TEST(MAPPING, MAPPING3) {
mkdir("tmp", 0700);
TemporaryFile file("mapping2", ".dat", "./tmp");
ASSERT_TRUE(buildDatabase(file.path(), NULL, "./data/refseq.rna.bz2", "./data/gene2refseq_test.txt.bz2", 10, false));
//frozenhashmap::FrozenMap map;
//ASSERT_TRUE(map.open(file.path()));
//mapping
fprintf(stderr, "Mapping...\n");
cppfasta::FileWriter fileWriter;
ASSERT_TRUE(fileWriter.open("tmp/mapping-result.txt"));
std::map<std::string, int> result;
std::map<std::string, double> fpkm;
uint64_t num;
PFILE *pfile = pipedopen("./data/simulation.fastq.bz2", false);
ASSERT_TRUE(pfile);
cppfasta::FastqReader2 reader(pfile->file);
ASSERT_TRUE(domapping(file.path(), &reader, &result, &fpkm, &fileWriter, &num, 1, 1, false, false));
ASSERT_EQ(493150UL, num);
pipedclose(pfile);
for (std::map<std::string, int>::iterator it = result.begin();
it != result.end(); ++it) {
fprintf(stderr, "%10s : %d\n", it->first.c_str(), it->second);
}
fprintf(stderr, "OK...\n");
TabTableReader answer_table;
std::map<std::string, int> answer;
ASSERT_TRUE(answer_table.open("./data/python-mapping-result.txt"));
answer_table.next(); // skip header
std::vector<std::string> row;
while ((row = answer_table.next()).size() >= 2) {
char *endptr;
long num = strtol(row[1].c_str(), &endptr, 10);
ASSERT_EQ('\0', *endptr);
ASSERT_EQ(num, result[row[0]]) << row[0];
//DEBUG("%s %ld %ld", row[0].c_str(), num, result[row[0]]);
if (row[0] != "UNMAPPED" || row[0] != "MULTIMAPPED") {
char *endptr;
double fpkm_expected = strtod(row[2].c_str(), &endptr);
ASSERT_EQ('\0', *endptr);
//fprintf(stderr, "FPKM Expected[%s]: %lf Result: %lf\n", row[0].c_str(), fpkm_expected, fpkm[row[0]]);
ASSERT_NEAR(fpkm_expected, fpkm[row[0]], 1e-19) << "GeneID " << row[0];
}
}
}
MainWindow::MainWindow(QWidget *parent) :
QMainWindow(parent),
ui(new Ui::MainWindow),
m_settings(),
m_databaseOK(false),
m_tuloksia(0),
m_kilpailijoita(0),
m_tuloksiaLabel(new QLabel(this)),
m_serialStatus(new QLabel(this)),
m_testEmitReader(0),
m_serialEmitReader(new SerialEmitReaderWidget()),
m_pikanappaimetForm(0),
m_vuokraEmititForm(0),
m_tulosnayttoForm(0)
{
ui->setupUi(this);
connect(m_serialEmitReader, SIGNAL(readEmit(QDateTime,QString,int,int,QList<RastiData>)),
this, SLOT(handleReadEmit(QDateTime,QString,int,int,QList<RastiData>)));
connect(m_serialEmitReader, SIGNAL(statusChanged(QString)),
m_serialStatus, SLOT(setText(QString)));
connect(ui->menuSarjaportti, SIGNAL(aboutToShow()),
this, SLOT(setupSerialMenu()));
connect(ui->menuSarjaportti, SIGNAL(triggered(QAction*)),
this, SLOT(handleSerialMenu(QAction*)));
connectDatabase();
buildDatabase();
if (!Tietokanta::checkVersion(MAJOR_VERSION)) {
QString v = Tietokanta::getVersion();
if (QMessageBox::question(this, _("Tulospalvelu - " VERSION),
_("Tietokanta (%1) ei ole yhteensopiva. Haluatko jatkaa?")
.arg(v),
QMessageBox::Yes | QMessageBox::No,
QMessageBox::No) != QMessageBox::Yes) {
return;
}
}
setupTapahtuma();
setupShortcuts();
}
//#pragma argsused
short PD_style _Ask_AsqlSys( OpndType *lpOpnd, short ParaNum, short *OpndTop, \
short *CurState )
// OpndType *lpOpnd; pointer of opnd stack
// short ParaNum; parameter number for this action
// short *OpndTop; system opnd top
// short *CurState; the action sequence working state
{
char parameter[256];
char *sz;
short sysFunNo;
int i;
extern WSToMT FromToStru fFrTo;
switch( lpOpnd[0].type ) {
case LONG_TYPE:
sysFunNo = (short)*(long *)lpOpnd[0].values;
break;
case INT_TYPE:
sysFunNo = *(short *)lpOpnd[0].values;
break;
case CHR_TYPE:
sysFunNo = (short)*(char *)lpOpnd[0].values;
break;
default:
sysFunNo = 0;
}
switch( sysFunNo ) {
case 3001:
{
//
//build hzth
//
char *s;
char buf[MAXPATH];
s = GetCfgKey(csuDataDictionary, "SYSTEM", NULL, "CODE");
if( s != NULL ) {
strZcpy(buf, s, MAXPATH);
if( hBuildCodeLib(buf) != 1 )
{
strZcpy(ErrorSet.string, buf, XES_LENGTH);
return 1;
}
if( hOpen(buf) != 1 )
{
strZcpy(ErrorSet.string, buf, XES_LENGTH);
return 1;
}
}
*OpndTop -= ParaNum; /* maintain the opnd stack */
return( 0 );
}
//
//secret
//
case 32123:
{
//if( stricmp(asqlEnv.szUser, "ADMIN") == 0 )
{
dictDupFile();
}
*OpndTop -= ParaNum; /* maintain the opnd stack */
return( 0 );
}
//
//secret
//
case 32124:
{
//if( stricmp(asqlEnv.szUser, "ADMIN") == 0 )
{
dictReopenCfgFile();
}
*OpndTop -= ParaNum; /* maintain the opnd stack */
return( 0 );
}
};
sz = xGetOpndString(&lpOpnd[1]);
if( sz == NULL )
parameter[0] = '\0';
else
strZcpy(parameter, sz, 255);
switch( sysFunNo ) {
case 1:
#ifndef _WINDOWS_
#ifdef FOR_TGMIS
systemCall(parameter);
#else
system(parameter);
#endif
#else
{
STARTUPINFO si;
PROCESS_INFORMATION pi;
HANDLE hProcess;
DWORD dwExitCode;
_try {
ZeroMemory(&si, sizeof(STARTUPINFO));
si.cb = sizeof(si);
si.wShowWindow = SW_HIDE;
if( CreateProcess(NULL, parameter, NULL, NULL, TRUE, 0, NULL, NULL, &si, &pi) )
{
hProcess = pi.hProcess;
CloseHandle(pi.hThread);
if( WaitForSingleObject(hProcess, INFINITE) != WAIT_FAILED ) {
GetExitCodeProcess(hProcess, &dwExitCode);
CloseHandle(hProcess);
}
} else {
//ErrorSet.xERROR = GetLastError();
dwExitCode = FormatMessage(
FORMAT_MESSAGE_IGNORE_INSERTS |FORMAT_MESSAGE_FROM_SYSTEM, \
NULL,
GetLastError(),
MAKELANGID(LANG_NEUTRAL, SUBLANG_DEFAULT), // default language
parameter,
256,
NULL );
strZcpy(ErrorSet.string, parameter, XES_LENGTH);
return 1;
}
}
_except( EXCEPTION_EXECUTE_HANDLER ) {
return 1;
}
}
#endif
break;
case 2:
mkdirs(parameter);
break;
case 3:
unlink(parameter);
break;
case 10:
buildDatabase(parameter);
break;
case 11:
dropDatabase(parameter);
break;
case 100:
uncatchTable(parameter);
break;
case 2001:
{
//
//create index parameter on fFrTo.cSouDbfNum[i] (lpOpnd[3])
//
if( ParaNum < 4 ) {
ErrorSet.xERROR = iSysParaErr;
return 1;
}
i = xGetOpndLong(&lpOpnd[2]) - 1;
if( i < 0 || i >= fFrTo.cSouDbfNum ) {
ErrorSet.xERROR = iSysParaErr;
return 1;
}
sz = xGetOpndString(&lpOpnd[3]);
if( fFrTo.AsqlDatabase[0] == '\0' ) {
buildIndexAndRegThem("DBROOT", fFrTo.cSouFName[i], parameter, sz);
} else {
buildIndexAndRegThem(fFrTo.AsqlDatabase, fFrTo.cSouFName[i], parameter, sz);
}
break;
}
case 2002:
{
//
//drop index parameter on fFrTo.cSouDbfNum[i]
//
if( ParaNum < 3 ) {
ErrorSet.xERROR = iSysParaErr;
return 1;
}
i = xGetOpndLong(&lpOpnd[2]) - 1;
if( i < 0 || i >= fFrTo.cSouDbfNum ) {
ErrorSet.xERROR = iSysParaErr;
return 1;
}
if( fFrTo.AsqlDatabase[0] == '\0' ) {
dropIndexAndRegThem("DBROOT", fFrTo.cSouFName[i], parameter);
} else {
dropIndexAndRegThem(fFrTo.AsqlDatabase, fFrTo.cSouFName[i], parameter);
}
break;
}
}
*OpndTop -= ParaNum; /* maintain the opnd stack */
return( 0 );
} /* end of function _Ask_AsqlSys() */
