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Added TsvDiff tool (#610)
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@marc-sturm
marc-sturm authored Dec 17, 2024
1 parent 8fdaabc commit f56ba84
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Showing 21 changed files with 475 additions and 68 deletions.
8 changes: 4 additions & 4 deletions src/ExportcBioportal/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -63,9 +63,9 @@ class ConcreteTool
int idx_icd10_catalog = samples.columnIndex("icd10_catalog");
int idx_oncotree_code = samples.columnIndex("oncotree_code");

for (int i=0; i< samples.rowCount(); i++)
for (int i=0; i< samples.count(); i++)
{
QStringList row = samples.row(i);
const QStringList& row = samples[i];
QString sample_id = db.sampleId(row[idx_tumor_name], true);

SampleMTBmetadata mtb_data;
Expand Down Expand Up @@ -177,9 +177,9 @@ class ConcreteTool
int idx_datatype = getIndex(headers, "datatype");
int idx_prio = getIndex(headers, "priority");

for (int i=0; i<attr_data.rowCount(); i++)
for (int i=0; i<attr_data.count(); i++)
{
QStringList row = attr_data.row(i);
const QStringList& row = attr_data[i];

SampleAttribute attr;
attr.name = row[idx_attr_name];
Expand Down
6 changes: 3 additions & 3 deletions src/GSvar/CohortExpressionDataWidget.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ void CohortExpressionDataWidget::loadExpressionData()
}

//set dimensions
ui_->tw_cohort_data->setRowCount(cohort_expression_data.rowCount());
ui_->tw_cohort_data->setRowCount(cohort_expression_data.count());
ui_->tw_cohort_data->setColumnCount(cohort_expression_data.headers().size());

// create header
Expand All @@ -69,9 +69,9 @@ void CohortExpressionDataWidget::loadExpressionData()
}

//fill table
for(int row_idx=0; row_idx<cohort_expression_data.rowCount(); ++row_idx)
for(int row_idx=0; row_idx<cohort_expression_data.count(); ++row_idx)
{
QStringList row = cohort_expression_data.row(row_idx);
const QStringList& row = cohort_expression_data[row_idx];
for (int col_idx = 0; col_idx < tsv_header.size(); ++col_idx)
{
if(col_idx > 0)
Expand Down
4 changes: 2 additions & 2 deletions src/GSvar/DiseaseCourseWidget.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -217,9 +217,9 @@ void DiseaseCourseWidget::createTableView()
{
for (int col_idx = 0; col_idx < table_data_.cfdna_samples.length(); ++col_idx)
{
if(table_data_.mrd_tables.at(col_idx).rowCount() > 0)
if(table_data_.mrd_tables.at(col_idx).count() > 0)
{
ui_->mrd->setItem(row_idx, col_idx, GUIHelper::createTableItem(table_data_.mrd_tables.at(col_idx).row(0).at(row_idx), Qt::AlignRight));
ui_->mrd->setItem(row_idx, col_idx, GUIHelper::createTableItem(table_data_.mrd_tables.at(col_idx)[0].at(row_idx), Qt::AlignRight));
continue;
}
ui_->mrd->setItem(row_idx, col_idx, GUIHelper::createTableItem(""));
Expand Down
52 changes: 26 additions & 26 deletions src/GSvar/ExpressionExonWidget.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,7 @@ void ExpressionExonWidget::loadExpressionFile()
qDebug() << "TSV parsed";

//init filter data
filter_result_ = FilterResult(expression_data_.rowCount());
filter_result_ = FilterResult(expression_data_.count());

QApplication::restoreOverrideCursor();
}
Expand Down Expand Up @@ -215,7 +215,7 @@ void ExpressionExonWidget::applyFilters()
ui_->tw_expression_table->setEnabled(false);

filter_result_.reset(true);
int filtered_lines = expression_data_.rowCount();
int filtered_lines = expression_data_.count();

QTime timer;
timer.start();
Expand All @@ -239,11 +239,11 @@ void ExpressionExonWidget::applyFilters()

if (gene_idx != -1)
{
for(int row_idx=0; row_idx<expression_data_.rowCount(); ++row_idx)
for(int row_idx=0; row_idx<expression_data_.count(); ++row_idx)
{
if (!filter_result_.flags()[row_idx]) continue;

filter_result_.flags()[row_idx] = variant_gene_set_.contains(expression_data_.row(row_idx).at(gene_idx).toUtf8().trimmed());
filter_result_.flags()[row_idx] = variant_gene_set_.contains(expression_data_[row_idx].at(gene_idx).toUtf8().trimmed());
}
}

Expand All @@ -265,12 +265,12 @@ void ExpressionExonWidget::applyFilters()
if (genes_joined.contains("*")) //with wildcards
{
QRegExp reg(genes_joined.replace("-", "\\-").replace("*", "[A-Z0-9-]*"));
for(int row_idx=0; row_idx<expression_data_.rowCount(); ++row_idx)
for(int row_idx=0; row_idx<expression_data_.count(); ++row_idx)
{
if (!filter_result_.flags()[row_idx]) continue;

// generate GeneSet from column text
GeneSet sv_genes = GeneSet::createFromText(expression_data_.row(row_idx).at(gene_idx).toUtf8(), ',');
GeneSet sv_genes = GeneSet::createFromText(expression_data_[row_idx].at(gene_idx).toUtf8(), ',');

bool match_found = false;
foreach(const QByteArray& sv_gene, sv_genes)
Expand All @@ -286,12 +286,12 @@ void ExpressionExonWidget::applyFilters()
}
else //without wildcards
{
for(int row_idx=0; row_idx<expression_data_.rowCount(); ++row_idx)
for(int row_idx=0; row_idx<expression_data_.count(); ++row_idx)
{
if (!filter_result_.flags()[row_idx]) continue;

// generate GeneSet from column text
GeneSet sv_genes = GeneSet::createFromText(expression_data_.row(row_idx).at(gene_idx).toUtf8(), ',');
GeneSet sv_genes = GeneSet::createFromText(expression_data_[row_idx].at(gene_idx).toUtf8(), ',');

filter_result_.flags()[row_idx] = sv_genes.intersectsWith(gene_whitelist);
}
Expand Down Expand Up @@ -321,12 +321,12 @@ void ExpressionExonWidget::applyFilters()
try
{
double min_rpb_value = ui_->sb_min_rpb->value();
for(int row_idx=0; row_idx<expression_data_.rowCount(); ++row_idx)
for(int row_idx=0; row_idx<expression_data_.count(); ++row_idx)
{
//skip already filtered
if (!filter_result_.flags()[row_idx]) continue;

QString value = expression_data_.row(row_idx).at(idx).toUtf8();
QString value = expression_data_[row_idx].at(idx).toUtf8();
if (value.isEmpty() || value == "n/a")
{
filter_result_.flags()[row_idx] = false;
Expand Down Expand Up @@ -364,12 +364,12 @@ void ExpressionExonWidget::applyFilters()
try
{
double min_srpb_value = ui_->sb_min_srpb_sample->value();
for(int row_idx=0; row_idx<expression_data_.rowCount(); ++row_idx)
for(int row_idx=0; row_idx<expression_data_.count(); ++row_idx)
{
//skip already filtered
if (!filter_result_.flags()[row_idx]) continue;

QString value = expression_data_.row(row_idx).at(idx).toUtf8();
QString value = expression_data_[row_idx].at(idx).toUtf8();
if (value.isEmpty() || value == "n/a")
{
filter_result_.flags()[row_idx] = false;
Expand Down Expand Up @@ -413,12 +413,12 @@ void ExpressionExonWidget::applyFilters()
}
else
{
for(int row_idx=0; row_idx<expression_data_.rowCount(); ++row_idx)
for(int row_idx=0; row_idx<expression_data_.count(); ++row_idx)
{
//skip already filtered
if (!filter_result_.flags()[row_idx]) continue;

QString biotype = expression_data_.row(row_idx).at(idx_biotype);
QString biotype = expression_data_[row_idx].at(idx_biotype);
filter_result_.flags()[row_idx] = selected_biotypes.contains(biotype.replace("_", " "));
}
}
Expand Down Expand Up @@ -454,13 +454,13 @@ void ExpressionExonWidget::applyFilters()
{
double min_expr_value = ui_->sb_low_expression->value();

for(int row_idx=0; row_idx<expression_data_.rowCount(); ++row_idx)
for(int row_idx=0; row_idx<expression_data_.count(); ++row_idx)
{
//skip already filtered
if (!filter_result_.flags()[row_idx]) continue;

QString value_sample = expression_data_.row(row_idx).at(idx_srpb).toUtf8();
QString value_mean_cohort = expression_data_.row(row_idx).at(idx_cohort_mean).toUtf8();
QString value_sample = expression_data_[row_idx].at(idx_srpb).toUtf8();
QString value_mean_cohort = expression_data_[row_idx].at(idx_cohort_mean).toUtf8();
if (value_sample.isEmpty() || value_sample == "n/a" || value_mean_cohort.isEmpty() || value_mean_cohort == "n/a")
{
filter_result_.flags()[row_idx] = false;
Expand Down Expand Up @@ -498,12 +498,12 @@ void ExpressionExonWidget::applyFilters()
try
{
double min_cohort_mean = ui_->sb_min_srpb_cohort->value();
for(int row_idx=0; row_idx<expression_data_.rowCount(); ++row_idx)
for(int row_idx=0; row_idx<expression_data_.count(); ++row_idx)
{
//skip already filtered
if (!filter_result_.flags()[row_idx]) continue;

QString value = expression_data_.row(row_idx).at(idx).toUtf8();
QString value = expression_data_[row_idx].at(idx).toUtf8();
if (value.isEmpty() || value == "n/a")
{
filter_result_.flags()[row_idx] = false;
Expand Down Expand Up @@ -541,12 +541,12 @@ void ExpressionExonWidget::applyFilters()
try
{
double min_logfc = ui_->sb_min_logfc->value();
for(int row_idx=0; row_idx<expression_data_.rowCount(); ++row_idx)
for(int row_idx=0; row_idx<expression_data_.count(); ++row_idx)
{
//skip already filtered
if (!filter_result_.flags()[row_idx]) continue;

QString value = expression_data_.row(row_idx).at(idx).toUtf8();
QString value = expression_data_[row_idx].at(idx).toUtf8();
if (value.isEmpty() || value == "n/a")
{
filter_result_.flags()[row_idx] = false;
Expand Down Expand Up @@ -584,12 +584,12 @@ void ExpressionExonWidget::applyFilters()
try
{
double min_zscore = ui_->sb_min_zscore->value();
for(int row_idx=0; row_idx<expression_data_.rowCount(); ++row_idx)
for(int row_idx=0; row_idx<expression_data_.count(); ++row_idx)
{
//skip already filtered
if (!filter_result_.flags()[row_idx]) continue;

QString value = expression_data_.row(row_idx).at(idx).toUtf8();
QString value = expression_data_[row_idx].at(idx).toUtf8();
if (value.isEmpty() || value == "n/a")
{
filter_result_.flags()[row_idx] = false;
Expand Down Expand Up @@ -780,12 +780,12 @@ void ExpressionExonWidget::updateTable()

// fill table
int table_row_idx = 0;
for(int file_line_idx=0; file_line_idx<expression_data_.rowCount(); ++file_line_idx)
for(int file_line_idx=0; file_line_idx<expression_data_.count(); ++file_line_idx)
{
if (!filter_result_.passing(file_line_idx)) continue;


QStringList row = expression_data_.row(file_line_idx);
const QStringList& row = expression_data_[file_line_idx];

//iterate over columns
for (int col_idx = 0; col_idx < column_names_.size(); ++col_idx)
Expand Down Expand Up @@ -834,7 +834,7 @@ void ExpressionExonWidget::updateTable()
ui_->tw_expression_table->sortByColumn(9, Qt::DescendingOrder);

//set number of filtered / total rows
ui_->l_filtered_rows->setText(QByteArray::number(filter_result_.flags().count(true)) + " / " + QByteArray::number(expression_data_.rowCount()));
ui_->l_filtered_rows->setText(QByteArray::number(filter_result_.flags().count(true)) + " / " + QByteArray::number(expression_data_.count()));

//optimize table view
GUIHelper::resizeTableCellWidths(ui_->tw_expression_table, 350);
Expand Down
28 changes: 14 additions & 14 deletions src/GSvar/ExpressionGeneWidget.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -126,7 +126,7 @@ void ExpressionGeneWidget::applyFilters(int max_rows)
if (filtering_in_progress_) return;
filtering_in_progress_ = true;
//skip if not necessary
int row_count = expression_data_.rowCount();
int row_count = expression_data_.count();
if (row_count == 0) return;

try
Expand Down Expand Up @@ -183,7 +183,7 @@ void ExpressionGeneWidget::applyFilters(int max_rows)
{
if (!filter_result_.flags()[row_idx]) continue;

filter_result_.flags()[row_idx] = variant_gene_set_.contains(expression_data_.row(row_idx).at(gene_idx).toUtf8().trimmed());
filter_result_.flags()[row_idx] = variant_gene_set_.contains(expression_data_[row_idx].at(gene_idx).toUtf8().trimmed());
}

qDebug() << filter_result_.countPassing();
Expand All @@ -204,7 +204,7 @@ void ExpressionGeneWidget::applyFilters(int max_rows)
if (!filter_result_.flags()[row_idx]) continue;

// generate GeneSet from column text
GeneSet sv_genes = GeneSet::createFromText(expression_data_.row(row_idx).at(gene_idx).toUtf8().trimmed(), ',');
GeneSet sv_genes = GeneSet::createFromText(expression_data_[row_idx].at(gene_idx).toUtf8().trimmed(), ',');

bool match_found = false;
foreach(const QByteArray& sv_gene, sv_genes)
Expand All @@ -225,7 +225,7 @@ void ExpressionGeneWidget::applyFilters(int max_rows)
if (!filter_result_.flags()[row_idx]) continue;

// generate GeneSet from column text
GeneSet sv_genes = GeneSet::createFromText(expression_data_.row(row_idx).at(gene_idx).toUtf8().trimmed(), ',');
GeneSet sv_genes = GeneSet::createFromText(expression_data_[row_idx].at(gene_idx).toUtf8().trimmed(), ',');

filter_result_.flags()[row_idx] = sv_genes.intersectsWith(gene_whitelist);
}
Expand All @@ -245,7 +245,7 @@ void ExpressionGeneWidget::applyFilters(int max_rows)
//skip already filtered
if (!filter_result_.flags()[row_idx]) continue;

QString value = expression_data_.row(row_idx).at(tpm_idx).trimmed();
QString value = expression_data_[row_idx].at(tpm_idx).trimmed();
if (value.isEmpty() || value == "n/a")
{
filter_result_.flags()[row_idx] = false;
Expand Down Expand Up @@ -281,7 +281,7 @@ void ExpressionGeneWidget::applyFilters(int max_rows)
//skip already filtered
if (!filter_result_.flags()[row_idx]) continue;

QString biotype = expression_data_.row(row_idx).at(idx_biotype).trimmed().replace("_", " ");
QString biotype = expression_data_[row_idx].at(idx_biotype).trimmed().replace("_", " ");
filter_result_.flags()[row_idx] = selected_biotypes.contains(biotype);
}

Expand All @@ -298,7 +298,7 @@ void ExpressionGeneWidget::applyFilters(int max_rows)
//skip already filtered
if (!filter_result_.flags()[row_idx]) continue;

QString value_sample = expression_data_.row(row_idx).at(tpm_idx);
QString value_sample = expression_data_[row_idx].at(tpm_idx);
if (value_sample.isEmpty() || value_sample == "n/a")
{
filter_result_.flags()[row_idx] = false;
Expand Down Expand Up @@ -340,7 +340,7 @@ void ExpressionGeneWidget::applyFilters(int max_rows)

//get gene and tpm value
bool in_db = false;
QByteArray ensg_number = expression_data_.row(row_idx).at(gene_id_idx).toUtf8().trimmed();
QByteArray ensg_number = expression_data_[row_idx].at(gene_id_idx).toUtf8().trimmed();
QByteArray gene_symbol;

if(ensg_mapping_.contains(ensg_number))
Expand All @@ -353,7 +353,7 @@ void ExpressionGeneWidget::applyFilters(int max_rows)
continue;
}
double tpm = 0.0;
QString value = expression_data_.row(row_idx).at(tpm_idx).toUtf8().trimmed();
QString value = expression_data_[row_idx].at(tpm_idx).toUtf8().trimmed();
if (!(value.isEmpty() || value == "n/a"))
{
tpm = Helper::toDouble(value);
Expand Down Expand Up @@ -777,7 +777,7 @@ void ExpressionGeneWidget::loadExpressionData()


//init filter mask
filter_result_ = FilterResult(expression_data_.rowCount());
filter_result_ = FilterResult(expression_data_.count());

QApplication::restoreOverrideCursor();
}
Expand Down Expand Up @@ -885,12 +885,12 @@ void ExpressionGeneWidget::updateTable(int max_rows)
}


for(int file_row_idx=0; file_row_idx<expression_data_.rowCount(); ++file_row_idx)
for(int file_row_idx=0; file_row_idx<expression_data_.count(); ++file_row_idx)
{
//skip rows which are filtered out
if(!filter_result_.flags()[file_row_idx]) continue;

QStringList row = expression_data_.row(file_row_idx);
const QStringList& row = expression_data_[file_row_idx];
QByteArray ensg_number = row.at(gene_id_idx).toUtf8();
QByteArray gene;
if (ensg_mapping_.contains(ensg_number)) gene = ensg_mapping_.value(ensg_number);
Expand Down Expand Up @@ -989,11 +989,11 @@ void ExpressionGeneWidget::updateTable(int max_rows)
//Set number of filtered / total rows
if (filter_result_.countPassing() >= max_rows)
{
ui_->filtered_rows->setText(QByteArray::number(max_rows) + "+ / " + QByteArray::number(expression_data_.rowCount()) + " (showing only first " + QByteArray::number(max_rows) + ")");
ui_->filtered_rows->setText(QByteArray::number(max_rows) + "+ / " + QByteArray::number(expression_data_.count()) + " (showing only first " + QByteArray::number(max_rows) + ")");
}
else
{
ui_->filtered_rows->setText(QByteArray::number(ui_->expression_data->rowCount()) + " / " + QByteArray::number(expression_data_.rowCount()));
ui_->filtered_rows->setText(QByteArray::number(ui_->expression_data->rowCount()) + " / " + QByteArray::number(expression_data_.count()));
}


Expand Down
6 changes: 3 additions & 3 deletions src/GSvar/FusionWidget.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -61,10 +61,10 @@ void FusionWidget::loadFusionData()
}

//fill table widget with expression data
ui_->fusions->setRowCount(fusion_data.rowCount());
for(int row_idx=0; row_idx<fusion_data.rowCount(); ++row_idx)
ui_->fusions->setRowCount(fusion_data.count());
for(int row_idx=0; row_idx<fusion_data.count(); ++row_idx)
{
QStringList row = fusion_data.row(row_idx);
const QStringList& row = fusion_data[row_idx];
for (int col_idx = 0; col_idx < column_names_.size(); ++col_idx)
{
if(numeric_columns_.at(col_idx))
Expand Down
6 changes: 3 additions & 3 deletions src/GSvar/PRSWidget.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -77,12 +77,12 @@ void PRSWidget::initGui()
}

//add contents
ui_.prs->setRowCount(prs_table_.rowCount());
for (int r=0; r<prs_table_.rowCount(); ++r)
ui_.prs->setRowCount(prs_table_.count());
for (int r=0; r<prs_table_.count(); ++r)
{
for (int c=0; c<headers.count(); ++c)
{
ui_.prs->setItem(r , c, GUIHelper::createTableItem(prs_table_.row(r)[c].trimmed()));
ui_.prs->setItem(r , c, GUIHelper::createTableItem(prs_table_[r][c].trimmed()));
}
}

Expand Down
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