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input.cpp
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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2009 Shaun Purcell //
// //
// This file is distributed under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#include <iostream>
#include <iomanip>
#include <fstream>
#include <sstream>
#include <map>
#include <algorithm>
#include <bitset>
#include <limits>
#include <cerrno>
#include "plink.h"
#include "options.h"
#include "helper.h"
#include "nlist.h"
#include "gvar.h"
extern ofstream LOG;
void Plink::readData()
{
//////////////////////
// Check files exist
if ( ! par::ped_from_stdin)
checkFileExists(par::pedfile);
checkFileExists(par::mapfile);
///////////////////////////////////////////////
// .map file
vector<bool> include;
vector<int> include_pos(0);
int nl_actual=0;
readMapFile(par::mapfile,
include,
include_pos,
nl_actual);
///////////////////////////////////////////////
// .ped
FILE * PED;
if ( ! par::ped_from_stdin )
{
PED = fopen64(par::pedfile.c_str(),"r");
if ( PED == NULL )
error("Problem opening PED file, errno = "+int2str(errno));
}
vector<Individual*> ambiguous;
int nmale = 0;
int nfemale = 0;
int nambig = 0;
int c=0; // number of individuals
string s2;
while( 1 )
{
// End of input stream?
if ( par::ped_from_stdin )
{
if ( cin.eof() )
break;
}
else
{
if ( feof(PED) )
break;
}
// Otherwise read in the next person
Individual * person = new Individual;
// Get first field
int f=0;
if ( par::ped_from_stdin)
cin >> person->fid;
else
if (readString(PED,person->fid )) f++;
// End of file?
if ( person->fid=="" )
{
delete person;
continue;
}
if ( person->fid=="FID" )
error("FID is a reserved ID... please select a different family ID");
// Is this line a comment?
if ( ! par::ped_from_stdin)
{
if (person->fid.substr(0,1)=="#")
{
// Ignore rest of line and advance to next line
while (fgetc(PED) != '\n' && !feof(PED)) {}
delete person;
continue;
}
}
// First 6 or 7 obligatory fields
if ( par::ped_skip_fid )
person->iid = person->fid;
else
{
if ( par::ped_from_stdin )
cin >> person->iid;
else
if ( readString(PED,person->iid )) f++;
}
if ( par::ped_skip_parents )
{
person->mat = person->pat = "0";
}
else
{
if ( par::ped_from_stdin )
{
cin >> person->pat >> person->mat;
}
else
{
if ( readString(PED, person->pat )) f++;
if ( readString(PED, person->mat )) f++;
}
}
if ( par::ped_skip_sex )
person->sexcode = "0";
else
{
if ( par::ped_from_stdin )
cin >> person->sexcode;
else
if ( readString(PED, person->sexcode)) f++;
}
string phenotype;
if ( par::ped_skip_pheno )
phenotype = par::missing_phenotype;
else
{
if ( par::ped_from_stdin )
cin >> phenotype;
else
if (readString(PED,phenotype)) f++;
}
// Are we using 0/1 coding?
if (par::coding01)
{
if ( phenotype == "1" )
phenotype = "2";
else if ( phenotype == "0" )
phenotype = "1";
else
phenotype = "0";
}
// Optional liability class
if (par::liability)
{
string dummy;
if ( par::ped_from_stdin )
cin >> dummy;
else
if (readString(PED,dummy)) f++;
}
// Skip last empty line that gets read
if (person->fid=="") break;
// Check sex
if (person->sexcode=="1")
{
person->sex = true; // male
nmale++;
}
else if (person->sexcode=="2")
{
person->sex = false; // female
nfemale++;
}
else
{
ambiguous.push_back(person);
nambig++;
if (!par::ignore_missing_sex)
person->missing = true;
}
//////////////////
// A non-founder?
person->founder =
(person->pat == "0" && person->mat == "0") ? true : false;
//////////////////////////////
// Test for quantitative trait
if (phenotype == par::missing_phenotype)
person->missing = true;
else
{
// Store in person->phenotype as number, checking for
// conversion failure
if ( ! from_string<double>( person->phenotype, phenotype, std::dec ) )
person->missing = true;
else
{
if (phenotype != "0" &&
phenotype != "1" &&
phenotype != "2" )
{
par::qt = true;
par::bt = false;
}
}
}
/////////////////////////////
// Add necessary locus space
if (!par::SNP_major)
{
person->one.resize(nl_actual);
person->two.resize(nl_actual);
}
/////////////////////
// Read genotypes now
int gn=0;
int i=0;
bool linedone = false;
bool fatal = false;
string fmsg;
while ( ! linedone )
{
string one="";
string two="";
if ( par::ped_from_stdin )
cin >> one >> two;
else
{
while (1)
{
char ch = fgetc(PED);
// Delimiter?
if (ch==' ' || ch=='\t' || ch=='\n' || ch=='\r' || feof(PED) )
{
if (ch=='\n' || ch=='\r' || feof(PED))
linedone = true;
// have we already seen something?
if (one.length()>0)
{
gn++;
break;
}
if (ch=='\n' || ch=='\r' || feof(PED))
break;
}
else
{
one += ch;
}
}
// Is this a compound genotype?
if ( par::compound_genotype_code )
{
// In this case, each allele must be exactly 1-character long
if ( one.length() != 2 )
error("Problem with compound genotype [ " + one + " ] should be two characters long\n");
two = one[1];
one = one[0];
// Add second allele
++gn;
}
else
{
// Second allele
if (!linedone)
while (1)
{
char ch = fgetc(PED);
// Delimiter?
if (ch==' ' || ch=='\t' || ch=='\n' || ch=='\r' || feof(PED) )
{
if (ch=='\n' || ch=='\r' || feof(PED))
linedone = true;
// have we already seen something?
if (two.length()>0)
{
gn++;
break;
}
if (ch=='\n' || ch=='\r' || feof(PED))
break;
}
else
{
two += ch;
}
}
}
if (linedone && one.length()==0 && two.length()==0 )
break;
}
/////////////////////////////////////
// Only consider loci to be included
if (include[i])
{
//////////////////////////////
// Look up genomic order,
// insert in slot k in locus[]
int k = include_pos[i];
Locus * loc = locus[k];
/////////////////////////////////////////
// Add allele names to list, if needed
// If allele is not missing...
if (one!=par::missing_genotype && two!=par::missing_genotype)
{
// ...and not already listed
if (one!=loc->allele1 && one!=loc->allele2)
{
// ...then add to first empty slot
if(loc->allele1=="") loc->allele1=one;
else if(loc->allele2=="") loc->allele2=one;
else {
// .. or show an error if no empty slots
if (!fatal)
fmsg = "Locus " +
loc->name + " has >2 alleles:\n individual "
+ person->fid + " " + person->iid
+ " has genotype [ " + one +" "+two+" ]\n"
+ " but we've already seen [ "
+ loc->allele1 + " ] and [ " + loc->allele2 + " ]\n";
fatal=true;
}
}
}
// Repeat for second allele, if different
if (two!=one)
{
// If allele is not missing...
if (one!=par::missing_genotype)
// ...and not already listed
if (two!=loc->allele1 && two!=loc->allele2)
{
// ...then add to first empty slot
if(loc->allele1=="") loc->allele1=two;
else if(loc->allele2=="") loc->allele2=two;
else {
if (!fatal)
fmsg = "Locus " +
loc->name + " has >2 alleles:\n individual "
+ person->fid + " " + person->iid
+ " has genotype [ " + one +" "+two+" ]\n"
+ " but we've already seen [ "
+ loc->allele1 + " ] and [ " + loc->allele2 + " ]\n";
fatal=true;
}
}
}
/////////////////////////////
// Add specific genotypes
if (par::SNP_major)
{
// 00 hom
if (one==loc->allele1 && two==loc->allele1)
{
SNP[k]->one.push_back(false);
SNP[k]->two.push_back(false);
}
// 01 het
else if (one!=par::missing_genotype &&
two!=par::missing_genotype &&
one!=two)
{
SNP[k]->one.push_back(false);
SNP[k]->two.push_back(true);
}
// 11 hom
else if (one==loc->allele2 && two==loc->allele2)
{
SNP[k]->one.push_back(true);
SNP[k]->two.push_back(true);
}
// 10 missing
else if (one==par::missing_genotype || two==par::missing_genotype)
{
SNP[k]->one.push_back(true);
SNP[k]->two.push_back(false);
}
}
else
{
// 00 hom
if (one==loc->allele1 && two==loc->allele1)
{
person->one[k]=false;
person->two[k]=false;
}
// 01 het
else if (one!=par::missing_genotype &&
two!=par::missing_genotype &&
one!=two)
{
person->one[k]=false;
person->two[k]=true;
}
// 11 hom
else if (one==loc->allele2 && two==loc->allele2)
{
person->one[k]=true;
person->two[k]=true;
}
// 10 missing
else if (one==par::missing_genotype || two==par::missing_genotype)
{
person->one[k]=true;
person->two[k]=false;
}
}
}
// Advance to next locus
i++;
if ( par::ped_from_stdin )
{
if ( i == include.size() )
linedone = true;
}
else
{
if ( i > include.size())
{
int ef = 1;
if ( ! par::ped_skip_fid ) ef++;
if ( ! par::ped_skip_parents ) ef+=2;
if ( ! par::ped_skip_sex ) ef++;
if ( ! par::ped_skip_pheno ) ef++;
if ( par::liability ) ef++;
fmsg += "\nProblem with line "
+int2str(c+1)+" in [ "+par::pedfile+" ]\n";
fmsg += "Expecting "
+int2str(ef) + " + 2 * " + int2str(include.size()) + " = " +
int2str(ef+2*include.size())+ " columns, but found more\n";
error(fmsg);
}
}
} // line done?
// check size of line length somewhere
if ( ! par::ped_from_stdin )
{
if ( gn != 2 * include.size() )
{
int ef = 1;
if ( ! par::ped_skip_fid ) ef++;
if ( ! par::ped_skip_parents ) ef+=2;
if ( ! par::ped_skip_sex ) ef++;
if ( ! par::ped_skip_pheno ) ef++;
if ( par::liability ) ef++;
fmsg += "\nA problem with line "
+int2str(c+1)+" in [ "+par::pedfile+" ]\n";
fmsg += "Expecting "+int2str(ef)
+" + 2 * " + int2str(include.size()) + " = " +
int2str(ef+2*include.size())+ " columns, but found " +
int2str(f+gn) + "\n";
fatal=true;
}
}
if (fatal)
error(fmsg);
// Increase person counter
c++;
// Add individual to list
sample.push_back(person);
}
// If a binary trait, now make 0 missing also
// i.e. if we never saw other than missing, 0, 1 or 2
if (par::bt)
for (int i=0; i<sample.size(); i++)
if ( sample[i]->phenotype == 0 )
sample[i]->missing = true;
// Display list of ambiguously-sexed individuals?
if (ambiguous.size()>0)
{
printLOG("Warning, found "
+int2str(ambiguous.size())
+" individuals with ambiguous sex codes\n");
if (!par::ignore_missing_sex)
printLOG("These individuals will be set to missing ( or use --allow-no-sex )\n");
string f = par::output_file_name + ".nosex";
printLOG("Writing list of these individuals to [ "+f+" ]\n");
ofstream AMB;
AMB.open(f.c_str(), ifstream::out);
for (int i=0; i<ambiguous.size(); i++)
AMB << ambiguous[i]->fid << "\t" << ambiguous[i]->iid << "\n";
AMB.close();
ambiguous.clear();
}
// Close PED file
if ( ! par::ped_from_stdin )
fclose(PED);
printLOG(int2str(c)+" individuals read from [ "+par::pedfile+" ] \n");
int nm=0;
for (int i=0;i<sample.size();i++)
if(!sample[i]->missing) nm++;
printLOG(int2str(nm)+" individuals with nonmissing phenotypes\n");
if (par::bt)
{
if (par::coding01)
printLOG("Assuming a disease phenotype (0=unaff, 1=aff, other=miss)\n");
else
{
printLOG("Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)\n");
if (par::missing_phenotype!="0")
printLOG("Missing phenotype value is also " + par::missing_phenotype + "\n");
}
int ncase = 0;
int ncontrol = 0;
int nmissing = 0;
for (int i=0; i<sample.size(); i++)
if ( sample[i]->missing )
nmissing++;
else if ( sample[i]->phenotype == 1 )
ncontrol++;
else if ( sample[i]->phenotype == 2 )
ncase++;
printLOG(int2str(ncase)+" cases, "
+int2str(ncontrol)+" controls and "
+int2str(nmissing)+" missing\n");
}
else
{
printLOG("Assuming a quantitative trait\n");
printLOG("Missing phenotype value is "
+ par::missing_phenotype + "\n");
}
// Display sex counts
printLOG(int2str(nmale)+" males, "+int2str(nfemale)
+" females, and "+int2str(nambig)+" of unspecified sex\n");
}
void Plink::readSet()
{
bool firsttime = true;
set<string> subset;
if ( par::use_subset )
{
printLOG("Reading a list of subsets from [ " + par::subsetfile + " ]\n");
checkFileExists( par::subsetfile );
ifstream IN(par::subsetfile.c_str(), ios::in);
while ( ! IN.eof() )
{
string gname;
IN >> gname;
if ( gname=="" )
continue;
subset.insert(gname);
}
printLOG("Read " + int2str( subset.size() ) + " sets to extract\n");
}
//////////////////////
// Clear current sets
// (i.e. after removing SNPs, the lookup numbers will be wrong so we
// need to reload)
if (snpset.size()>0)
{
firsttime = false;
for (int i=0; i<snpset.size();i++)
snpset[i].clear();
snpset.clear();
setname.clear();
}
//////////////////
// Load SET file
checkFileExists(par::setfile);
ifstream SET;
SET.open(par::setfile.c_str());
SET.clear();
// Temporary vector of SNP numbers
vector<int> s;
// First set name
string name;
SET >> name;
// Make map of locus name with 'l' number
map<string,int> mlocus;
for (int l=0;l<nl_all;l++)
mlocus.insert(make_pair(locus[l]->name,l));
map<string,int>::iterator ilocus;
while(!SET.eof())
{
string t;
SET >> t;
if (t=="END" || t=="end" || SET.fail() ) // End of SET
{
if ( SET.fail() )
printLOG("Warning: the set-file did not end with the END keyword\n");
if ( ( ! par::use_subset ) ||
subset.find(name) != subset.end() )
{
// Save set
snpset.push_back(s);
// Save set name
setname.push_back(name);
}
// Get next set name
SET >> name;
// Clear buffer
s.resize(0);
}
else
{
// Lookup locus name
ilocus = mlocus.find(t);
if (ilocus != mlocus.end())
s.push_back(ilocus->second);
}
}
if (firsttime)
printLOG(int2str(snpset.size())
+ " sets read from [ "
+ par::setfile + " ] \n");
}
bool Plink::readClusterFile(bool verbose)
{
checkFileExists(par::include_cluster_filename);
ifstream CLST(par::include_cluster_filename.c_str(), ios::in);
// Make map of family/individual IDs. Originally, set to not be
// permuted: i.e. if an individual does not appear in the --within
// file, then they will not be permuted. Otherwise, all individuals
// are permuted.
map<string,Individual*> uid;
map<string,Individual*>::iterator ii;
map<string,int>::iterator ik;
for (int i=0; i<sample.size(); i++)
{
uid.insert(make_pair(sample[i]->fid+"_"+sample[i]->iid,sample[i]));
sample[i]->sol = -1;
}
int cnt=0;
int k=0;
kname.resize(0);
kmap.clear();
while (!CLST.eof())
{
string pfid, piid;
string cluster;
char cline[par::MAX_LINE_LENGTH];
CLST.getline(cline,par::MAX_LINE_LENGTH,'\n');
// convert to string
string sline = cline;
if (sline=="") continue;
string buf;
stringstream ss(sline);
vector<string> tokens;
while (ss >> buf)
tokens.push_back(buf);
// Trying to read past last column
if (tokens.size() < 2+par::mult_clst)
{
if (! par::bmatch )
{
for (int i0=0; i0<tokens.size(); i0++)
printLOG(tokens[i0]+" ");
printLOG("\n");
}
CLST.close();
return false;
}
pfid = tokens[0];
piid = tokens[1];
cluster = tokens[1 + par::mult_clst];
// Find individual
ii = uid.find(pfid+"_"+piid);
if (ii != uid.end() )
{
// Is this cluster on list?
ik = kmap.find(cluster);
if ( ik != kmap.end() ) // already on list
(ii->second)->sol = ik->second;
else // add to list
{
kmap.insert(make_pair(cluster,k));
(ii->second)->sol = k;
kname.push_back(cluster);
k++;
}
cnt++;
}
}
CLST.close();
// Assign to Family-like groups of pointers (e.g. to enable DFAM routine)
klist.clear();
for (int j=0;j<k;j++)
klist.push_back( new Cluster );
for (int i=0; i<n; i++)
{
if ( sample[i]->sol > -1 )
klist[sample[i]->sol]->person.push_back(sample[i]);
}
if ( verbose )
printLOG(int2str( cnt ) + " of " + int2str(n) +
" individuals assigned to "
+ int2str(k) + " cluster(s)\n");
nk = k;
return true;
}
bool Plink::readPhenoFile()
{
// Assume binary trait unless we find out otherwise
par::qt = false;
par::bt = true;
printLOG( "Reading alternate phenotype from [ "
+ par::pheno_filename + " ] \n");
checkFileExists(par::pheno_filename);
ifstream PHE(par::pheno_filename.c_str(), ios::in);
// Make map of family/individual IDs
// and initially set all individuals as missing
map<string,Individual*> uid;
map<string,Individual*>::iterator ii;
for (int i=0; i<sample.size(); i++)
{
uid.insert(make_pair(sample[i]->fid+"_"+sample[i]->iid,sample[i]));
sample[i]->phenotype = -9;
sample[i]->missing = true;
}
// Read in phenotype labels, if --pheno-name has been used
if ( par::name_pheno != "" )
{
string pfid, piid, ph;
char cline[par::MAX_LINE_LENGTH];
PHE.getline(cline,par::MAX_LINE_LENGTH,'\n');
string sline = cline;
if (sline!="")
{
string buf;
stringstream ss(sline);
vector<string> tokens;
while (ss >> buf)
tokens.push_back(buf);
if ( tokens[0] != "FID" )
error("First header field must be FID");
if ( tokens[1] != "IID" )
error("Second header field must be IID");
par::mult_pheno = -1;
for ( int i=2; i<tokens.size(); i++)
if ( tokens[i] == par::name_pheno )
par::mult_pheno = i - 1;
if ( par::mult_pheno == -1 )
error("Did not find phenotype [ "
+ par::name_pheno
+ " ] in [ "
+ par::pheno_filename
+ " ]");
}
}
int ccount = -1;
while (!PHE.eof())
{
string pfid, piid, ph;
char cline[par::MAX_LINE_LENGTH];
PHE.getline(cline,par::MAX_LINE_LENGTH,'\n');
// convert to string
string sline = cline;
if (sline=="") continue;
string buf;
stringstream ss(sline);
vector<string> tokens;
while (ss >> buf)
tokens.push_back(buf);
if ( ccount < 0 )
ccount = tokens.size();
else if ( ccount != tokens.size() )
error("Wrong number of columns in file [ "+par::pheno_filename
+" ] line :\n"+sline);
if (tokens.size() < 2+par::mult_pheno)
{
if ( par::all_pheno )
{
printLOG("Processed all phenotypes\n");
return false;
}
else
error("Problem with [ "+par::pheno_filename
+" ] -- not enough columns :\n"+sline);
}
pfid = tokens[0];
piid = tokens[1];
// Skip header, if --pheno-name not used but should have been
// (shouldn't matter in any case, as no individual with FID
// of "FID" should be allowed
if ( pfid == "FID" ||
piid == "IID" )
{
phenotype_name = tokens[1 + par::mult_pheno];
continue;
}
ph = tokens[1 + par::mult_pheno];
// Are we using 0/1 coding?
if (par::coding01)
{
if ( ph == "1" )
ph = "2";
else if ( ph == "0" )
ph = "1";
else