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Merge branch 'master' of https://github.com/imgag/ngs-bits
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@marc-sturm
marc-sturm committed Jan 16, 2025
2 parents 3233d0f + 5a0c934 commit b7cea4a
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Showing 2 changed files with 177 additions and 108 deletions.
283 changes: 175 additions & 108 deletions src/GSvar/RepeatExpansionWidget.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ RepeatExpansionWidget::RepeatExpansionWidget(QWidget* parent, const RepeatLocusL
, ngsd_user_logged_in_(LoginManager::active())
, rc_enabled_(ngsd_user_logged_in_ && report_config_!=nullptr && !report_config_->isFinalized())
{
ui_.setupUi(this);
ui_.setupUi(this);
ui_.filter_hpo->setEnabled(ngsd_user_logged_in_);
ui_.filter_hpo->setEnabled(!GlobalServiceProvider::filterWidget()->phenotypes().isEmpty());

Expand Down Expand Up @@ -78,17 +78,17 @@ RepeatExpansionWidget::RepeatExpansionWidget(QWidget* parent, const RepeatLocusL
ui_.table->setColumnHidden(GUIHelper::columnIndex(ui_.table, "statistical cutoff"), true);
}

if (!res_.isEmpty())
{
displayRepeats();
loadMetaDataFromNGSD();
GUIHelper::resizeTableCellWidths(ui_.table, 300);
GUIHelper::resizeTableCellHeightsToMinimum(ui_.table);
colorRepeatCountBasedOnCutoffs();
colorRepeatCountConfidenceInterval();
updateRowVisibility();
setReportConfigHeaderIcons();
}
if (!res_.isEmpty())
{
displayRepeats();
loadMetaDataFromNGSD();
GUIHelper::resizeTableCellWidths(ui_.table, 300);
GUIHelper::resizeTableCellHeightsToMinimum(ui_.table);
colorRepeatCountBasedOnCutoffs();
colorRepeatCountConfidenceInterval();
updateRowVisibility();
setReportConfigHeaderIcons();
}
}

void RepeatExpansionWidget::showContextMenu(QPoint pos)
Expand Down Expand Up @@ -347,6 +347,19 @@ QString RepeatExpansionWidget::getRepeatId(NGSD& db, int row, bool throw_if_fail
return QString::number(id);
}

QString RepeatExpansionWidget::getRepeatExpansionFieldById(DBTable& table_data, QString field, QString& id)
{
for (int i=0; i<table_data.rowCount(); i++)
{
if (table_data.row(i).id()==id)
{
int column_index = table_data.columnIndex(field);
return table_data.row(i).value(column_index).trimmed();
}
}
return "";
}

void RepeatExpansionWidget::setCellDecoration(int row, QString column, QString tooltip, QColor bg_color)
{
//determine column index
Expand Down Expand Up @@ -417,7 +430,7 @@ void RepeatExpansionWidget::displayRepeats()
{
// fill table widget with variants/repeat expansions
ui_.table->setRowCount(res_.count());
for(int row_idx=0; row_idx<res_.count(); ++row_idx)
for(int row_idx=0; row_idx<res_.count(); ++row_idx)
{
const RepeatLocus& re = res_[row_idx];

Expand Down Expand Up @@ -471,101 +484,155 @@ void RepeatExpansionWidget::loadMetaDataFromNGSD()
{
if (!ngsd_user_logged_in_) return;

NGSD db;

//get infos from NGSD
for (int row=0; row<ui_.table->rowCount(); ++row)
{
//check if repeat is in NGSD
QString id = getRepeatId(db, row, false);
if (id.isEmpty())
{
setCellDecoration(row, "repeat ID", "Repeat not found in NGSD", orange_);
continue;
}

//max_normal
QVariant tmp = db.getValue("SELECT max_normal FROM repeat_expansion WHERE id=" + id);
QString max_normal = tmp.isNull() ? "" : tmp.toString().trimmed();
setCell(row, "max. normal", max_normal);

//min_pathogenic
tmp = db.getValue("SELECT min_pathogenic FROM repeat_expansion WHERE id=" + id);
QString min_pathogenic = tmp.isNull() ? "" : tmp.toString().trimmed();
setCell(row, "min. pathogenic", min_pathogenic);

//inheritance
QString inheritance = db.getValue("SELECT inheritance FROM repeat_expansion WHERE id=" + id).toString().trimmed();
setCell(row, "inheritance", inheritance);

//location
QString location = db.getValue("SELECT location FROM repeat_expansion WHERE id=" + id).toString().trimmed();
setCell(row, "location", location);

//diseases
QString disease_names = db.getValue("SELECT disease_names FROM repeat_expansion WHERE id=" + id).toString().trimmed();
setCell(row, "diseases", disease_names);

//OMIM IDs
QStringList disease_ids_omim = db.getValue("SELECT disease_ids_omim FROM repeat_expansion WHERE id=" + id).toString().split(",");
for(int i=0; i<disease_ids_omim.count(); ++i)
{
QString id = disease_ids_omim[i].trimmed();
if (id.isEmpty()) continue;
QStringList names;
SqlQuery query = db.getQuery();
query.exec("SELECT phenotype FROM omim_phenotype WHERE phenotype LIKE '%" + id + "%'");
while (query.next())
{
QString name = query.value(0).toString();
name.replace(id, "");
name.replace("(3)", "");
name = name.trimmed();
while(name.endsWith(',') || name.endsWith(' ')) name.chop(1);
if (!name.isEmpty()) names << name;
}
if (!names.isEmpty())
{
disease_ids_omim[i] = id + " - " + names.join("/");
}
}
setCell(row, "OMIM disease IDs", disease_ids_omim.join("; "));

//comments
QString comments = db.repeatExpansionComments(id.toInt());
QTableWidgetItem* item = setCell(row, "comments", "");
if (!comments.isEmpty())
{
setCellDecoration(row, "comments", comments);
item->setIcon(QIcon(":/Icons/Info.png"));
}

//HPO terms
QStringList hpo_terms = db.getValue("SELECT hpo_terms FROM repeat_expansion WHERE id=" + id).toString().split(",");
for(int i=0; i<hpo_terms.count(); ++i)
{
QString id = hpo_terms[i].trimmed();
QString name = db.getValue("SELECT name FROM hpo_term WHERE hpo_id LIKE '" + id + "'", true).toString();
if (!name.isEmpty()) id += " - " + name;
hpo_terms[i] = id;
}
setCell(row, "HPO terms", hpo_terms.join("; "));

//type
QString type = db.getValue("SELECT type FROM repeat_expansion WHERE id=" + id).toString().trimmed();
setCell(row, "type", type);

//type
bool inhouse_testing = db.getValue("SELECT inhouse_testing FROM repeat_expansion WHERE id=" + id).toBool();
setCell(row, "in-house testing", inhouse_testing ? "yes" : "no");

//statistical cutoff
if (!sys_type_cutoff_col_.isEmpty())
{
QString cutoff = db.getValue("SELECT "+sys_type_cutoff_col_+" FROM repeat_expansion WHERE id=" + id).toString().trimmed();
setCell(row, "statistical cutoff", cutoff);
}
}
NGSD db;
SqlQuery re_query = db.getQuery();
re_query.exec("SELECT * FROM repeat_expansion");
DBTable re_table = db.createTable("repeat_expansion", "SELECT * FROM repeat_expansion");

//get infos from NGSD
for (int row=0; row<ui_.table->rowCount(); ++row)
{
//check if repeat is in NGSD
QString region = getCell(row, "region");
QString repeat_unit = getCell(row, "repeat unit");

QString id;
for (int re_index=0; re_index<re_table.rowCount(); re_index++)
{
int region_index = re_table.columnIndex("region");
int repeat_unit_index = re_table.columnIndex("repeat_unit");

if (re_table.row(re_index).value(region_index)==region && re_table.row(re_index).value(repeat_unit_index)==repeat_unit)
{
id = re_table.row(re_index).id();
}
}
if (id.isEmpty())
{
setCellDecoration(row, "repeat ID", "Repeat not found in NGSD", orange_);
continue;
}

//max_normal
QString max_normal = getRepeatExpansionFieldById(re_table, "max_normal", id);
setCell(row, "max. normal", max_normal);

//min_pathogenic
QString min_pathogenic = getRepeatExpansionFieldById(re_table, "min_pathogenic", id);
setCell(row, "min. pathogenic", min_pathogenic);

//inheritance
QString inheritance = getRepeatExpansionFieldById(re_table, "inheritance", id);
setCell(row, "inheritance", inheritance);

//location
QString location = getRepeatExpansionFieldById(re_table, "location", id);
setCell(row, "location", location);

//diseases
QString disease_names = getRepeatExpansionFieldById(re_table, "disease_names", id);
setCell(row, "diseases", disease_names);

//OMIM IDs
QStringList disease_ids_omim = getRepeatExpansionFieldById(re_table, "disease_ids_omim", id).split(",");
QString omim_like_clause = "";
QString omim_when_clause = "";
for (const QString &id : disease_ids_omim)
{
QString disease_id = id.trimmed();
if (disease_id.isEmpty()) continue;
if (!omim_like_clause.isEmpty())
{
omim_like_clause += " OR ";
omim_when_clause += " ";
}
omim_like_clause += "phenotype LIKE '%" + disease_id + "%'";
omim_when_clause += "WHEN phenotype LIKE '%" + disease_id + "%' THEN '" + disease_id + "'";
}
if (!omim_when_clause.isEmpty()) omim_when_clause = ", CASE " + omim_when_clause + " ELSE NULL END AS matched_disease_id";

QStringList names;
if (!omim_when_clause.isEmpty() && !omim_like_clause.isEmpty())
{
SqlQuery omim_query = db.getQuery();
omim_query.exec("SELECT phenotype" + omim_when_clause + " FROM omim_phenotype WHERE " + omim_like_clause);
while (omim_query.next())
{
QString disease_id = omim_query.value(1).toString().trimmed();
QString name = omim_query.value(0).toString().trimmed();
name.replace(disease_id, "");
name.replace("(3)", "");
name = name.trimmed();
while(name.endsWith(',') || name.endsWith(' ')) name.chop(1);
if (!name.isEmpty()) names << disease_id + " - " + name;
}
}
setCell(row, "OMIM disease IDs", names.join("; "));

//comments
QStringList comments_list = getRepeatExpansionFieldById(re_table, "comments", id).replace("<br>", "\n").trimmed().split("\n");
for (int comment_index=0; comment_index<comments_list.count(); ++comment_index)
{
QString line = comments_list[comment_index].trimmed();
if (line.startsWith('#') && line.endsWith('#'))
{
comments_list[comment_index] = "<b>" + line.mid(1, line.length()-2) + "</b>";
}
}

QString comments = comments_list.join("<br>");
QTableWidgetItem* item = setCell(row, "comments", "");
if (!comments.isEmpty())
{
setCellDecoration(row, "comments", comments);
item->setIcon(QIcon(":/Icons/Info.png"));
}

//HPO terms
QStringList hpo_terms = getRepeatExpansionFieldById(re_table, "hpo_terms", id).split(",");
QString hpo_like_clause = "";
for (const QString &term : hpo_terms)
{
if (!hpo_like_clause.isEmpty()) hpo_like_clause += " OR ";
hpo_like_clause += "hpo_id LIKE '" + term.trimmed() + "'";
}
if (!hpo_like_clause.isEmpty())
{
QSqlQuery hpo_query = db.getQuery();
hpo_query.exec("SELECT hpo_id, name FROM hpo_term WHERE " + hpo_like_clause);

int hpo_terms_counter = -1;
while(hpo_query.next())
{
hpo_terms_counter++;
QString name = hpo_query.value(1).toString();
if (!name.isEmpty())
{
hpo_terms[hpo_terms_counter] = hpo_query.value(0).toString().trimmed() + " - " + name;
}
else
{
hpo_terms[hpo_terms_counter] = hpo_query.value(0).toString().trimmed();
}
}
}
setCell(row, "HPO terms", hpo_terms.join("; "));

//type
QString type = getRepeatExpansionFieldById(re_table, "type", id);
setCell(row, "type", type);

//inhouse_testing
QString inhouse_testing = getRepeatExpansionFieldById(re_table, "inhouse_testing", id)=="1" ? "yes" : "no";
setCell(row, "in-house testing", inhouse_testing);

//statistical cutoff
if (!sys_type_cutoff_col_.isEmpty())
{
QString cutoff = getRepeatExpansionFieldById(re_table, sys_type_cutoff_col_, id);
setCell(row, "statistical cutoff", cutoff);
}
}
}

void RepeatExpansionWidget::colorRepeatCountBasedOnCutoffs()
Expand Down
2 changes: 2 additions & 0 deletions src/GSvar/RepeatExpansionWidget.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,8 @@ private slots:
///Returns the text value of a cell.
QString getCell(int row, QString column);
QString getRepeatId(NGSD& db, int row, bool throw_if_fails=true);
//Returns a value from RE table by ID
QString getRepeatExpansionFieldById(DBTable& table_data, QString field, QString& id);

///Sets the cell decoration
void setCellDecoration(int row, QString column, QString tooltip, QColor bg_color=QColor());
Expand Down

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