iMatrix *readmatrix(std::string filename,const std::string delim=",;: \t"){
///@param filename A filename to read.@param delim A string of delimiters.
std::vector<std::string> tokens;
const int SIZE=500000;
char buffer[SIZE];
std::ifstream pFile (filename.c_str(),std::ios::in);
if(!pFile){
std::cout <<"Problems opening file" <<filename<<std::endl;
exit(0);
}
std::string tmp_string;
int doFirstRow =1;
int itemsInFirstRow=0;
int numRows =0;
while(!pFile.eof()){
pFile.getline(buffer,SIZE);
tmp_string = std::string(buffer);
if(doFirstRow){
//if file has a emptystart line
itemsInFirstRow = get_lexemes(tmp_string,tokens,delim);
if (itemsInFirstRow==0)
continue;
// printf("items in first rwo:%d\n",itemsInFirstRow);
doFirstRow=0;
numRows++;
}
else{
int nItems = get_lexemes(tmp_string,tokens,delim);
//if line is empty
if(nItems==0)
continue;
numRows++;
if(nItems!=itemsInFirstRow){
printf("row length mismatch at line:%d numitems is:%d shouldn't be:%d\t will exit\n",numRows,itemsInFirstRow,nItems);
exit(0);
}
}
}
iMatrix *data_ = allocIntMatrix(numRows,itemsInFirstRow);
//now we have a token array of string coerce the types now
typecast_stringarray_to_int_matrix(tokens,data_);
//copy(tokens.begin(), tokens.end(), ostream_iterator<string>(cout, ", "));
printf("\t-> Dimension of genotype datafile is (%d,%d)\n",data_->x,data_->y);
return data_;
}
iMatrix *readmatrix_filty_memory(std::string filename,const std::string delim=",;: \t"){
///@param filename A filename to read.@param delim A string of delimiters.
std::vector<std::string> tokens;
const int SIZE = MAX_ELEMS_PER_LINE;//defined in conf.h
char buffer[SIZE];
std::ifstream pFile (filename.c_str(),std::ios::in);
if(!pFile){
fileError(filename);
exit(0);
}
std::string tmp_string;
int doFirstRow =1;
int itemsInFirstRow=0;
int numRows =0;
while(!pFile.eof()){
pFile.getline(buffer,SIZE);
tmp_string = std::string(buffer);
if(doFirstRow){
//if file has a emptystart line
itemsInFirstRow = get_lexemes(tmp_string,tokens,delim);
if (itemsInFirstRow==0)
continue;
// printf("items in first rwo:%d\n",itemsInFirstRow);
doFirstRow=0;
numRows++;
}
else{
int nItems = get_lexemes(tmp_string,tokens,delim);
//if line is empty
if(nItems==0)
continue;
numRows++;
if(nItems!=itemsInFirstRow){
printf("row length mismatch at line:%d numitems is:%d shouldn't be:%d\t will exit\n",numRows,itemsInFirstRow,nItems);
exit(0);
}
}
}
flush_print("\r\t-> File has been read in now, will now typecheck... ");
iMatrix *data_ = allocIntMatrix(numRows,itemsInFirstRow);
//now we have a token array of string coerce the types now
typecast_stringarray_to_int_matrix(tokens,data_);
//copy(tokens.begin(), tokens.end(), ostream_iterator<string>(cout, ", "));
return data_;
}
iMatrix *bed_to_iMatrix(const char* file, int nrow,int ncol) {
const unsigned char recode[4] = {'\x01', '\x00', '\x02', '\x03'};
const unsigned char mask = '\x03';
FILE *in = fopen(file, "r");
if (!in){
printf("Couln't open input file: %s", file);
exit(0);
}
unsigned char start[3];
if (fread(start, 1, 3, in)!=3){
printf("Failed to read first 3 bytes");
exit(0);
}
if (start[0]!='\x6C' || start[1]!='\x1B'){
printf("Input file does not appear to be a .bed file (%X, %X)",
start[0], start[1]);
exit(0);
}
/* Create output object */
iMatrix *returnMat = allocIntMatrix(nrow,ncol);
int ncell = nrow*ncol;
unsigned char *result = new unsigned char[nrow*ncol];
memset(result, 0x00, ncell);
/* Read in data */
int snp_major = start[2];
int part=0, ij=0, i=0, j=0;
while (1) {
unsigned char byte;
if (!part) {
if (feof(in) || !fread(&byte, 1, 1, in)) {
printf("Unexpected end of file reached");
exit(0);
}
part = 4;
}
unsigned char code = byte & mask;
byte = byte >> 2;
part--;
result[ij] = recode[code];
returnMat->matrix[i][j] = result[ij];
if(returnMat->matrix[i][j]==3)
returnMat->matrix[i][j]=1;
else if(returnMat->matrix[i][j]==1)
returnMat->matrix[i][j]=3;
else if(returnMat->matrix[i][j]<0 || returnMat->matrix[i][j]>3){
printf("Problem in bed file at position=(%d,%d)=%d\n",i,j,returnMat->matrix[i][j]);
exit(0);
}
// printf("(%d,%d)=%d ",i,j,result[ij]);
if (snp_major) {
ij++;
i++;
if (i==nrow) {
i = part = 0;
j++;
if (j==ncol)
break;
}
}
else {
ij += nrow;
j++;
if (j==ncol){
j = part = 0;
i++;
if (i==nrow)
break;
ij = i;
}
}
}
fclose(in);
delete [] result;
return returnMat;
}
iMatrix *readmatrix(std::string filename,const std::string delim=",;: \t"){
///@param filename A filename to read.@param delim A string of delimiters.
if(0){
printf("\t-> will try to open postfile: \"%s\" ... \n",filename.c_str());
fflush(stdout);
}
const int SIZE = MAX_ELEMS_PER_LINE;
char buffer[SIZE];
std::ifstream pFile (filename.c_str(),std::ios::in);
if(!pFile){
std::cout <<"Problems opening file" <<filename<<std::endl;
exit(0);
}
int doFirstRow =1;
int itemsInFirstRow=0;
int numRows =0;
flush_print("Checking consistency of file...");
while(!pFile.eof()){
std::vector<std::string> tokens;
std::string tmp_string;
pFile.getline(buffer,SIZE);
tmp_string = std::string(buffer);
if(doFirstRow){
//if file has a emptystart line
itemsInFirstRow = get_lexemes(tmp_string,tokens,delim);
if (itemsInFirstRow==0)
continue;
// printf("items in first rwo:%d\n",itemsInFirstRow);
doFirstRow=0;
numRows++;
}
else{
int nItems = get_lexemes(tmp_string,tokens,delim);
//if line is empty
if(nItems==0)
continue;
numRows++;
if(nItems!=itemsInFirstRow){
printf("row length mismatch at line:%d numitems is:%d shouldn't be:%d\t will exit\n",numRows,itemsInFirstRow,nItems);
exit(0);
}
}
if ((numRows%20 )==0){
printf("\r\t-> Checking consistency of file: (checking number of items at line: %d )",numRows);
fflush(stdout);
}
}
pFile.close();
fflush(stdout);
iMatrix *mat = allocIntMatrix(numRows,itemsInFirstRow);
numRows = 0;
std::ifstream pFile2 (filename.c_str(),std::ios::in);
while(!pFile2.eof()){
if ((numRows%5 )==0){
printf("\r\t-> Checking consistency of file: (Now reading in data at line: %d/%d ) ",numRows,mat->x);
fflush(stdout);
}
std::vector<std::string> tokens;
std::string tmp_string;
pFile2.getline(buffer,SIZE);
tmp_string = std::string(buffer);
int itemsInRow = get_lexemes(tmp_string,tokens,delim);
if (itemsInRow==0)
continue;
for(unsigned int i=0; i <tokens.size();i++){
mat->matrix[numRows][i] = to_int(tokens[i]);
if(mat->matrix[numRows][i]<0||mat->matrix[numRows][i]>3){
printf("\n\t-> Error in genotype data: (%d,%d)=%d, value should be between 0 and 3.\n",numRows,i,mat->matrix[numRows][i]);
exit(0);
}
}
numRows++;
}
pFile2.close();
//copy(tokens.begin(), tokens.end(), ostream_iterator<string>(cout, ", "));
fflush(stdout);
return mat;
}
