
|
||||
found_equal = false;
|
||||
found_nchar = false;
|
||||
} else if (stri == "matrix") {
|
||||
eulnum = lnum + 1;
|
||||
}
|
||||
}
|
||||
}
|
||||
// go back
|
||||
matrixfile.clear();
|
||||
matrixfile.seekg(0);
|
||||
// create class
|
||||
Sample sam(ntax,nchar);
|
||||
Sample sam(ntax, nchar);
|
||||
// some temp, z is line number, l is the string arrary number
|
||||
int z=0; int l=0;
|
||||
int z = 0;
|
||||
int l = 0;
|
||||
// read line by line
|
||||
while(getline(matrixfile,snall)){
|
||||
// convert to word
|
||||
istringstream istr(snall);
|
||||
// limit the read line number
|
||||
if(z>(eulnum-1)&&z<(eulnum+sam.ntax)){
|
||||
istr >> sam.taxas[l];
|
||||
istr >> sam.chars[l];
|
||||
l++;
|
||||
}
|
||||
z++;
|
||||
while (getline(matrixfile, snall)) {
|
||||
// convert to word
|
||||
istringstream istr(snall);
|
||||
// limit the read line number
|
||||
if (z > (eulnum - 1) && z < (eulnum + sam.ntax)) {
|
||||
istr >> sam.taxas[l];
|
||||
istr >> sam.chars[l];
|
||||
l++;
|
||||
}
|
||||
z++;
|
||||
}
|
||||
return sam;
|
||||
}
|
||||
string add_space (char x, string str_old) {
|
||||
int i;
|
||||
string str_new;
|
||||
for (i=0; i<str_old.length(); i++) {
|
||||
if (str_old[i] != x) {
|
||||
str_new=str_new+str_old[i];
|
||||
} else {
|
||||
str_new=str_new+" "+str_old[i]+" ";
|
||||
}
|
||||
}
|
||||
return str_new;
|
||||
string add_space(char x, string str_old) {
|
||||
int i;
|
||||
string str_new;
|
||||
for (i = 0; i < str_old.length(); i++) {
|
||||
if (str_old[i] != x) {
|
||||
str_new = str_new + str_old[i];
|
||||
} else {
|
||||
str_new = str_new + " " + str_old[i] + " ";
|
||||
}
|
||||
}
|
||||
return str_new;
|
||||
}
|
||||
|
||||
string to_lower(string stri){
|
||||
transform(stri.begin(),stri.end(),stri.begin(),::tolower);
|
||||
string to_lower(string stri) {
|
||||
transform(stri.begin(), stri.end(), stri.begin(), ::tolower);
|
||||
return stri;
|
||||
}
|
||||
|
||||
void writeFas(class Sample sam, char* otn){
|
||||
void writeFas(class Sample sam, char* otn) {
|
||||
ofstream matrixfile(otn);
|
||||
for(int i=0;i<sam.ntax;i++){
|
||||
matrixfile << ">" << sam.taxas[i] << endl;
|
||||
matrixfile << sam.chars[i] << endl;
|
||||
}
|
||||
for (int i = 0; i < sam.ntax; i++) {
|
||||
matrixfile << ">" << sam.taxas[i] << endl;
|
||||
matrixfile << sam.chars[i] << endl;
|
||||
}
|
||||
matrixfile.close();
|
||||
}
|
||||
|
||||
void writePhy(class Sample sam, char* otn){
|
||||
void writePhy(class Sample sam, char* otn) {
|
||||
ofstream matrixfile(otn);
|
||||
matrixfile << sam.ntax << " " << sam.nchar << endl;
|
||||
for(int i=0;i<sam.ntax;i++){
|
||||
matrixfile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
|
||||
}
|
||||
matrixfile << sam.ntax << " " << sam.nchar << endl;
|
||||
for (int i = 0; i < sam.ntax; i++) {
|
||||
matrixfile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
|
||||
}
|
||||
matrixfile.close();
|
||||
}
|
||||
|
||||
void writeNex(class Sample sam, char* otn){
|
||||
void writeNex(class Sample sam, char* otn) {
|
||||
ofstream matrixfile(otn);
|
||||
string datatype;
|
||||
datatype = checktype(sam.chars[0]);
|
||||
matrixfile << "#NEXUS" << endl;
|
||||
matrixfile << "Begin data;" << endl << "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax << ";" << endl << "\tFormat datatype=" << datatype << " missing=? gap=-;" << endl << "\tMatrix" << endl;
|
||||
for(int i2=0;i2<sam.ntax;i2++){
|
||||
matrixfile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
|
||||
}
|
||||
matrixfile << "\t;" << endl << "End;" << endl;
|
||||
matrixfile << "#NEXUS" << endl;
|
||||
matrixfile << "Begin data;" << endl
|
||||
<< "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax
|
||||
<< ";" << endl
|
||||
<< "\tFormat datatype=" << datatype << " missing=? gap=-;" << endl
|
||||
<< "\tMatrix" << endl;
|
||||
for (int i2 = 0; i2 < sam.ntax; i2++) {
|
||||
matrixfile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
|
||||
}
|
||||
matrixfile << "\t;" << endl << "End;" << endl;
|
||||
matrixfile.close();
|
||||
}
|
||||
|
||||
string checktype(string str){
|
||||
string checktype(string str) {
|
||||
// some var
|
||||
float a, c, t, g, zero, one, two, dna, standard;
|
||||
char ca='a', cc='c', ct='t', cg='g', czero='0', cone='1', ctwo='2';
|
||||
char ca = 'a', cc = 'c', ct = 't', cg = 'g', czero = '0', cone = '1',
|
||||
ctwo = '2';
|
||||
string datatype;
|
||||
// count fre
|
||||
a = countfre(str, ca);
|
||||
|
|
@ -292,131 +301,134 @@ string checktype(string str){
|
|||
one = countfre(str, cone);
|
||||
two = countfre(str, ctwo);
|
||||
// summary dna or morphology
|
||||
dna = a+c+t+g;
|
||||
standard = zero+one+two;
|
||||
dna = a + c + t + g;
|
||||
standard = zero + one + two;
|
||||
// use percentage to test
|
||||
if((dna/str.length())>0.7){
|
||||
datatype = "dna";
|
||||
} else if ((standard/str.length())>0.7){
|
||||
datatype = "standard";
|
||||
if ((dna / str.length()) > 0.7) {
|
||||
datatype = "dna";
|
||||
} else if ((standard / str.length()) > 0.7) {
|
||||
datatype = "standard";
|
||||
} else {
|
||||
datatype = "protein";
|
||||
datatype = "protein";
|
||||
}
|
||||
return datatype;
|
||||
}
|
||||
|
||||
int countfre(string str, char c){
|
||||
int countfre(string str, char c) {
|
||||
int num;
|
||||
str = to_lower(str);
|
||||
num = count(str.begin(),str.end(),c);
|
||||
num = count(str.begin(), str.end(), c);
|
||||
return num;
|
||||
}
|
||||
|
||||
void writeTnt(class Sample sam, char* otn){
|
||||
void writeTnt(class Sample sam, char* otn) {
|
||||
ofstream matrixfile(otn);
|
||||
matrixfile << "xread" << endl << "\' \'" << endl;
|
||||
matrixfile << sam.nchar << " " << sam.ntax << endl;
|
||||
for(int i=0;i<sam.ntax;i++){
|
||||
matrixfile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
|
||||
}
|
||||
matrixfile << "proc / ;" << endl;
|
||||
matrixfile << "xread" << endl << "\' \'" << endl;
|
||||
matrixfile << sam.nchar << " " << sam.ntax << endl;
|
||||
for (int i = 0; i < sam.ntax; i++) {
|
||||
matrixfile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
|
||||
}
|
||||
matrixfile << "proc / ;" << endl;
|
||||
matrixfile.close();
|
||||
}
|
||||
|
||||
|
||||
Basic_arg procargs (int nargs, char ** arg, char* itn, char* otn){
|
||||
int i, sta = 0, intype=0, outype=0;
|
||||
Basic_arg procargs(int nargs, char** arg, char* itn, char* otn) {
|
||||
int i, sta = 0, intype = 0, outype = 0;
|
||||
string para, inputfile, outputfile;
|
||||
//no arg, show help
|
||||
if (nargs==1){
|
||||
// no arg, show help
|
||||
if (nargs == 1) {
|
||||
show_help(0);
|
||||
exit(0);
|
||||
sta=2;
|
||||
sta = 2;
|
||||
}
|
||||
//recognize arg
|
||||
for (i=1;i<nargs;i++){
|
||||
//to string
|
||||
string para (arg[i]);
|
||||
if ( para =="-h"| para=="--help" ) {
|
||||
show_help(1);
|
||||
sta=2;
|
||||
}
|
||||
else if ( para =="-i"| para=="--input"){
|
||||
i++;
|
||||
itn=arg[i];
|
||||
string inputfile (arg[i]);
|
||||
intype = checkextension(inputfile);
|
||||
sta++;
|
||||
}
|
||||
else if ( para =="-o"| para=="--output"){
|
||||
i++;
|
||||
otn=arg[i];
|
||||
string outputfile (arg[i]);
|
||||
outype = checkextension(outputfile);
|
||||
sta++;
|
||||
// recognize arg
|
||||
for (i = 1; i < nargs; i++) {
|
||||
// to string
|
||||
string para(arg[i]);
|
||||
if (para == "-h" | para == "--help") {
|
||||
show_help(1);
|
||||
sta = 2;
|
||||
} else if (para == "-i" | para == "--input") {
|
||||
i++;
|
||||
itn = arg[i];
|
||||
string inputfile(arg[i]);
|
||||
intype = checkextension(inputfile);
|
||||
sta++;
|
||||
} else if (para == "-o" | para == "--output") {
|
||||
i++;
|
||||
otn = arg[i];
|
||||
string outputfile(arg[i]);
|
||||
outype = checkextension(outputfile);
|
||||
sta++;
|
||||
} else {
|
||||
cout << "MiMi\tUnknown arguments, please use -h to check" << endl;
|
||||
exit(0);
|
||||
}
|
||||
}
|
||||
if(sta!=2){
|
||||
cout << "MiMi\tInput and Output can't be empty" << endl;
|
||||
exit(0);
|
||||
if (sta != 2) {
|
||||
cout << "MiMi\tInput and Output can't be empty" << endl;
|
||||
exit(0);
|
||||
}
|
||||
Basic_arg arguvar(intype,outype,itn,otn);
|
||||
return arguvar;
|
||||
Basic_arg arguvar(intype, outype, itn, otn);
|
||||
return arguvar;
|
||||
}
|
||||
|
||||
int checkextension(string str){
|
||||
int loc, type;
|
||||
string extension;
|
||||
loc = str.rfind('.');
|
||||
if(loc){
|
||||
extension = str.substr(loc+1);
|
||||
} else {
|
||||
cout << "MiMi\tPlease sepecifc the extension name" << endl;
|
||||
exit(0);
|
||||
}
|
||||
extension = to_lower(extension);
|
||||
if(extension=="fas"|extension=="fasta"){
|
||||
type = 1;
|
||||
} else if (extension=="nex"|extension=="nexus"){
|
||||
type = 2;
|
||||
} else if (extension=="phy"|extension=="phylip"){
|
||||
type = 3;
|
||||
} else if (extension=="tnt"|extension=="ss"){
|
||||
type = 4;
|
||||
} else {
|
||||
cout << "MiMi\tUnknown format" << endl;
|
||||
exit(0);
|
||||
}
|
||||
return type;
|
||||
}
|
||||
|
||||
void show_help (int help_num){
|
||||
|
||||
|
||||
|
||||
if (help_num == 0){
|
||||
cout << "MiMi, GPL, Guoyi Zhang, 2023.\nPlease use -h to see more help" << endl;
|
||||
int checkextension(string str) {
|
||||
int loc, type;
|
||||
string extension;
|
||||
loc = str.rfind('.');
|
||||
if (loc) {
|
||||
extension = str.substr(loc + 1);
|
||||
} else {
|
||||
cout << "\n ／l、 \t. . . .\n（ﾟ､ ｡ ７ \t|\\/|*|\\/|*\n l ~ヽ \t| ||| ||\n じしf_,)ノ\t| ||| ||\n" << endl;
|
||||
cout << "Morphology into Molecules into\n" << "GPL\tGuoyi\tZhang,\t2023\n" << endl;
|
||||
cout << "-h\t--help;\n-i\t--input\t\t${filename};\n-o\t--output\t${filename};\n" << endl;
|
||||
cout << "Accepted format:\nfas\tfasta;\nnex\tnexus\nphy\tphylip\ntnt\tss" << endl;
|
||||
cout << "MiMi\tPlease sepecifc the extension name" << endl;
|
||||
exit(0);
|
||||
}
|
||||
extension = to_lower(extension);
|
||||
if (extension == "fas" | extension == "fasta") {
|
||||
type = 1;
|
||||
} else if (extension == "nex" | extension == "nexus") {
|
||||
type = 2;
|
||||
} else if (extension == "phy" | extension == "phylip") {
|
||||
type = 3;
|
||||
} else if (extension == "tnt" | extension == "ss") {
|
||||
type = 4;
|
||||
} else {
|
||||
cout << "MiMi\tUnknown format" << endl;
|
||||
exit(0);
|
||||
}
|
||||
return type;
|
||||
}
|
||||
|
||||
void show_help(int help_num) {
|
||||
if (help_num == 0) {
|
||||
cout << "MiMi, GPL, Guoyi Zhang, 2023.\nPlease use -h to see more help"
|
||||
<< endl;
|
||||
} else {
|
||||
cout << "\n ／l、 \t. . . .\n（ﾟ､ ｡ ７ \t|\\/|*|\\/|*\n l ~ヽ "
|
||||
" \t| ||| ||\n じしf_,)ノ\t| ||| ||\n"
|
||||
<< endl;
|
||||
cout << "Morphology into Molecules into\n"
|
||||
<< "GPL;\tGuoyi Zhang;\t2023\n"
|
||||
<< endl;
|
||||
cout << "-h\t--help;\n-i\t--input\t\t${filename};\n-o\t--output\t${"
|
||||
"filename};\n"
|
||||
<< endl;
|
||||
cout
|
||||
<< "Accepted formats:\nfas\tfasta;\nnex\tnexus;\nphy\tphylip;\ntnt\tss;"
|
||||
<< endl;
|
||||
}
|
||||
}
|
||||
|
||||
Sample read_input (char* itn, int intype){
|
||||
Sample read_input(char* itn, int intype) {
|
||||
int ntax, nchar;
|
||||
Sample sam(ntax,nchar);
|
||||
Sample sam(ntax, nchar);
|
||||
ifstream matrixfile;
|
||||
matrixfile.open(itn);
|
||||
if (matrixfile.is_open()){
|
||||
if (intype==1) sam = readFas(itn);
|
||||
if (intype==2) sam = readNex(itn);
|
||||
if (intype==3) sam = readPhy(itn);
|
||||
if (intype==4) sam = readTnt(itn);
|
||||
if (matrixfile.is_open()) {
|
||||
if (intype == 1) sam = readFas(itn);
|
||||
if (intype == 2) sam = readNex(itn);
|
||||
if (intype == 3) sam = readPhy(itn);
|
||||
if (intype == 4) sam = readTnt(itn);
|
||||
} else {
|
||||
cout << "MiMi\tInput file can't be open" << endl;
|
||||
exit(0);
|
||||
|
|
@ -424,48 +436,47 @@ Sample read_input (char* itn, int intype){
|
|||
return sam;
|
||||
}
|
||||
|
||||
void write_output (class Sample sam, char* otn, int outype){
|
||||
void write_output(class Sample sam, char* otn, int outype) {
|
||||
ofstream matrixfile(otn);
|
||||
if (matrixfile.is_open()) {
|
||||
if (outype==1) writeFas(sam,otn);
|
||||
if (outype==2) writeNex(sam,otn);
|
||||
if (outype==3) writePhy(sam,otn);
|
||||
if (outype==4) writeTnt(sam,otn);
|
||||
if (outype == 1) writeFas(sam, otn);
|
||||
if (outype == 2) writeNex(sam, otn);
|
||||
if (outype == 3) writePhy(sam, otn);
|
||||
if (outype == 4) writeTnt(sam, otn);
|
||||
} else {
|
||||
cout << "MiMi\tOutput file can't be open" << endl;
|
||||
exit(0);
|
||||
}
|
||||
}
|
||||
|
||||
bool checkalign(class Sample sam){
|
||||
int a=0, b=0, x=0;
|
||||
bool checkalign(class Sample sam) {
|
||||
int a = 0, b = 0, x = 0;
|
||||
a = sam.nchar;
|
||||
bool aligned = true;
|
||||
for(int i=0;i<sam.ntax;i++){
|
||||
b=sam.chars[i].length();
|
||||
if(a==b){
|
||||
x++;
|
||||
}
|
||||
for (int i = 0; i < sam.ntax; i++) {
|
||||
b = sam.chars[i].length();
|
||||
if (a == b) {
|
||||
x++;
|
||||
}
|
||||
}
|
||||
if (x!=sam.ntax){
|
||||
aligned = false;
|
||||
if (x != sam.ntax) {
|
||||
aligned = false;
|
||||
}
|
||||
return aligned;
|
||||
}
|
||||
|
||||
|
||||
int main(int argc, char **argv){
|
||||
int main(int argc, char** argv) {
|
||||
char *itn, *otn;
|
||||
Basic_arg arguvar = procargs (argc, argv, itn, otn);
|
||||
if(arguvar.intype!=0&&arguvar.outype!=0){
|
||||
Sample sam = read_input(arguvar.itn,arguvar.intype);
|
||||
cout << "MiMi:\tInput\tfinished" << endl;
|
||||
if(!checkalign(sam)){
|
||||
cout << "MiMi:\tInput file should be aligned" << endl;
|
||||
exit(0);
|
||||
}
|
||||
write_output(sam,arguvar.otn,arguvar.outype);
|
||||
cout << "MiMi:\tOutput\tfinished" << endl;
|
||||
Basic_arg arguvar = procargs(argc, argv, itn, otn);
|
||||
if (arguvar.intype != 0 && arguvar.outype != 0) {
|
||||
Sample sam = read_input(arguvar.itn, arguvar.intype);
|
||||
cout << "MiMi:\tInput\tfinished" << endl;
|
||||
if (!checkalign(sam)) {
|
||||
cout << "MiMi:\tInput file should be aligned" << endl;
|
||||
exit(0);
|
||||
}
|
||||
write_output(sam, arguvar.otn, arguvar.outype);
|
||||
cout << "MiMi:\tOutput\tfinished" << endl;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in a new issue