void GenerateDNASequenceTask::run( ) {
if ( seed < 0 ) {
qsrand( QDateTime::currentDateTime( ).toTime_t( ) );
} else {
qsrand( seed );
}
dbiRef = AppContext::getDbiRegistry( )->getSessionTmpDbiRef( stateInfo );
CHECK_OP( stateInfo, );
DbiConnection con( dbiRef, stateInfo );
CHECK_OP( stateInfo, );
results.reserve( count );
for ( int seqCount = 0; seqCount < count; seqCount++ ) {
U2SequenceImporter seqImporter( QVariantMap( ), true );
QByteArray sequenceChunk;
if( window > length ) {
window = length;
}
seqImporter.startSequence(stateInfo, dbiRef, U2ObjectDbi::ROOT_FOLDER, QString( "default" ), false);
CHECK_OP_BREAK( stateInfo );
for( int chunkCount = 0; chunkCount < length / window && !isCanceled( );
chunkCount++ )
{
DNASequenceGenerator::generateSequence( baseContent, window, sequenceChunk );
seqImporter.addBlock( sequenceChunk.constData( ), sequenceChunk.length( ), stateInfo );
CHECK_OP_BREAK( stateInfo );
const int currentProgress = int( 100 * ( seqCount + chunkCount * double ( window )
/ double ( length ) ) / double( count ) );
stateInfo.setProgress( currentProgress );
}
// append last chunk
DNASequenceGenerator::generateSequence( baseContent, length % window, sequenceChunk );
seqImporter.addBlock( sequenceChunk.constData( ), sequenceChunk.length( ), stateInfo );
CHECK_OP_BREAK( stateInfo );
U2Sequence seq = seqImporter.finalizeSequence( stateInfo );
CHECK_OP_BREAK( stateInfo );
results.append( seq );
stateInfo.setProgress( seqCount / count * 100 );
}
}
QModelIndex GTUtilsSharedDatabaseDocument::getItemIndex(HI::GUITestOpStatus &os, Document *databaseDoc, const QString &itemPath, bool mustExist) {
Q_UNUSED(os);
GT_CHECK_RESULT(NULL != databaseDoc, "databaseDoc is NULL", QModelIndex());
GT_CHECK_RESULT(!itemPath.isEmpty(), "Folder path is empty", QModelIndex());
const QStringList folders = itemPath.split(U2ObjectDbi::PATH_SEP, QString::SkipEmptyParts);
QModelIndex itemIndex = GTUtilsProjectTreeView::findIndex(os, databaseDoc->getName());
CHECK(!folders.isEmpty(), itemIndex);
GTGlobals::FindOptions options;
options.depth = 1;
options.failIfNotFound = mustExist;
foreach (const QString& folder, folders) {
itemIndex = GTUtilsProjectTreeView::findIndex(os, folder, itemIndex, options);
CHECK_OP_BREAK(os);
CHECK_BREAK(itemIndex.isValid());
}
/**
* FASTQ format specification: http://maq.sourceforge.net/fastq.shtml
*/
static void load(IOAdapter* io, const U2DbiRef& dbiRef, const QVariantMap& hints, const GUrl& docUrl, QList<GObject*>& objects, U2OpStatus& os,
int gapSize, int predictedSize, QString& writeLockReason) {
DbiOperationsBlock opBlock(dbiRef, os);
CHECK_OP(os, );
Q_UNUSED(opBlock);
writeLockReason.clear();
bool merge = gapSize!=-1;
QByteArray sequence;
QByteArray qualityScores;
QStringList headers;
QSet<QString> uniqueNames;
QVector<U2Region> mergedMapping;
QByteArray gapSequence((merge ? gapSize : 0), 0);
sequence.reserve(predictedSize);
qualityScores.reserve(predictedSize);
// for lower case annotations
GObjectReference sequenceRef;
qint64 sequenceStart = 0;
U2SequenceImporter seqImporter(hints, true);
const QString folder = hints.value(DocumentFormat::DBI_FOLDER_HINT, U2ObjectDbi::ROOT_FOLDER).toString();
int seqNumber = 0;
int progressUpNum = 0;
const int objectsCountLimit = hints.contains(DocumentReadingMode_MaxObjectsInDoc) ? hints[DocumentReadingMode_MaxObjectsInDoc].toInt() : -1;
const bool settingsMakeUniqueName = !hints.value(DocumentReadingMode_DontMakeUniqueNames, false).toBool();
while (!os.isCoR()) {
//read header
QString sequenceName = readSequenceName(os, io, '@');
// check for eof while trying to read another FASTQ block
if (io->isEof()) {
break;
}
CHECK_OP_BREAK(os);
if(sequenceName.isEmpty()){
sequenceName = "Sequence";
}
if ((merge == false) || (seqNumber == 0)) {
QString objName = sequenceName;
if (settingsMakeUniqueName) {
objName = (merge) ? "Sequence" : TextUtils::variate(sequenceName, "_", uniqueNames);
objName.squeeze();
uniqueNames.insert(objName);
}
seqImporter.startSequence(dbiRef, folder, objName, false, os);
CHECK_OP_BREAK(os);
}
//read sequence
if (merge && sequence.length() > 0) {
seqImporter.addDefaultSymbolsBlock(gapSize,os);
sequenceStart += sequence.length();
sequenceStart+=gapSize;
CHECK_OP_BREAK(os);
}
sequence.clear();
readSequence(os, io, sequence);
MemoryLocker lSequence(os, qCeil(sequence.size()/(1000*1000)));
CHECK_OP_BREAK(os);
Q_UNUSED(lSequence);
seqImporter.addBlock(sequence.data(),sequence.length(),os);
CHECK_OP_BREAK(os);
QString qualSequenceName = readSequenceName(os, io, '+');
if (!qualSequenceName.isEmpty()) {
static const QString err = U2::FastqFormat::tr("Not a valid FASTQ file: %1, sequence name differs from quality scores name: %2 and %3");
CHECK_EXT_BREAK(sequenceName == qualSequenceName,
os.setError(err.arg(docUrl.getURLString()).arg(sequenceName).arg(qualSequenceName)));
}
// read qualities
qualityScores.clear();
readQuality(os, io, qualityScores, sequence.size());
CHECK_OP_BREAK(os);
static const QString err = U2::FastqFormat::tr("Not a valid FASTQ file: %1. Bad quality scores: inconsistent size.").arg(docUrl.getURLString());
CHECK_EXT_BREAK(sequence.length() == qualityScores.length(), os.setError(err));
seqNumber++;
progressUpNum++;
if (merge) {
headers.append(sequenceName);
mergedMapping.append(U2Region(sequenceStart, sequence.length() ));
}
else {
if (objectsCountLimit > 0 && objects.size() >= objectsCountLimit) {
os.setError(FastqFormat::tr("File \"%1\" contains too many sequences to be displayed. "
"However, you can process these data using instruments from the menu <i>Tools -> NGS data analysis</i> "
"or pipelines built with Workflow Designer.")
.arg(io->getURL().getURLString()));
break;
}
U2Sequence u2seq = seqImporter.finalizeSequenceAndValidate(os);
CHECK_OP_BREAK(os);
sequenceRef = GObjectReference(io->getURL().getURLString(), u2seq.visualName, GObjectTypes::SEQUENCE, U2EntityRef(dbiRef, u2seq.id));
U2SequenceObject* seqObj = new U2SequenceObject(u2seq.visualName, U2EntityRef(dbiRef, u2seq.id));
CHECK_EXT_BREAK(seqObj != NULL, os.setError("U2SequenceObject is NULL"));
seqObj->setQuality(DNAQuality(qualityScores));
objects << seqObj;
U1AnnotationUtils::addAnnotations(objects, seqImporter.getCaseAnnotations(), sequenceRef, NULL, hints);
}
if (PROGRESS_UPDATE_STEP == progressUpNum) {
progressUpNum = 0;
os.setProgress(io->getProgress());
}
}
CHECK_OP_EXT(os, qDeleteAll(objects); objects.clear(), );
bool emptyObjects = objects.isEmpty();
CHECK_EXT(!emptyObjects || merge, os.setError(Document::tr("Document is empty.")), );
SAFE_POINT(headers.size() == mergedMapping.size(), "headers <-> regions mapping failed!", );
if (!merge) {
return;
}
U2Sequence u2seq = seqImporter.finalizeSequenceAndValidate(os);
CHECK_OP(os,);
sequenceRef = GObjectReference(io->getURL().getURLString(), u2seq.visualName, GObjectTypes::SEQUENCE, U2EntityRef(dbiRef, u2seq.id));
U1AnnotationUtils::addAnnotations(objects, seqImporter.getCaseAnnotations(), sequenceRef, NULL, hints);
objects << new U2SequenceObject(u2seq.visualName, U2EntityRef(dbiRef, u2seq.id));
objects << DocumentFormatUtils::addAnnotationsForMergedU2Sequence(sequenceRef, dbiRef, headers, mergedMapping, hints);
if (headers.size() > 1) {
writeLockReason = DocumentFormat::MERGED_SEQ_LOCK;
}
}
static void load(IOAdapter* io, const U2DbiRef& dbiRef, const QVariantMap& fs, QList<GObject*>& objects,
int gapSize, QString& writeLockReason, U2OpStatus& os)
{
DbiOperationsBlock opBlock(dbiRef, os);
CHECK_OP(os, );
Q_UNUSED(opBlock);
static char fastaCommentStartChar = FastaFormat::FASTA_COMMENT_START_SYMBOL;
MemoryLocker memoryLocker(os, 1);
CHECK_OP(os, );
writeLockReason.clear();
QByteArray readBuff(DocumentFormat::READ_BUFF_SIZE + 1, 0);
char* buff = readBuff.data();
qint64 len = 0;
bool merge = gapSize != -1;
QStringList headers;
QSet<QString> uniqueNames;
QVector<U2Region> mergedMapping;
// for lower case annotations
GObjectReference sequenceRef;
//skip leading whites if present
bool lineOk = true;
static QBitArray nonWhites = ~TextUtils::WHITES;
io->readUntil(buff, DocumentFormat::READ_BUFF_SIZE, nonWhites, IOAdapter::Term_Exclude, &lineOk);
CHECK_EXT(!io->hasError(), os.setError(io->errorString()), );
U2SequenceImporter seqImporter(fs, true);
const QString folder = fs.value(DocumentFormat::DBI_FOLDER_HINT, U2ObjectDbi::ROOT_FOLDER).toString();
qint64 sequenceStart = 0;
int sequenceNumber = 0;
DbiConnection con(dbiRef, os);
bool headerReaded = false;
QStringList emptySeqNames;
const int objectsCountLimit = fs.contains(DocumentReadingMode_MaxObjectsInDoc) ? fs[DocumentReadingMode_MaxObjectsInDoc].toInt() : -1;
const bool settingsMakeUniqueName = !fs.value(DocumentReadingMode_DontMakeUniqueNames, false).toBool();
while (!os.isCoR()) {
//skip start comments and read header
if(!headerReaded){
do{
len = io->readLine(buff, DocumentFormat::READ_BUFF_SIZE);
CHECK_EXT(!io->hasError(), os.setError(io->errorString()), );
}while(buff[0] == fastaCommentStartChar && len > 0);
}
if (len == 0 && io->isEof()) { //end if stream
break;
}
CHECK_EXT(!io->hasError(), os.setError(io->errorString()), );
CHECK_EXT_BREAK(lineOk, os.setError(FastaFormat::tr("Line is too long")));
QString headerLine = QString(QByteArray(buff+1, len-1)).trimmed();
CHECK_EXT_BREAK(buff[0] == FastaFormat::FASTA_HEADER_START_SYMBOL, os.setError(FastaFormat::tr("First line is not a FASTA header")));
//read sequence
if (sequenceNumber == 0 || !merge) {
QString objName = headerLine;
if(objName.isEmpty()){
objName = "Sequence";
}
if (settingsMakeUniqueName) {
objName = (merge) ? "Sequence" : TextUtils::variate(objName, "_", uniqueNames);
objName.squeeze();
memoryLocker.tryAcquire(2*objName.size());
CHECK_OP_BREAK(os);
uniqueNames.insert(objName);
}
seqImporter.startSequence(os, dbiRef, folder, objName, false);
CHECK_OP_BREAK(os);
sequenceRef = GObjectReference(io->getURL().getURLString(), objName, GObjectTypes::SEQUENCE);
}
if (sequenceNumber >= 1 && merge) {
seqImporter.addDefaultSymbolsBlock(gapSize, os);
sequenceStart += gapSize;
CHECK_OP_BREAK(os);
}
int sequenceLen = 0;
while (!os.isCoR()) {
do {
len = io->readLine(buff, DocumentFormat::READ_BUFF_SIZE);
CHECK_EXT(!io->hasError(), os.setError(io->errorString()), );
} while (len <= 0 && !io->isEof());
CHECK_EXT(!io->hasError(), os.setError(io->errorString()), );
if (len <= 0 && io->isEof()) {
break;
}
CHECK_EXT(!io->hasError(), os.setError(io->errorString()), );
buff[len] = 0;
if(buff[0] != fastaCommentStartChar && buff[0] != FastaFormat::FASTA_HEADER_START_SYMBOL){
len = TextUtils::remove(buff, len, TextUtils::WHITES);
if(len > 0){
seqImporter.addBlock(buff, len, os);
sequenceLen += len;
}
}else if( buff[0] == FastaFormat::FASTA_HEADER_START_SYMBOL){
headerReaded = true;
break;
}
CHECK_OP_BREAK(os);
os.setProgress(io->getProgress());
}
if (merge) {
memoryLocker.tryAcquire(headerLine.size());
CHECK_OP_BREAK(os);
headers.append(headerLine);
mergedMapping.append(U2Region(sequenceStart, sequenceLen));
} else {
if (objectsCountLimit > 0 && objects.size() >= objectsCountLimit) {
os.setError(FastaFormat::tr("File \"%1\" contains too many sequences to be displayed. "
"However, you can process these data using instruments from the menu <i>Tools -> NGS data analysis</i> "
"or pipelines built with Workflow Designer.")
.arg(io->getURL().getURLString()));
break;
}
memoryLocker.tryAcquire(800);
CHECK_OP_BREAK(os);
U2Sequence seq = seqImporter.finalizeSequenceAndValidate(os);
if (os.hasError() && os.getError() == U2SequenceImporter::EMPTY_SEQUENCE_ERROR) {
os.setError("");
emptySeqNames << headerLine;
continue;
}
sequenceRef.entityRef = U2EntityRef(dbiRef, seq.id);
//TODO parse header
U2StringAttribute attr(seq.id, DNAInfo::FASTA_HDR, headerLine);
con.dbi->getAttributeDbi()->createStringAttribute(attr, os);
CHECK_OP_BREAK(os);
objects << new U2SequenceObject(seq.visualName, U2EntityRef(dbiRef, seq.id));
CHECK_OP_BREAK(os);
U1AnnotationUtils::addAnnotations(objects, seqImporter.getCaseAnnotations(), sequenceRef, NULL, fs);
}
sequenceStart += sequenceLen;
sequenceNumber++;
ioLog.trace(QString("Sequence #%1 is processed").arg(sequenceNumber));
}
CHECK_OP_EXT(os, qDeleteAll(objects); objects.clear(), );
CHECK_EXT(!objects.isEmpty() || merge, os.setError(Document::tr("Document is empty.")), );
SAFE_POINT(headers.size() == mergedMapping.size(), "headers <-> regions mapping failed!", );
ioLog.trace("All sequences are processed");
if (!emptySeqNames.isEmpty()) {
QString warningMessage;
warningMessage.append(FastaFormat::tr("Loaded sequences: %1.\n").arg(sequenceNumber));
warningMessage.append(FastaFormat::tr("Skipped sequences: %1.\n").arg(emptySeqNames.size()));
warningMessage.append(FastaFormat::tr("The following sequences are empty:\n%1").arg(emptySeqNames.join(",\n")));
os.addWarning(warningMessage);
}
if (!merge) {
return;
}
U2Sequence seq = seqImporter.finalizeSequenceAndValidate(os);
CHECK_OP(os, );
sequenceRef.entityRef = U2EntityRef(dbiRef, seq.id);
U1AnnotationUtils::addAnnotations(objects, seqImporter.getCaseAnnotations(), sequenceRef, NULL, fs);
objects << new U2SequenceObject(seq.visualName, U2EntityRef(dbiRef, seq.id));
objects << DocumentFormatUtils::addAnnotationsForMergedU2Sequence( sequenceRef, dbiRef, headers, mergedMapping, fs );
if (headers.size() > 1) {
writeLockReason = QObject::tr("Document sequences were merged");
}
}
