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SMR_data_p2.cpp
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SMR_data_p2.cpp
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//
// SMR_data_p2.cpp
// SMR_CPP
//
// Created by Futao Zhang on 10/06/2016.
// Copyright (c) 2016 Futao Zhang. All rights reserved.
//
#include "SMR_data_p2.h"
FILE* techeQTLfile=NULL;
namespace SMRDATA
{
double adjSE(double beta,double p)
{
if(p==1)
{
return 1e10;
}
else
{
double z2=qchisq(p, 1);
return fabs(beta/sqrt(z2));
}
}
// below for txt 2 besd
int read_probeinfolst(vector<probeinfolst> &prbiflst,char* syllabusName)
{
ifstream flptr(syllabusName);
if (!flptr) {
printf("ERROR: can not open the file %s to read.\n",syllabusName);
exit(EXIT_FAILURE);
}
printf( "Reading eQTL probe information from \"%s\".\n", syllabusName);
map<string, int> probe_map;
map<string, int> probe_cp_map;
map<string, int> probe_cpb_map;
long mapsize=0;
char buf[MAX_LINE_SIZE];
flptr.getline(buf, MAX_LINE_SIZE); //header
if(buf[0]=='\0')
{
printf("ERROR: the first row of the file %s is empty.\n",syllabusName);
exit(EXIT_FAILURE);
}
vector<string> vs_buf;
int col_num = split_string(buf, vs_buf, ", \t\n");
to_upper(vs_buf[0]);
if(vs_buf[0]!="CHR") {
printf("ERROR: %s should have headers that start with \"Chr\".\n", syllabusName);
exit(EXIT_FAILURE);
}
int lineNum(0);
while(!flptr.eof())
{
flptr.getline(buf,MAX_LINE_SIZE);
if(buf[0]!='\0') lineNum++;
}
flptr.clear(ios::goodbit);
flptr.seekg (0, ios::beg);
flptr.getline(buf, MAX_LINE_SIZE); //header
int fcount=0;
while(!flptr.eof())
{
flptr.getline(buf,MAX_LINE_SIZE);
if(buf[0]!='\0'){
vs_buf.clear();
col_num = split_string(buf, vs_buf, ", \t\n");
if(col_num!=7 && col_num!=8) {
printf("ERROR: column number is not correct in row %d with probe name %s.\n", fcount+2, vs_buf[1].c_str());
exit(EXIT_FAILURE);
}
if(vs_buf[1]=="NA" || vs_buf[1]=="na")
{
printf("ERROR: probe name is missing in row %d.\n", fcount+2);
exit(EXIT_FAILURE);
}
to_upper(vs_buf[0]);
to_upper(vs_buf[3]);
if(vs_buf[0]=="NA" || vs_buf[3]=="NA")
{
printf("ERROR: probe chromosome information or probe position information of probe %s is missing in row %d.\n", vs_buf[1].c_str(),fcount+2);
exit(EXIT_FAILURE);
}
if(vs_buf[6]=="NA" || vs_buf[6]=="na")
{
printf("ERROR: ESD file path of probe %s is missing in row %d.\n", vs_buf[1].c_str(),fcount+2);
exit(EXIT_FAILURE);
}
string cpstr=vs_buf[0]+":"+vs_buf[1];
string cpbstr=vs_buf[0]+":"+vs_buf[1]+":"+vs_buf[3];
probe_cp_map.insert(pair<string,int>(cpstr,fcount));
probe_cpb_map.insert(pair<string,int>(cpbstr,fcount));
probe_map.insert(pair<string,int>(vs_buf[6],fcount));
if(probe_cp_map.size()!=probe_cpb_map.size())
{
printf("ERROR: probe %s has multiple positions.\n",vs_buf[1].c_str() );
exit(EXIT_FAILURE);
}
if(mapsize==probe_map.size())
{
printf("ERROR: Duplicated ESD file name found for %s.\n",vs_buf[6].c_str() );
exit(EXIT_FAILURE);
} else {
mapsize=probe_map.size();
}
probeinfolst tmpinfo;
int tmpchr;
if(vs_buf[0]=="X" || vs_buf[0]=="x") tmpchr=23;
else if(vs_buf[0]=="Y" || vs_buf[0]=="y") tmpchr=24;
else tmpchr=atoi(vs_buf[0].c_str());
tmpinfo.probechr=tmpchr;
strcpy2(&tmpinfo.probeId, vs_buf[1]);
tmpinfo.gd=atoi(vs_buf[2].c_str());
tmpinfo.bp=atoi(vs_buf[3].c_str());
strcpy2(&tmpinfo.genename, vs_buf[4]);
tmpinfo.orien=vs_buf[5].c_str()[0];
strcpy2(&tmpinfo.esdpath, vs_buf[6]);
if(col_num==8){
strcpy2(&tmpinfo.bfilepath, vs_buf[7]);
} else tmpinfo.bfilepath=NULL;
prbiflst.push_back(tmpinfo);
fcount++;
}
}
flptr.close();
printf("%d ESD files of total %ld probes to be included from \"%s\".\n",lineNum, probe_cp_map.size(), syllabusName);
return lineNum;
}
void read_smr_sa(vector<string> &rs,vector<int> &chr, vector<int> &bp, vector<string> &a1, vector<string> &a2, vector<float> &freq,vector<float> &beta,vector<float> &se,string esdpath)
{
gzFile gzfile=NULL;
ifstream flptr;
bool gzflag=has_suffix(esdpath, "gz");
if(gzflag)
{
gzfile = gzopen(esdpath.c_str(), "rb");
if (!(gzfile)) {
fprintf (stderr, "%s: Error: can not open the file %s\n",
esdpath.c_str(), strerror (errno));
exit (EXIT_FAILURE);
}
}
else
{
flptr.open(esdpath.c_str());
if (!flptr) throw ("Error: can not open the file [" + esdpath + "] to read.");
}
cout << "Reading eQTL summary data from [" + string(esdpath) + "]." << endl;
char buf[MAX_LINE_SIZE];
int lineNum(0);
if(gzflag) gzgets(gzfile, buf, MAX_LINE_SIZE); //head
else flptr.getline(buf,MAX_LINE_SIZE);// the header
/* check headers */
if(buf[0]=='\0')
{
printf("ERROR: the first row of the file %s is empty.\n",esdpath.c_str());
exit(EXIT_FAILURE);
}
vector<string> vs_buf;
int col_num = split_string(buf, vs_buf, ", \t\n");
to_upper(vs_buf[0]);
if(vs_buf[0]!="CHR") {
printf("ERROR: the headers should start with \"Chr\"");
exit(EXIT_FAILURE);
}
map<string, int> currs_map;
long currssize=0;
while(!flptr.eof() && !gzeof(gzfile))
{
if(gzflag) gzgets(gzfile, buf, MAX_LINE_SIZE);
else flptr.getline(buf,MAX_LINE_SIZE);
if(buf[0]!='\0'){
vs_buf.clear();
col_num = split_string(buf, vs_buf, ", \t\n");
if(col_num!=9) {
printf("ERROR: column number is not correct in row %d.!", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[1]=="NA" || vs_buf[1]=="na"){
printf("ERROR: the SNP name is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
string tmpstr=vs_buf[0]+":"+vs_buf[1];
currs_map.insert(pair<string,int>(tmpstr,lineNum));
if(currssize<currs_map.size())
{
if(vs_buf[0]=="NA" || vs_buf[0]=="na"){
printf("ERROR: the chromosome is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
int tmpchr;
if(vs_buf[0]=="X" || vs_buf[0]=="x") tmpchr=23;
else if(vs_buf[0]=="Y" || vs_buf[0]=="y") tmpchr=24;
else tmpchr=atoi(vs_buf[0].c_str());
chr.push_back(tmpchr);
rs.push_back(vs_buf[1]);
if(vs_buf[2]=="NA" || vs_buf[2]=="na"){
printf("ERROR: the SNP position is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
bp.push_back(atoi(vs_buf[2].c_str()));
to_upper(vs_buf[3]);
a1.push_back(vs_buf[3]);
to_upper(vs_buf[4]);
a2.push_back(vs_buf[4]);
if(vs_buf[5].compare("NA") && vs_buf[5].compare("na"))
{
float fq=atof(vs_buf[5].c_str());
if(fq<=0 || fq>=1)
{
printf("ERROR: allele frequency should be between 0 and 1 in row %d.\n",lineNum+2);
exit(EXIT_FAILURE);
}
freq.push_back(fq);
} else {
freq.push_back(-9);
}
to_upper(vs_buf[6]);
to_upper(vs_buf[7]);
to_upper(vs_buf[8]);
if(vs_buf[6].compare("NA") && (vs_buf[7].compare("NA") || vs_buf[8].compare("NA"))){
beta.push_back(atof(vs_buf[6].c_str()));
if(vs_buf[8]=="NA") se.push_back(atof(vs_buf[7].c_str()));
else {
double betatmp=atof(vs_buf[6].c_str());
double ptmp=atof(vs_buf[8].c_str());
if(ptmp<0)
{
printf("ERROR: p-value should be positive in row %d.\n",lineNum+2);
printf("%s\n",buf);
exit(EXIT_FAILURE);
}
if(ptmp==0) {
ptmp=__DBL_MIN__;
printf("WARNING: p-value of 0 found in row %d and changed to min double value %e.\n",lineNum+2,__DBL_MIN__);
printf("%s\n",buf);
}
if((ptmp<MIN_PVAL_ADJUSTED && vs_buf[7]!="NA") || ptmp==1) se.push_back(atof(vs_buf[7].c_str()));
else se.push_back(adjSE(betatmp, ptmp));
}
} else {
printf("WARNING: this row is omitted because beta is missing or both SE and P are missing (\"NA\").\n");
printf("%s\n",buf);
beta.push_back(-9);
se.push_back(-9);
}
lineNum++;
currssize=currs_map.size();
} else {
printf("WARNING: duplicated SNP ID %s in file %s. The duplicated entry is omitted:\n", vs_buf[1].c_str(),esdpath.c_str());
printf("%s.\n",buf);
}
}
}
if(gzflag) gzclose(gzfile);
else flptr.close();
cout << lineNum << " SNPs to be included from [" + string(esdpath) + "]." << endl;
}
void read_smr_sa(vector<snpinfolst> &snpinfo,string esdpath)
{
gzFile gzfile=NULL;
ifstream flptr;
bool gzflag=has_suffix(esdpath, "gz");
if(gzflag)
{
gzfile = gzopen(esdpath.c_str(), "rb");
if (!(gzfile)) {
fprintf (stderr, "%s: Couldn't open file %s\n",
esdpath.c_str(), strerror (errno));
exit (EXIT_FAILURE);
}
}
else
{
flptr.open(esdpath.c_str());
if (!flptr) throw ("Error: can not open the file [" + esdpath + "] to read.");
}
cout << "Reading eQTL information from [" + string(esdpath) + "]." << endl;
char buf[MAX_LINE_SIZE];
int lineNum(0);
if(gzflag) gzgets(gzfile, buf, MAX_LINE_SIZE); //head
else flptr.getline(buf,MAX_LINE_SIZE);// the header
/* check headers */
if(buf[0]=='\0')
{
printf("ERROR: the first row of the file %s is empty.\n",esdpath.c_str());
exit(EXIT_FAILURE);
}
vector<string> vs_buf;
int col_num = split_string(buf, vs_buf, ", \t\n");
to_upper(vs_buf[0]);
if(vs_buf[0]!="CHR") {
printf("ERROR: the headers should start with \"Chr\"");
exit(EXIT_FAILURE);
}
map<string, int> currs_map;
long currssize=0;
while(!flptr.eof() && !gzeof(gzfile))
{
snpinfolst tmpesd;
if(gzflag) gzgets(gzfile, buf, MAX_LINE_SIZE);
else flptr.getline(buf,MAX_LINE_SIZE);
if(buf[0]!='\0'){
vs_buf.clear();
col_num = split_string(buf, vs_buf, ", \t\n");
if(col_num!=9) {
printf("ERROR: the number of columns is incorrect in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[1]=="NA" || vs_buf[1]=="na"){
printf("ERROR: the SNP name is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
string tmpstr=vs_buf[0]+":"+vs_buf[1];
currs_map.insert(pair<string,int>(tmpstr,lineNum));
if(currssize<currs_map.size())
{
if(vs_buf[0]=="NA" || vs_buf[0]=="na"){
printf("ERROR: the chromosome is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[0]=="X" || vs_buf[0]=="x") tmpesd.snpchr=23;
else if(vs_buf[0]=="Y" || vs_buf[0]=="y") tmpesd.snpchr=24;
else tmpesd.snpchr=atoi(vs_buf[0].c_str());
strcpy2(&tmpesd.snprs,vs_buf[1]);
if(vs_buf[2]=="NA" || vs_buf[2]=="na"){
printf("ERROR: the SNP position is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
tmpesd.bp=atoi(vs_buf[2].c_str());
to_upper(vs_buf[3]);
strcpy2(&tmpesd.a1,vs_buf[3]);
to_upper(vs_buf[4]);
strcpy2(&tmpesd.a2,vs_buf[4]);
if(vs_buf[5].compare("NA") && vs_buf[5].compare("na"))
{
float fq=atof(vs_buf[5].c_str());
if(fq<=0 || fq>=1)
{
printf("ERROR: freq should be between 0 and 1 in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
tmpesd.freq=fq;
} else {
tmpesd.freq=-9;
}
to_upper(vs_buf[6]);
to_upper(vs_buf[7]);
to_upper(vs_buf[8]);
if(vs_buf[6].compare("NA") && (vs_buf[7].compare("NA") || vs_buf[8].compare("NA"))){
tmpesd.beta=atof(vs_buf[6].c_str());
if(vs_buf[8]=="NA") tmpesd.se=atof(vs_buf[7].c_str());
else {
double betatmp=atof(vs_buf[6].c_str());
double ptmp=atof(vs_buf[8].c_str());
if(ptmp<0)
{
printf("ERROR: p-value should be positive in row %d.\n",lineNum+2);
printf("%s\n",buf);
exit(EXIT_FAILURE);
}
if(ptmp==0) {
ptmp=__DBL_MIN__;
printf("WARNING: p-value of 0 found in row %d and changed to min double value %e.\n",lineNum+2,__DBL_MIN__);
printf("%s\n",buf);
}
if((ptmp<MIN_PVAL_ADJUSTED && vs_buf[7]!="NA") || ptmp==1) tmpesd.se=atof(vs_buf[7].c_str());
else tmpesd.se=adjSE(betatmp, ptmp);
}
snpinfo.push_back(tmpesd);
} else {
printf("WARNING: this row is omitted because beta is missing or both SE and P are missing (\"NA\").\n");
printf("%s\n",buf);
tmpesd.beta=-9;
tmpesd.se=-9;
}
lineNum++;
currssize=currs_map.size();
} else {
printf("WARNING: duplicated SNP ID %s in file %s. The duplicated entry is omitted:\n", vs_buf[1].c_str(),esdpath.c_str());
printf("%s.\n",buf);
}
}
}
if(gzflag) gzclose(gzfile);
else flptr.close();
cout << lineNum << " SNPs infomation to be included from [" + string(esdpath) + "]." << endl;
}
void read_plink_qassoc_gz(vector<string> &rs,vector<int> &chr,vector<int> &bp, vector<float> &beta,vector<float> &se,string esdpath){
cout << "Reading summary information from [" + esdpath + "]." << endl;
char tbuf[MAX_LINE_SIZE];
gzFile gzfile = gzopen(esdpath.c_str(), "rb");
if (!(gzfile)) {
fprintf (stderr, "%s: Couldn't open file %s\n",
esdpath.c_str(), strerror (errno));
exit (EXIT_FAILURE);
}
int lineNum(0);
gzgets(gzfile, tbuf, MAX_LINE_SIZE); //head
if(tbuf[0]=='\0')
{
printf("ERROR: the first row of the file %s is empty.\n",esdpath.c_str());
exit(EXIT_FAILURE);
}
vector<string> vs_buf;
int col_num = split_string(tbuf, vs_buf, ", \t\n");
to_upper(vs_buf[0]);
if(vs_buf[0]!="CHR") {
printf("ERROR: the headers should start with \"CHR\"");
exit(EXIT_FAILURE);
}
while(!gzeof(gzfile))
{
gzgets(gzfile, tbuf, MAX_LINE_SIZE);
if(tbuf[0]!='\0'){
vs_buf.clear();
int col_num = split_string(tbuf, vs_buf, ", \t\n");
if(col_num!=9) {
printf("ERROR: the number of columns is incorrect in row %d.!", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[0]=="NA" || vs_buf[0]=="na"){
printf("ERROR: the chromosome is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[1]=="NA" || vs_buf[1]=="na"){
printf("ERROR: the SNP name is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
int tmpchr;
if(vs_buf[0]=="X" || vs_buf[0]=="x") tmpchr=23;
else if(vs_buf[0]=="Y" || vs_buf[0]=="y") tmpchr=24;
else tmpchr=atoi(vs_buf[0].c_str());
chr.push_back(tmpchr);
rs.push_back(vs_buf[1]);
if(vs_buf[2]=="NA" || vs_buf[2]=="na"){
printf("ERROR: the SNP position is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
bp.push_back(atoi(vs_buf[2].c_str()));
to_upper(vs_buf[4]);
to_upper(vs_buf[5]);
to_upper(vs_buf[8]);
if(vs_buf[4].compare("NA") && (vs_buf[5].compare("NA") || vs_buf[8].compare("NA")))
{
beta.push_back(atof(vs_buf[4].c_str()));
if(vs_buf[8]=="NA") se.push_back(atof(vs_buf[5].c_str()));
else {
double betatmp=atof(vs_buf[4].c_str());
double ptmp=atof(vs_buf[8].c_str());
if(ptmp<0)
{
printf("ERROR: p-value should be positive in row %d.\n",lineNum+2);
printf("%s\n",tbuf);
exit(EXIT_FAILURE);
}
if(ptmp==0) {
ptmp=__DBL_MIN__;
printf("WARNING: p-value of 0 found in row %d and changed to min double value %e.\n",lineNum+2,__DBL_MIN__);
printf("%s\n",tbuf);
}
if((ptmp<MIN_PVAL_ADJUSTED && vs_buf[5]!="NA") || ptmp==1) se.push_back(atof(vs_buf[5].c_str()));
else se.push_back(adjSE(betatmp, ptmp));
}
} else {
printf("WARNING: this row is omitted because beta is missing or both SE and P are missing (\"NA\").\n");
printf("%s\n",tbuf);
beta.push_back(-9);
se.push_back(-9);
}
lineNum++;
}
}
gzclose(gzfile);
cout << lineNum << " SNPs summary info to be included from [" + esdpath + "]." << endl;
}
void read_plink_qassoc(vector<string> &rs,vector<int> &chr, vector<int> &bp, vector<float> &beta,vector<float> &se,string esdpath){
ifstream flptr(esdpath.c_str());
if (!flptr) throw ("Error: can not open the file [" + string(esdpath) + "] to read.");
cout << "Reading eQTL information from [" + string(esdpath) + "]." << endl;
char buf[MAX_LINE_SIZE];
int lineNum(0);
flptr.getline(buf,MAX_LINE_SIZE);
if(buf[0]=='\0')
{
printf("ERROR: the first row of the file %s is empty.\n",esdpath.c_str());
exit(EXIT_FAILURE);
}
vector<string> vs_buf;
int col_num = split_string(buf, vs_buf, ", \t\n");
to_upper(vs_buf[0]);
if(vs_buf[0]!="CHR") {
printf("ERROR: the headers should start with \"CHR\"");
exit(EXIT_FAILURE);
}
while(!flptr.eof())
{
flptr.getline(buf,MAX_LINE_SIZE);
if(buf[0]!='\0'){
vs_buf.clear();
int col_num = split_string(buf, vs_buf, ", \t\n");
if(col_num!=9) {
printf("ERROR: the number of columns is incorrect in row %d.!", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[0]=="NA" || vs_buf[0]=="na"){
printf("ERROR: the chromosome is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[1]=="NA" || vs_buf[1]=="na"){
printf("ERROR: the SNP name is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
int tmpchr;
if(vs_buf[0]=="X" || vs_buf[0]=="x") tmpchr=23;
else if(vs_buf[0]=="Y" || vs_buf[0]=="y") tmpchr=24;
else tmpchr=atoi(vs_buf[0].c_str());
chr.push_back(tmpchr);
rs.push_back(vs_buf[1]);
if(vs_buf[2]=="NA" || vs_buf[2]=="na"){
printf("ERROR: the SNP position is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
bp.push_back(atoi(vs_buf[2].c_str()));
to_upper(vs_buf[4]);
to_upper(vs_buf[5]);
to_upper(vs_buf[8]);
if(vs_buf[4].compare("NA") && (vs_buf[5].compare("NA") || vs_buf[8].compare("NA")))
{
beta.push_back(atof(vs_buf[4].c_str()));
if(vs_buf[8]=="NA") se.push_back(atof(vs_buf[5].c_str()));
else {
double betatmp=atof(vs_buf[4].c_str());
double ptmp=atof(vs_buf[8].c_str());
if(ptmp<0)
{
printf("ERROR: p-value should be positive in row %d.\n",lineNum+2);
printf("%s\n",buf);
exit(EXIT_FAILURE);
}
if(ptmp==0) {
ptmp=__DBL_MIN__;
printf("WARNING: p-value of 0 found in row %d and changed to min double value %e.\n",lineNum+2,__DBL_MIN__);
printf("%s\n",buf);
}
if((ptmp<MIN_PVAL_ADJUSTED && vs_buf[5]!="NA") || ptmp==1) se.push_back(atof(vs_buf[5].c_str()));
else se.push_back(adjSE(betatmp, ptmp));
}
} else {
printf("WARNING: this row is omitted because beta is missing or both SE and P are missing (\"NA\").\n");
printf("%s\n",buf);
beta.push_back(-9);
se.push_back(-9);
}
lineNum++;
}
}
flptr.close();
cout << lineNum << " SNPs summary info to be included from [" + esdpath + "]." << endl;
}
void read_plink_qassoc(vector<snpinfolst> &snpinfo,string esdpath)
{
gzFile gzfile=NULL;
ifstream flptr;
bool gzflag=has_suffix(esdpath, "gz");
if(gzflag)
{
gzfile = gzopen(esdpath.c_str(), "rb");
if (!(gzfile)) {
fprintf (stderr, "%s: Couldn't open file %s\n",
esdpath.c_str(), strerror (errno));
exit (EXIT_FAILURE);
}
}
else
{
flptr.open(esdpath.c_str());
if (!flptr) throw ("Error: can not open the file [" + esdpath + "] to read.");
}
cout << "Reading eQTL information from [" + string(esdpath) + "]." << endl;
char buf[MAX_LINE_SIZE];
int lineNum(0);
if(gzflag) gzgets(gzfile, buf, MAX_LINE_SIZE); //head
else flptr.getline(buf,MAX_LINE_SIZE);// the header
if(buf[0]=='\0')
{
printf("ERROR: the first row of the file %s is empty.\n",esdpath.c_str());
exit(EXIT_FAILURE);
}
vector<string> vs_buf;
int col_num = split_string(buf, vs_buf, ", \t\n");
to_upper(vs_buf[0]);
if(vs_buf[0]!="CHR") {
printf("ERROR: the headers should start with \"CHR\"");
exit(EXIT_FAILURE);
}
while(!flptr.eof() && !gzeof(gzfile))
{
snpinfolst tmpesd;
if(gzflag) gzgets(gzfile, buf, MAX_LINE_SIZE);
else flptr.getline(buf,MAX_LINE_SIZE);
if(buf[0]!='\0'){
vs_buf.clear();
int col_num = split_string(buf, vs_buf, ", \t\n");
if(col_num!=9) {
printf("ERROR: the number of columns is incorrect in row %d.!", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[0]=="NA" || vs_buf[0]=="na"){
printf("ERROR: the chromosome is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[1]=="NA" || vs_buf[1]=="na"){
printf("ERROR: the SNP name is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[0]=="X" || vs_buf[0]=="x") tmpesd.snpchr=23;
else if(vs_buf[0]=="Y" || vs_buf[0]=="y") tmpesd.snpchr=24;
else tmpesd.snpchr=atoi(vs_buf[0].c_str());
strcpy2(&tmpesd.snprs,vs_buf[1]);
if(vs_buf[2]=="NA" || vs_buf[2]=="na"){
printf("ERROR: the SNP position is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
tmpesd.bp=atoi(vs_buf[2].c_str());
to_upper(vs_buf[4]);
to_upper(vs_buf[5]);
to_upper(vs_buf[8]);
if(vs_buf[4].compare("NA") && (vs_buf[5].compare("NA") || vs_buf[8].compare("NA")))
{
tmpesd.beta=atof(vs_buf[4].c_str());
if(vs_buf[8]=="NA") tmpesd.se=atof(vs_buf[5].c_str());
else {
double betatmp=atof(vs_buf[4].c_str());
double ptmp=atof(vs_buf[8].c_str());
if(ptmp<0)
{
printf("ERROR: p-value should be positive in row %d.\n",lineNum+2);
printf("%s\n",buf);
exit(EXIT_FAILURE);
}
if(ptmp==0) {
ptmp=__DBL_MIN__;
printf("WARNING: p-value of 0 found in row %d and changed to min double value %e.\n",lineNum+2,__DBL_MIN__);
printf("%s\n",buf);
}
if((ptmp<MIN_PVAL_ADJUSTED && vs_buf[5]!="NA") || ptmp==1) tmpesd.se=atof(vs_buf[5].c_str());
else tmpesd.se=adjSE(betatmp, ptmp);
}
snpinfo.push_back(tmpesd);
} else {
printf("WARNING: this row is omitted because beta is missing or both SE and P are missing (\"NA\").\n");
printf("%s\n",buf);
tmpesd.beta=-9;
tmpesd.se=-9;
}
lineNum++;
}
}
if(gzflag) gzclose(gzfile);
else flptr.close();
cout << lineNum << " SNPs summary info to be included from [" + esdpath + "]." << endl;
}
void read_merlin_qassoc_gz(vector<string> &rs,vector<int> &chr,vector<string> &a1, vector<string> &a2, vector<float> freq, vector<float> &beta,vector<float> &se,string esdpath){
cout << "Reading summary information from [" + esdpath + "]." << endl;
char tbuf[MAX_LINE_SIZE];
gzFile gzfile = gzopen(esdpath.c_str(), "rb");
if (!(gzfile)) {
fprintf (stderr, "%s: Couldn't open file %s\n",
esdpath.c_str(), strerror (errno));
exit (EXIT_FAILURE);
}
int lineNum(0);
gzgets(gzfile, tbuf, MAX_LINE_SIZE); //head
if(tbuf[0]=='\0')
{
printf("ERROR: the first row of the file %s is empty.\n",esdpath.c_str());
exit(EXIT_FAILURE);
}
vector<string> vs_buf;
int col_num = split_string(tbuf, vs_buf, ", \t\n");
to_upper(vs_buf[0]);
if(vs_buf[0]!="CHR") {
printf("ERROR: the headers should start with \"CHR\"");
exit(EXIT_FAILURE);
}
while(!gzeof(gzfile))
{
gzgets(gzfile, tbuf, MAX_LINE_SIZE);
if(tbuf[0]!='\0'){
vs_buf.clear();
int col_num = split_string(tbuf, vs_buf, ", \t\n");
if(col_num!=11) {
printf("ERROR: the number of columns is incorrect in row %d.!", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[0]=="NA" || vs_buf[0]=="na"){
printf("ERROR: the chromosome is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[1]=="NA" || vs_buf[1]=="na"){
printf("ERROR: the SNP name is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
int tmpchr;
if(vs_buf[0]=="X" || vs_buf[0]=="x") tmpchr=23;
else if(vs_buf[0]=="Y" || vs_buf[0]=="y") tmpchr=24;
else tmpchr=atoi(vs_buf[0].c_str());
chr.push_back(tmpchr);
rs.push_back(vs_buf[1]);
to_upper(vs_buf[2]);
a1.push_back(vs_buf[2]);
to_upper(vs_buf[3]);
a2.push_back(vs_buf[3]);
if(vs_buf[4].compare("NA") || vs_buf[4].compare("na"))
{
float fq=atof(vs_buf[4].c_str());
if(fq<=1e-8 || fq>=1)
{
printf("ERROR: Allele frequency should be between 0 and 1 in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
freq.push_back(fq);
} else {
freq.push_back(-9);
}
to_upper(vs_buf[6]);
to_upper(vs_buf[7]);
to_upper(vs_buf[10]);
if(vs_buf[6].compare("NA") && (vs_buf[7].compare("NA") || vs_buf[10].compare("NA")))
{
beta.push_back(atof(vs_buf[6].c_str()));
if(vs_buf[10]=="NA") se.push_back(atof(vs_buf[7].c_str()));
else {
double betatmp=atof(vs_buf[6].c_str());
double ptmp=atof(vs_buf[10].c_str());
if(ptmp<0)
{
printf("ERROR: p-value should be positive in row %d.\n",lineNum+2);
printf("%s\n",tbuf);
exit(EXIT_FAILURE);
}
if(ptmp==0) {
ptmp=__DBL_MIN__;
printf("WARNING: p-value of 0 found in row %d and changed to min double value %e.\n",lineNum+2,__DBL_MIN__);
printf("%s\n",tbuf);
}
if((ptmp<MIN_PVAL_ADJUSTED && vs_buf[7]!="NA") || ptmp==1) se.push_back(atof(vs_buf[7].c_str()));
else se.push_back(adjSE(betatmp, ptmp));
}
} else {
printf("WARNING: this row is omitted because beta is missing or both SE and P are missing (\"NA\").\n");
printf("%s\n",tbuf);
beta.push_back(-9);
se.push_back(-9);
}
lineNum++;
}
}
gzclose(gzfile);
cout << lineNum << " SNPs summary info to be included from [" + esdpath + "]." << endl;
}
void read_gemma_qassoc(vector<string> &rs,vector<int> &chr, vector<int> &bp, vector<string> &a1, vector<string> &a2, vector<float> freq, vector<float> &beta,vector<float> &se,string esdpath)
{
gzFile gzfile=NULL;
ifstream flptr;
bool gzflag=has_suffix(esdpath, "gz");
if(gzflag)
{
gzfile = gzopen(esdpath.c_str(), "rb");
if (!(gzfile)) {
fprintf (stderr, "%s: Couldn't open file %s\n",
esdpath.c_str(), strerror (errno));
exit (EXIT_FAILURE);
}
}
else
{
flptr.open(esdpath.c_str());
if (!flptr) throw ("Error: can not open the file [" + esdpath + "] to read.");
}
cout << "Reading eQTL information from [" + string(esdpath) + "]." << endl;
char buf[MAX_LINE_SIZE];
int lineNum(0);
if(gzflag) gzgets(gzfile, buf, MAX_LINE_SIZE); //head
else flptr.getline(buf,MAX_LINE_SIZE);// the header
/* check headers */
if(buf[0]=='\0')
{
printf("ERROR: the first row of the file %s is empty.\n",esdpath.c_str());
exit(EXIT_FAILURE);
}
vector<string> vs_buf;
int col_num = split_string(buf, vs_buf, ", \t\n");
to_upper(vs_buf[0]);
if(vs_buf[0]!="CHR") {
printf("ERROR: the headers should start with \"chr\"");
exit(EXIT_FAILURE);
}
while(!flptr.eof() && !gzeof(gzfile))
{
if(gzflag) gzgets(gzfile, buf, MAX_LINE_SIZE);
else flptr.getline(buf,MAX_LINE_SIZE);
if(buf[0]!='\0'){
vs_buf.clear();
int col_num = split_string(buf, vs_buf, ", \t\n");
if(col_num!=11) {
printf("ERROR: the number of columns is incorrect in row %d.!", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[0]=="NA" || vs_buf[0]=="na"){
printf("ERROR: the chromosome is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[1]=="NA" || vs_buf[1]=="na"){
printf("ERROR: the SNP name is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
int tmpchr;
if(vs_buf[0]=="X" || vs_buf[0]=="x") tmpchr=23;
else if(vs_buf[0]=="Y" || vs_buf[0]=="y") tmpchr=24;
else tmpchr=atoi(vs_buf[0].c_str());
chr.push_back(tmpchr);
rs.push_back(vs_buf[1]);
if(vs_buf[2]=="NA" || vs_buf[2]=="na"){
printf("ERROR: the SNP position is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
bp.push_back(atoi(vs_buf[2].c_str()));
to_upper(vs_buf[4]);
a1.push_back(vs_buf[4]);
to_upper(vs_buf[5]);
a2.push_back(vs_buf[5]);
if(vs_buf[6].compare("NA") && vs_buf[6].compare("na"))
{
float fq=atof(vs_buf[6].c_str());
if(fq<0 || fq>1)
{
printf("ERROR: freq should be between 0 and 1 in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
freq.push_back(fq);
} else {
freq.push_back(-9);
}
to_upper(vs_buf[7]);
to_upper(vs_buf[8]);
to_upper(vs_buf[10]);
if(vs_buf[7].compare("NA") && (vs_buf[8].compare("NA") || vs_buf[10].compare("NA"))) {
beta.push_back(atof(vs_buf[7].c_str()));
if(vs_buf[10]=="NA") se.push_back(atof(vs_buf[8].c_str()));
else {
double betatmp=atof(vs_buf[7].c_str());
double ptmp=atof(vs_buf[10].c_str());
if(ptmp<0)
{
printf("ERROR: p-value should be positive in row %d.\n",lineNum+2);
printf("%s\n",buf);
exit(EXIT_FAILURE);
}
if(ptmp==0) {
ptmp=__DBL_MIN__;
printf("WARNING: p-value of 0 found in row %d and changed to min double value %e.\n",lineNum+2,__DBL_MIN__);
printf("%s\n",buf);
}
if((ptmp<MIN_PVAL_ADJUSTED && vs_buf[8]!="NA") || ptmp==1) se.push_back(atof(vs_buf[8].c_str()));
else se.push_back(adjSE(betatmp, ptmp));
}
} else {
printf("WARNING: this row is omitted because beta is missing or both SE and P are missing (\"NA\").\n");
printf("%s\n",buf);
beta.push_back(-9);
se.push_back(-9);
}
lineNum++;
}
}
cout << lineNum << " SNPs infomation to be included from [" + string(esdpath) + "]." << endl;
if(gzflag) gzclose(gzfile);
else flptr.close();
}
void read_bolt_qassoc(vector<string> &rs,vector<int> &chr, vector<int> &bp, vector<string> &a1, vector<string> &a2, vector<float> freq, vector<float> &beta,vector<float> &se,string esdpath)
{
gzFile gzfile=NULL;
ifstream flptr;
bool gzflag=has_suffix(esdpath, "gz");
if(gzflag)
{
gzfile = gzopen(esdpath.c_str(), "rb");
if (!(gzfile)) {
fprintf (stderr, "%s: Couldn't open file %s\n",
esdpath.c_str(), strerror (errno));
exit (EXIT_FAILURE);
}
}
else
{
flptr.open(esdpath.c_str());
if (!flptr) throw ("Error: can not open the file [" + esdpath + "] to read.");
}
cout << "Reading eQTL information from [" + string(esdpath) + "]." << endl;
char buf[MAX_LINE_SIZE];
int lineNum(0);
if(gzflag) gzgets(gzfile, buf, MAX_LINE_SIZE); //head
else flptr.getline(buf,MAX_LINE_SIZE);// the header
/* check headers */
if(buf[0]=='\0')
{
printf("ERROR: the first row of the file %s is empty.\n",esdpath.c_str());
exit(EXIT_FAILURE);
}
vector<string> vs_buf;
int col_num = split_string(buf, vs_buf, ", \t\n");
to_upper(vs_buf[0]);
if(vs_buf[0]!="SNP") {
printf("ERROR: the headers should start with \"SNP\"");
exit(EXIT_FAILURE);
}
while(!flptr.eof() && !gzeof(gzfile))
{
if(gzflag) gzgets(gzfile, buf, MAX_LINE_SIZE);
else flptr.getline(buf,MAX_LINE_SIZE);
if(buf[0]!='\0'){
vs_buf.clear();
int col_num = split_string(buf, vs_buf, ", \t\n");
if(col_num!=12) {
printf("ERROR: the number of columns is incorrect in row %d.\n", lineNum+2);
printf("\t%s\n",buf);
exit(EXIT_FAILURE);
}
if(vs_buf[0]=="NA" || vs_buf[0]=="na"){
printf("ERROR: the SNP name is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
if(vs_buf[1]=="NA" || vs_buf[1]=="na"){
printf("ERROR: the chromosome is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
int tmpchr;
if(vs_buf[1]=="X" || vs_buf[1]=="x") tmpchr=23;
else if(vs_buf[1]=="Y" || vs_buf[1]=="y") tmpchr=24;
else tmpchr=atoi(vs_buf[1].c_str());
chr.push_back(tmpchr);
rs.push_back(vs_buf[0]);
if(vs_buf[2]=="NA" || vs_buf[2]=="na"){
printf("ERROR: the SNP position is \'NA\' in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
bp.push_back(atoi(vs_buf[2].c_str()));
to_upper(vs_buf[4]);
a1.push_back(vs_buf[4]);
to_upper(vs_buf[5]);
a2.push_back(vs_buf[5]);
if(vs_buf[6].compare("NA") && vs_buf[6].compare("na"))
{
float fq=atof(vs_buf[6].c_str());
if(fq<=1e-8 || fq>=1)
{
printf("ERROR: Allele frequency should be between 0 and 1 in row %d.\n", lineNum+2);
exit(EXIT_FAILURE);
}
freq.push_back(fq);
} else {
freq.push_back(-9);
}
to_upper(vs_buf[8]);
to_upper(vs_buf[9]);
to_upper(vs_buf[11]);
if(vs_buf[8].compare("NA") && (vs_buf[9].compare("NA") || vs_buf[11].compare("NA"))) {
beta.push_back(atof(vs_buf[8].c_str()));
if(vs_buf[11]=="NA") se.push_back(atof(vs_buf[9].c_str()));