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D_stat_tv.cpp
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/*
Rauf Salamzade
DATE - 07/03/13
PROGRAM NAME - D_stat_0.6.cpp
DESCRIPTION - C++ implementation of D_stat_0.6.py by James Cahill
""
This version is for fasta files, they should be aligned and ordered correctly
If you want to calculate this D stat: D(Indiv1,Indiv2,Admix,OG)
Input is as follows:
python D_stat_0.5.py Indiv1.fa Indiv2.fa Admix.fa OG.fa block_size > D_I1_I2_Ad_OG.dstat
""
*/
#include <iostream>
#include <fstream>
#include <string>
#include <sstream>
using namespace std;
/* Example Run For Edser:
./D_stat_0.6 \
/mnt/tank/projects/bears_asymetric_hybridization/fastas_30/Den_all.fa \
/mnt/tank/projects/bears_asymetric_hybridization/fastas_30/Swe_all.fa \
/mnt/tank/projects/bears_asymetric_hybridization/fastas_30/WH1_all.fa \
/mnt/tank/projects/bears_asymetric_hybridization/fastas_30/Uam_all.fa \
1000 \
> ABBA_BABA_Den_Swe_WH1_Uam.out
*/
string scaffoldName(string val) {
string result;
for (int i=0; i < val.length(); i++) {
if (i != 0) {
result += val.at(i);
}
i++;
}
return result;
}
string doubleToString(double val) {
string result;
ostringstream convertd;
convertd << val;
result = convertd.str();
return result;
}
string integerToString(int val) {
string result;
ostringstream convert;
convert << val;
result = convert.str();
return result;
}
int main (int argc, char* argv[]) {
if ( argv[1]==NULL ) {
cerr << "ERROR: Incorrect number of arguments provided" << endl;
return 1;
}
else if ( (argv[1][0]=='-' && argv[1][1]=='h') || (argv[1][0]=='-' && argv[1][1]=='-' && argv[1][2]=='h') ) {
cout << "Input format:" << endl;
cout << "./a.out same_spp_1 same_spp_2 admix_spp outgroup_spp block_size" << endl;
cout << "all input files should be aligned fastas generated with pu2fa by Ed Green" << endl;
cout << "block_size should be an integer measured in bases" << endl;
return 0;
}
else if ( argv[1]==NULL || argv[2]==NULL || argv[3]==NULL || argv[4]==NULL || argv[5]==NULL ) {
cerr << "ERROR: Incorrect number of arguments provided" << endl;
return 1;
}
else {
ifstream file1;
ifstream file2;
ifstream adfile;
ifstream ogfile;
file1.open (argv[1]);
file2.open (argv[2]);
adfile.open (argv[3]);
ogfile.open (argv[4]);
istringstream ss(argv[5]);
int block;
if (!(ss >> block)) {
cerr << "Invalid block argument: " << argv[5] << '\n';
return 1;
}
string scaffold = "";
int AAAA = 0;
int BAAA = 0;
int ABAA = 0;
int AABA = 0;
int BBAA = 0;
int BABA = 0;
int ABBA = 0;
int BBBA = 0;
int BCAA = 0;
int BACA = 0;
int ABCA = 0;
int BBCA = 0;
int BCBA = 0;
int BCCA = 0;
int BCDA = 0;
int total = 0;
int count = 0;
int counter = 0;
string line1;
string line2;
string line3;
string line4;
string last1;
string last2;
string adlast;
string oglast;
cout << "scaffold\tend_block\tD_stat\tABBA\tBABA\tAAAA\tBAAA\tABAA\tAABA\tBBAA\tBBBA\tBCAA\tBACA\tABCA\tBBCA\tBCBA\tBCCA\tBCDA" << endl;
//cout << "scaffold1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0" << endl;
if ( file1.is_open() && file2.is_open() && adfile.is_open() && ogfile.is_open() ) {
while ( file1.good() && file2.good() && adfile.good() && ogfile.good() ) {
if (counter == 0) {
getline (file1,line1);
getline (file2,line2);
getline (adfile, line3);
getline (ogfile, line4);
}
if ( line1.find(">") == 0 || line2.find(">") == 0 || line3.find(">") == 0 || line4.find(">") == 0) {
if (counter != 0) {
if ( (ABBA+BABA) != 0) {
string out = scaffold.substr(1) + "\t" + integerToString(total) + "\t" + doubleToString( ( (double)ABBA-(double)BABA ) / ( (double)ABBA+(double)BABA ) ) + "\t" + integerToString(ABBA) + "\t" + integerToString(BABA) + "\t" + integerToString(AAAA) + "\t" + integerToString(BAAA) + "\t" + integerToString(ABAA) + "\t" + integerToString(AABA) + "\t" + integerToString(BBAA) + "\t" + integerToString(BBBA) + "\t" + integerToString(BCAA) + "\t" + integerToString(BACA) + "\t" + integerToString(ABCA) + "\t" + integerToString(BBCA) + "\t" + integerToString(BCBA) + "\t" + integerToString(BCCA) + "\t" + integerToString(BCDA);
cout << out << endl;
} else {
string out = scaffold.substr(1) + "\t" + integerToString(total) + "\t" + "0" + "\t" + integerToString(ABBA) + "\t" + integerToString(BABA) + "\t" + integerToString(AAAA) + "\t" + integerToString(BAAA) + "\t" + integerToString(ABAA) + "\t" + integerToString(AABA) + "\t" + integerToString(BBAA) + "\t" + integerToString(BBBA) + "\t" + integerToString(BCAA) + "\t" + integerToString(BACA) + "\t" + integerToString(ABCA) + "\t" + integerToString(BBCA) + "\t" + integerToString(BCBA) + "\t" + integerToString(BCCA) + "\t" + integerToString(BCDA);
cout << out << endl;
}
}
total=0;
while ( line1.find(">") != 0 ) {
getline(file1,line1);
}
while ( line2.find(">") != 0 ) {
getline(file2,line2);
}
while ( line3.find(">") != 0 ) {
getline(adfile,line3);
}
while ( line4.find(">") != 0 ) {
getline(ogfile,line4);
}
if ( (line1.compare(line2)!=0) or (line1.compare(line3)!=0) or (line1.compare(line4)!=0) or (line2.compare(line3)!=0) or (line2.compare(line4)!=0) or (line3.compare(line4)!=0) ) {
cout << "ERROR: FASTA files do not have scaffolds in the same order" << endl;
return(1);
}
scaffold = line1;
AAAA = 0;
BAAA = 0;
ABAA = 0;
AABA = 0;
BBAA = 0;
BABA = 0;
ABBA = 0;
BBBA = 0;
BCAA = 0;
BACA = 0;
ABCA = 0;
BBCA = 0;
BCBA = 0;
BCCA = 0;
BCDA = 0;
last1 = "";
last2 = "";
adlast = "";
oglast = "";
for(int i = 0 ; i < line1.length() ; i++) {
last1 += line1[i];
last2 += line2[i];
adlast += line3[i];
oglast += line4[i];
}
getline (file1,line1);
getline (file2,line2);
getline (adfile, line3);
getline (ogfile, line4);
count = 0;
}
else {
if ( (last1.length() == last2.length()) && (last1.length() == last2.length()) && (last1.length() == adlast.length()) && (last1.length() == oglast.length()) ) {
while ( (count < line1.length()) && (count < line2.length()) && (count < line3.length()) && (count < line4.length()) ) {
total++;
if ( line1[count]!='N' && line2[count]!='N' && line3[count]!='N' && line4[count]!='N') {
if ( line1[count]==line4[count] ) {
if ( line2[count]==line4[count] ) {
if ( line3[count]==line4[count] ) {
AAAA++;
} else {
AABA++;
}
}
else {
if ( line3[count]==line4[count] ) {
ABAA++;
} else if ( line2[count]==line3[count] ) {
if (line1[count]=='A' and line2[count]=='C') {
ABBA++;
} else if (line1[count]=='A' and line2[count]=='T') {
ABBA++;
} else if (line1[count]=='C' and line2[count]=='A') {
ABBA++;
} else if (line1[count]=='C' and line2[count]=='G') {
ABBA++;
} else if (line1[count]=='G' and line2[count]=='C') {
ABBA++;
} else if (line1[count]=='G' and line2[count]=='T') {
ABBA++;
} else if (line1[count]=='T' and line2[count]=='A') {
ABBA++;
} else if (line1[count]=='T' and line2[count]=='G') {
ABBA++;
}
} else {
ABCA++;
}
}
}
else {
if ( line2[count]==line4[count] ) {
if ( line3[count]==line4[count] ) {
BAAA++;
} else if ( line1[count]==line3[count] ) {
if (line1[count]=='A' and line2[count]=='C') {
BABA++;
} else if (line1[count]=='A' and line2[count]=='T') {
BABA++;
} else if (line1[count]=='C' and line2[count]=='A') {
BABA++;
} else if (line1[count]=='C' and line2[count]=='G') {
BABA++;
} else if (line1[count]=='G' and line2[count]=='C') {
BABA++;
} else if (line1[count]=='G' and line2[count]=='T') {
BABA++;
} else if (line1[count]=='T' and line2[count]=='A') {
BABA++;
} else if (line1[count]=='T' and line2[count]=='G') {
BABA++;
}
} else {
BACA++;
}
}
else if ( line1[count]==line2[count] ) {
if ( line1[count]==line3[count] ) {
BBBA++;
} else if ( line3[count]==line4[count] ) {
BBAA++;
} else {
BBCA++;
}
}
else {
if ( line1[count]==line3[count] ) {
BCBA++;
} else if ( line2[count]==line3[count] ) {
BCCA++;
} else if ( line3[count]==line4[count] ) {
BCAA++;
} else {
BCDA++;
}
}
}
}
if ( total%block==0 ) {
if ( (ABBA+BABA) != 0 ) {
string out = scaffold.substr(1) + "\t" + integerToString(total) + "\t" + doubleToString( ( (double)ABBA-(double)BABA ) / ( (double)ABBA+(double)BABA ) ) + "\t" + integerToString(ABBA) + "\t" + integerToString(BABA) + "\t" + integerToString(AAAA) + "\t" + integerToString(BAAA) + "\t" + integerToString(ABAA) + "\t" + integerToString(AABA) + "\t" + integerToString(BBAA) + "\t" + integerToString(BBBA) + "\t" + integerToString(BCAA) + "\t" + integerToString(BACA) + "\t" + integerToString(ABCA) + "\t" + integerToString(BBCA) + "\t" + integerToString(BCBA) + "\t" + integerToString(BCCA) + "\t" + integerToString(BCDA);
cout << out << endl;
} else {
string out = scaffold.substr(1) + "\t" + integerToString(total) + "\t" + "0" + "\t" + integerToString(ABBA) + "\t" + integerToString(BABA) + "\t" + integerToString(AAAA) + "\t" + integerToString(BAAA) + "\t" + integerToString(ABAA) + "\t" + integerToString(AABA) + "\t" + integerToString(BBAA) + "\t" + integerToString(BBBA) + "\t" + integerToString(BCAA) + "\t" + integerToString(BACA) + "\t" + integerToString(ABCA) + "\t" + integerToString(BBCA) + "\t" + integerToString(BCBA) + "\t" + integerToString(BCCA) + "\t" + integerToString(BCDA);
cout << out << endl;
}
AAAA = 0;
BAAA = 0;
ABAA = 0;
AABA = 0;
BBAA = 0;
BABA = 0;
ABBA = 0;
BBBA = 0;
BCAA = 0;
BACA = 0;
ABCA = 0;
BBCA = 0;
BCBA = 0;
BCCA = 0;
BCDA = 0;
}
count++;
}
} else {
cout << "ERROR: FASTA file lines should be of equal length" << endl;
return(1);
}
count = 0;
last1 = "";
last2 = "";
adlast = "";
oglast = "";
for(int i = 0 ; i < line1.length() ; i++) {
last1 += line1[i];
last2 += line2[i];
adlast += line3[i];
oglast += line4[i];
}
getline (file1,line1);
getline (file2,line2);
getline (adfile, line3);
getline (ogfile, line4);
}
counter++;
}
if ( (ABBA+BABA) != 0 ) {
string out = scaffold.substr(1) + "\t" + integerToString(total) + "\t" + doubleToString( ( (double)ABBA-(double)BABA ) / ( (double)ABBA+(double)BABA ) ) + "\t" + integerToString(ABBA) + "\t" + integerToString(BABA) + "\t" + integerToString(AAAA) + "\t" + integerToString(BAAA) + "\t" + integerToString(ABAA) + "\t" + integerToString(AABA) + "\t" + integerToString(BBAA) + "\t" + integerToString(BBBA) + "\t" + integerToString(BCAA) + "\t" + integerToString(BACA) + "\t" + integerToString(ABCA) + "\t" + integerToString(BBCA) + "\t" + integerToString(BCBA) + "\t" + integerToString(BCCA) + "\t" + integerToString(BCDA);
cout << out << endl;
} else {
string out = scaffold.substr(1) + "\t" + integerToString(total) + "\t" + "0" + "\t" + integerToString(ABBA) + "\t" + integerToString(BABA) + "\t" + integerToString(AAAA) + "\t" + integerToString(BAAA) + "\t" + integerToString(ABAA) + "\t" + integerToString(AABA) + "\t" + integerToString(BBAA) + "\t" + integerToString(BBBA) + "\t" + integerToString(BCAA) + "\t" + integerToString(BACA) + "\t" + integerToString(ABCA) + "\t" + integerToString(BBCA) + "\t" + integerToString(BCBA) + "\t" + integerToString(BCCA) + "\t" + integerToString(BCDA);
cout << out << endl;
}
file1.close();
file2.close();
adfile.close();
ogfile.close();
}
else {
cout << "ERROR: Unable to open file(s)" << endl;
}
return 0;
}
}