Пример #1
0
bool NGSD::removeColumnIfPresent(VariantList& variants, QString name, bool exact_name_match)
{
	int index = variants.annotationIndexByName(name, exact_name_match, false);
	if (index==-1) return false;

	variants.removeAnnotation(index);
	return true;
}
Пример #2
0
QString LovdUploadFile::getAnnotation(const VariantList& vl, const Variant& variant, QString key)
{
    return variant.annotations()[vl.annotationIndexByName(key)];
}
Пример #3
0
void NGSD::annotate(VariantList& variants, QString filename)
{
	initProgress("NGSD annotation", true);

	//get sample ids
	QString s_id = sampleId(filename, false);
	QString ps_id = processedSampleId(filename, false);
	QString sys_id = getValue("SELECT processing_system_id FROM processed_sample WHERE id='" + processedSampleId(filename, false) + "'").toString();

	//check if we could determine the sample
	bool found_in_db = true;
	if (s_id=="" || ps_id=="" || sys_id=="")
	{
		Log::warn("Could not find processed sample in NGSD by name '" + filename + "'. Annotation will be incomplete because processing system could not be determined!");
		found_in_db = false;
	}

	//get sample ids that have processed samples with the same processing system (not same sample, variants imported, same processing system, good quality of sample, not tumor)
	QSet<int> sys_sample_ids;
	SqlQuery tmp = getQuery();
	tmp.exec("SELECT DISTINCT s.id FROM processed_sample as ps, sample s WHERE ps.processing_system_id='" + sys_id + "' AND ps.sample_id=s.id AND s.tumor='0' AND s.quality='good' AND s.id!='" + s_id + "' AND (SELECT count(id) FROM detected_variant as dv WHERE dv.processed_sample_id = ps.id)>0");
	while(tmp.next())
	{
		sys_sample_ids.insert(tmp.value(0).toInt());
	}

	//remove all NGSD-specific columns
	QList<VariantAnnotationHeader> headers = variants.annotations();
	foreach(const VariantAnnotationHeader& header, headers)
	{
		if (header.name().startsWith("ihdb_"))
		{
			removeColumnIfPresent(variants, header.name(), true);
		}
	}
	removeColumnIfPresent(variants, "classification", true);
	removeColumnIfPresent(variants, "classification_comment", true);
	removeColumnIfPresent(variants, "validated", true);
	removeColumnIfPresent(variants, "comment", true);

	//get required column indices
	QString num_samples = QString::number(sys_sample_ids.count());
	int ihdb_hom_idx = addColumn(variants, "ihdb_hom", "Homozygous variant counts in NGSD for the same processing system (" + num_samples + " samples).");
	int ihdb_het_idx = addColumn(variants, "ihdb_het", "Heterozyous variant counts in NGSD for the same processing system (" + num_samples + " samples).");
	int ihdb_wt_idx  = addColumn(variants, "ihdb_wt", "Wildtype variant counts in NGSD for the same processing system (" + num_samples + " samples).");
	int ihdb_all_hom_idx = addColumn(variants, "ihdb_allsys_hom", "Homozygous variant counts in NGSD independent of the processing system.");
	int ihdb_all_het_idx =  addColumn(variants, "ihdb_allsys_het", "Heterozygous variant counts in NGSD independent of the processing system.");
	int class_idx = addColumn(variants, "classification", "Classification from the NGSD.");
	int clacom_idx = addColumn(variants, "classification_comment", "Classification comment from the NGSD.");
	int valid_idx = addColumn(variants, "validated", "Validation information from the NGSD. Validation results of other samples are listed in brackets!");
	if (variants.annotationIndexByName("comment", true, false)==-1) addColumn(variants, "comment", "Comments from the NGSD. Comments of other samples are listed in brackets!");
	int comment_idx = variants.annotationIndexByName("comment", true, false);

	//(re-)annotate the variants
	SqlQuery query = getQuery();
	for (int i=0; i<variants.count(); ++i)
	{
		//QTime timer;
		//timer.start();

		//variant id
		Variant& v = variants[i];
		QByteArray v_id = variantId(v, false).toLatin1();

		//variant classification
		QVariant classification = getValue("SELECT class FROM variant_classification WHERE variant_id='" + v_id + "'", true);
		if (!classification.isNull())
		{
			v.annotations()[class_idx] = classification.toByteArray().replace("n/a", "");
			v.annotations()[clacom_idx] = getValue("SELECT comment FROM variant_classification WHERE variant_id='" + v_id + "'", true).toByteArray().replace("\n", " ").replace("\t", " ");
		}
		//int t_v = timer.elapsed();
		//timer.restart();

		//detected variant infos
		int dv_id = -1;
		QByteArray comment = "";
		if (found_in_db)
		{
			query.exec("SELECT id, comment FROM detected_variant WHERE processed_sample_id='" + ps_id + "' AND variant_id='" + v_id + "'");
			if (query.size()==1)
			{
				query.next();
				dv_id = query.value(0).toInt();
				comment = query.value(1).toByteArray();
			}
		}

		//validation info
		int vv_id = -1;
		QByteArray val_status = "";
		if (found_in_db)
		{
			query.exec("SELECT id, status FROM variant_validation WHERE sample_id='" + s_id + "' AND variant_id='" + v_id + "'");
			if (query.size()==1)
			{
				query.next();
				vv_id = query.value(0).toInt();
				val_status = query.value(1).toByteArray().replace("n/a", "");
			}
		}

		//int t_dv = timer.elapsed();
		//timer.restart();

		//validation info other samples
		int tps = 0;
		int fps = 0;
		query.exec("SELECT id, status FROM variant_validation WHERE variant_id='"+v_id+"' AND status!='n/a'");
		while(query.next())
		{
			if (query.value(0).toInt()==vv_id) continue;
			if (query.value(1).toByteArray()=="true positive") ++tps;
			else if (query.value(1).toByteArray()=="false positive") ++fps;
		}
		if (tps>0 || fps>0)
		{
			if (val_status=="") val_status = "n/a";
			val_status += " (" + QByteArray::number(tps) + "xTP, " + QByteArray::number(fps) + "xFP)";
		}
		//int t_val = timer.elapsed();
		//timer.restart();

		//comments other samples
		QList<QByteArray> comments;
		query.exec("SELECT id, comment FROM detected_variant WHERE variant_id='"+v_id+"' AND comment IS NOT NULL");
		while(query.next())
		{
			if (query.value(0).toInt()==dv_id) continue;
			QByteArray tmp = query.value(1).toByteArray().trimmed();
			if (tmp!="") comments.append(tmp);
		}
		if (comments.size()>0)
		{
			if (comment=="") comment = "n/a";
			comment += " (";
			for (int i=0; i<comments.count(); ++i)
			{
				if (i>0)
				{
					comment += ", ";
				}
				comment += comments[i];
			}
			comment += ")";
		}
		//int t_com = timer.elapsed();
		//timer.restart();

		//genotype counts
		int allsys_hom_count = 0;
		int allsys_het_count = 0;
		int sys_hom_count = 0;
		int sys_het_count = 0;
		QSet<int> s_ids_done;
		int s_id_int = s_id.toInt();
		query.exec("SELECT dv.genotype, ps.sample_id FROM detected_variant as dv, processed_sample ps WHERE dv.processed_sample_id=ps.id AND dv.variant_id='" + v_id + "'");
		while(query.next())
		{
			//skip this sample id
			int current_sample = query.value(1).toInt();
			if (current_sample==s_id_int) continue;

			//skip already seen samples (there could be several processings of the same sample because of different processing systems or because of experment repeats due to quality issues)
			if (s_ids_done.contains(current_sample)) continue;
			s_ids_done.insert(current_sample);

			QByteArray current_geno = query.value(0).toByteArray();
			if (current_geno=="hom")
			{
				++allsys_hom_count;
				if (sys_sample_ids.contains(current_sample))
				{
					++sys_hom_count;
				}
			}
			else if (current_geno=="het")
			{
				++allsys_het_count;
				if (sys_sample_ids.contains(current_sample))
				{
					++sys_het_count;
				}
			}
		}
		//qDebug() << (v.isSNV() ? "S" : "I") << query.size() << t_v << t_dv << t_val << t_com << timer.elapsed();

		v.annotations()[ihdb_all_hom_idx] = QByteArray::number(allsys_hom_count);
		v.annotations()[ihdb_all_het_idx] = QByteArray::number(allsys_het_count);
		if (found_in_db)
		{
			v.annotations()[ihdb_hom_idx] = QByteArray::number((double)sys_hom_count / sys_sample_ids.count(), 'f', 4);
			v.annotations()[ihdb_het_idx] =  QByteArray::number((double)sys_het_count / sys_sample_ids.count(), 'f', 4);
			v.annotations()[ihdb_wt_idx] =  QByteArray::number((double)(sys_sample_ids.count() - sys_hom_count - sys_het_count) / sys_sample_ids.count(), 'f', 4);
			v.annotations()[valid_idx] = val_status;
			v.annotations()[comment_idx] = comment.replace("\n", " ").replace("\t", " ");
		}
		else
		{
			v.annotations()[ihdb_hom_idx] = "n/a";
			v.annotations()[ihdb_het_idx] = "n/a";
			v.annotations()[ihdb_wt_idx] = "n/a";
			v.annotations()[valid_idx] = "n/a";
			v.annotations()[comment_idx] = "n/a";
		}

		emit updateProgress(100*i/variants.count());
	}
}