static void WriteHeader(MetabolizerPhenotypingEngine *eng, affx::TsvFile &tsv, int idx, std::ofstream &str)
{
// Output the header
str << "# For research use only. Not for diagnostic purposes." << std::endl;
str << "#%report-guid=" << affxutil::Guid::GenerateNewGuid() << std::endl;
str << "#%Program=" << MET_PROGRAM_NAME << std::endl;
str << "#%Version=" << MET_PROGRAM_VERSION << std::endl;
str << "#%Date=" << Util::getTimeStamp() << std::endl;
str << "#%MetabolizerFile=" << eng->getOpt("metabolizer-file") << std::endl;
str << "#%AlleleFile=" << eng->getOpt("allele-file") << std::endl;
for (int i=0; i<(int)eng->PhenotypeCallDescs().size(); i++)
str << "#%PhenotypeCallDesc=" << eng->PhenotypeCallDescs()[i] << std::endl;
for (int i=0; i<(int)eng->UserInformation().size(); i++)
str << "#%Info=" << eng->UserInformation()[i] << std::endl;
str << "Index" << "\t"
<< "CHP File" << "\t"
<< "Gene" << "\t"
<< "Phenotype Call" << "\t"
<< "Gene Activity" << "\t"
<< "Known Call" << "\t"
<< "Unknown Call" << "\t"
<< "Interpretation Code";
int n = tsv.getColumnCount(0);
for (int i=idx; i<n; i++)
{
std::string name = tsv.getColumnName(0, i);
str << "\t" << name;
}
str << std::endl;
}
void
affx::TsvFileDiff::open_residuals(const std::string& filename,
affx::TsvFile& tsv1,
affx::TsvFile& tsv2)
{
// no file
if (filename=="") {
return;
}
//
m_residuals_tsv=new affx::TsvFile();
//
for (int clvl=0;clvl<tsv1.getLevelCount();clvl++) {
for (int cidx=0;cidx<tsv1.getColumnCount(clvl);cidx++) {
std::string cname=tsv1.getColumnName(clvl,cidx); // +"_res";
m_residuals_tsv->defineColumn(clvl,cidx,cname);
}
}
//
m_residuals_tsv->addHeader("apt-file-type","tsv-diff-residuals");
m_residuals_tsv->addHeader("tsv-diff-input-file1",tsv1.getFileName());
m_residuals_tsv->addHeader("tsv-diff-input-file2",tsv2.getFileName());
m_residuals_tsv->addHeader("file-guid",affxutil::Guid::GenerateNewGuid());
//
if (m_residuals_tsv->getLevelCount()==1) {
m_residuals_tsv->writeTsv_v1(filename);
} else {
m_residuals_tsv->writeTsv_v2(filename);
}
}
static int FindStartingAttributeColumnIndex(affx::TsvFile &tsv)
{
int n = tsv.getColumnCount(0);
int idx = n;
for (int i=0; i<n; i++)
{
std::string name = tsv.getColumnName(0, i);
if (name == "Override Comment")
{
idx = i+1;
break;
}
}
return idx;
}
