add: nexus input function
This commit is contained in:
parent
b0e35fa3d1
commit
f01844d2a8
183
main.cpp
183
main.cpp
|
|
@ -30,17 +30,18 @@ void show_help(int help_num);
|
|||
Sample read_input();
|
||||
Sample readFas();
|
||||
Sample readPhy();
|
||||
Sample readTnt();
|
||||
Sample readNex();
|
||||
void write_output(class Sample sam);
|
||||
void writeFas(class Sample sam);
|
||||
void writePhy(class Sample sam);
|
||||
void writeTnt(class Sample sam);
|
||||
void writeNexus(class Sample sam);
|
||||
void writeNex(class Sample sam);
|
||||
bool isNum(string strnum);
|
||||
string to_lower(string stri);
|
||||
string add_space (char x, string str_old);
|
||||
|
||||
Sample readPhy(){
|
||||
// unsigned ntax, nchar;
|
||||
// string *taxas, *chars;
|
||||
// Sample sam(ntax, nchar);
|
||||
int num=0;
|
||||
//read file
|
||||
ifstream seqfile;
|
||||
seqfile.open(fn);
|
||||
|
|
@ -71,6 +72,7 @@ Sample readFas(){
|
|||
int ntax, nchar, lnum;
|
||||
ifstream seqfile;
|
||||
seqfile.open(fn);
|
||||
// check line number and taxa number
|
||||
ntax = 0;
|
||||
string temln;
|
||||
for(lnum=0;getline(seqfile,temln);lnum++){
|
||||
|
|
@ -81,7 +83,7 @@ Sample readFas(){
|
|||
cout << "lnum= " << lnum << ", ntax= " << ntax << endl;
|
||||
seqfile.clear();
|
||||
seqfile.seekg(0);
|
||||
|
||||
// check the nchar
|
||||
string *str_a = new string;
|
||||
string *str_b = new string;
|
||||
int r = lnum/ntax;
|
||||
|
|
@ -96,12 +98,12 @@ Sample readFas(){
|
|||
str_a = nullptr;
|
||||
delete str_b;
|
||||
str_b = nullptr;
|
||||
|
||||
cout << "ntax= " << ntax << ", nchar= " << nchar << endl;
|
||||
seqfile.clear();
|
||||
seqfile.seekg(0);
|
||||
|
||||
// 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){
|
||||
|
|
@ -121,19 +123,153 @@ Sample readFas(){
|
|||
delete str_c;
|
||||
str_c = nullptr;
|
||||
seqfile.close();
|
||||
int lennum;
|
||||
for(lennum=0;lennum<sam.ntax;lennum++){
|
||||
cout << "tax" << lennum << " is " << sam.taxas[lennum] << "; seq" << lennum << " is " << sam.chars[lennum] << endl;
|
||||
}
|
||||
return sam;
|
||||
}
|
||||
|
||||
Sample readTnt(){
|
||||
int ntax, nchar;
|
||||
ifstream seqfile;
|
||||
seqfile.open(fn);
|
||||
// get nchar and ntax
|
||||
string stri, sntax, snchar;
|
||||
for(int i=0;i<1;){
|
||||
getline(seqfile,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);
|
||||
// get class
|
||||
int lennum;
|
||||
for(lennum=0;lennum<sam.ntax;lennum++){
|
||||
getline(seqfile,stri);
|
||||
istringstream istr(stri);
|
||||
istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
|
||||
cout << "tax" << lennum << " is " << sam.taxas[lennum] << "; seq" << lennum << " is " << sam.chars[lennum] << endl;
|
||||
}
|
||||
seqfile.close();
|
||||
return sam;
|
||||
}
|
||||
|
||||
bool isNum(string strnum) {
|
||||
char* p;
|
||||
strtol(strnum.c_str(), &p, 10);
|
||||
return *p == 0;
|
||||
}
|
||||
|
||||
Sample readNex(){
|
||||
int ntax, nchar;
|
||||
// open file
|
||||
ifstream seqfile;
|
||||
seqfile.open(fn);
|
||||
// some tem
|
||||
string snall, stri, str_a, str_b;
|
||||
bool found = false;
|
||||
bool found_ntax = false;
|
||||
bool found_nchar = false;
|
||||
bool found_equal = false;
|
||||
char x = '=';
|
||||
int lnum, e, eulnum;
|
||||
e = 0;
|
||||
// getline line by line
|
||||
for(lnum=0;getline(seqfile,snall);lnum++){
|
||||
str_a = to_lower(snall);
|
||||
str_b = add_space(x,str_a);
|
||||
istringstream istr(str_b);
|
||||
// convert to words
|
||||
// e will enter the ntax/nchar function just after statisfy the `=`
|
||||
while(istr>> stri){
|
||||
if(stri=="dimensions"){
|
||||
found = true;
|
||||
}
|
||||
|
||||
if(stri=="ntax"){
|
||||
found_ntax = true;
|
||||
}
|
||||
if(stri=="nchar"){
|
||||
found_nchar = true;
|
||||
}
|
||||
if(stri=="="){
|
||||
found_equal = true;
|
||||
}
|
||||
if (found_ntax&&found_equal){
|
||||
e++;
|
||||
if(e>1){
|
||||
if(stri.back()==';'){
|
||||
stri.pop_back();
|
||||
found = false;
|
||||
}
|
||||
ntax = stoi(stri);
|
||||
found_equal = false;
|
||||
found_ntax = false;
|
||||
e=0;
|
||||
}
|
||||
}
|
||||
|
||||
if (found_nchar&&found_equal){
|
||||
e++;
|
||||
if(e>1){
|
||||
if(stri.back()==';'){
|
||||
stri.pop_back();
|
||||
found = false;
|
||||
}
|
||||
nchar = stoi(stri);
|
||||
found_equal = false;
|
||||
found_nchar = false;
|
||||
e=0;
|
||||
}
|
||||
}
|
||||
if(stri=="matrix"){
|
||||
// get the position of matrix
|
||||
eulnum = lnum+1;
|
||||
}
|
||||
}
|
||||
}
|
||||
// go back
|
||||
seqfile.clear();
|
||||
seqfile.seekg(0);
|
||||
// create class
|
||||
Sample sam(ntax,nchar);
|
||||
// some temp, z is line number, l is the string arrary number
|
||||
int z=0; int l=0;
|
||||
// read line by line
|
||||
while(getline(seqfile,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];
|
||||
cout << "tax" << l << " is " << sam.taxas[l] << "; seq" << l << " is " << sam.chars[l] << "; l=" << l << endl;
|
||||
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 to_lower(string stri){
|
||||
transform(stri.begin(),stri.end(),stri.begin(),::tolower);
|
||||
return stri;
|
||||
}
|
||||
|
||||
void writeFas(class Sample sam){
|
||||
ofstream outputFile(otn);
|
||||
if (outputFile.is_open()) {
|
||||
|
|
@ -160,14 +296,16 @@ void writePhy(class Sample sam){
|
|||
outputFile.close();
|
||||
}
|
||||
|
||||
void writeNexus(class Sample sam){
|
||||
void writeNex(class Sample sam){
|
||||
ofstream outputFile(otn);
|
||||
if (outputFile.is_open()) {
|
||||
outputFile << "#NEXUS" << endl << "Begin TAXA;" << endl << "\tDimensions ntax=" << sam.ntax << ";" << endl << "\tTaxLabels";
|
||||
for(int i1=0;i1<sam.ntax;i1++){
|
||||
outputFile << " " << sam.taxas[i1] << endl;
|
||||
}
|
||||
outputFile << ";" << endl << "End;" << endl << endl << "Begin data;" << endl << "\tDimensions nchar=" << sam.nchar << ";" << endl << "\tFormat datatype=dna missing=? gap=-;" << endl << "\tMatrix" << endl;
|
||||
outputFile << "#NEXUS" << endl;
|
||||
// outputFile << "Begin TAXA;" << endl << "\tDimensions ntax=" << sam.ntax << ";" << endl << "\tTaxLabels";
|
||||
// for(int i1=0;i1<sam.ntax;i1++){
|
||||
// outputFile << " " << sam.taxas[i1];
|
||||
// }
|
||||
// outputFile << ";" << endl << "End;" << endl << endl;
|
||||
outputFile << "Begin data;" << endl << "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax << ";" << endl << "\tFormat datatype=dna missing=? gap=-;" << endl << "\tMatrix" << endl;
|
||||
for(int i2=0;i2<sam.ntax;i2++){
|
||||
outputFile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
|
||||
}
|
||||
|
|
@ -180,9 +318,9 @@ void writeNexus(class Sample sam){
|
|||
|
||||
void writeTnt(class Sample sam){
|
||||
ofstream outputFile(otn);
|
||||
if (outputFile.is_open()) {
|
||||
if (outputFile.is_open()) {
|
||||
outputFile << "xread" << endl << "\' \'" << endl;
|
||||
outputFile << sam.nchar << " " << sam.ntax << endl;
|
||||
outputFile << "\' \'" << endl;
|
||||
for(int i=0;i<sam.ntax;i++){
|
||||
outputFile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
|
||||
}
|
||||
|
|
@ -218,6 +356,7 @@ void procargs (int nargs, char ** arg){ //*arg 视为整体，是字符串指针
|
|||
if (*cp=='f') {intype=1; cout << "intype is fasta, " << intype << endl;}
|
||||
if (*cp=='n') intype=2;
|
||||
if (*cp=='p') {intype=3; cout << "intype is phylip, " << intype << endl;}
|
||||
if (*cp=='t') {intype=4;}
|
||||
break;
|
||||
case 'h': show_help(1); break;
|
||||
case 'i': cp++; fn = cp; break;
|
||||
|
|
@ -246,13 +385,15 @@ Sample read_input (void){
|
|||
int ntax, nchar;
|
||||
Sample sam(ntax,nchar);
|
||||
if (intype==1) sam = readFas();
|
||||
if (intype==2) sam = readNex();
|
||||
if (intype==3) sam = readPhy();
|
||||
if (intype==4) sam = readTnt();
|
||||
return sam;
|
||||
}
|
||||
|
||||
void write_output (class Sample sam){
|
||||
if (outype==1) writeFas(sam);
|
||||
if (outype==2) writeNexus(sam);
|
||||
if (outype==2) writeNex(sam);
|
||||
if (outype==3) writePhy(sam);
|
||||
if (outype==4) writeTnt(sam);
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue