Adding capability to fetch PanelApp panel names and the number of gen…

…es for each confidence level from the DB. Displaying this as a filter option on the short variant and GBS query pages.
KCCG · Mar 27, 2018 · f6a1965 · f6a1965
1 parent dbbfad0
commit f6a1965
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Showing 6 changed files with 218 additions and 73 deletions.
diff --git a/actions/action_gbs_analysis.php b/actions/action_gbs_analysis.php
@@ -221,11 +221,11 @@
 
 	} elseif ($_SESSION["gbs_analysis_type"] == "svfusions") {		
 		// Store the lists selected in the multi-select box so they can be restored on the query page (only used for this)
-		if (isset($_POST["svfusions_gene_list_selection"])) {
+		if (isset($_POST["gbs_gene_list_selection"])) {
-			$_SESSION["gbs_svfusions_gene_list_selection"] = $_POST["svfusions_gene_list_selection"];
+			$_SESSION["gbs_gbs_gene_list_selection"] = $_POST["gbs_gene_list_selection"];
 		// If no list was selected reset to nothing (in case some were selected before)
 		} else {
-			$_SESSION["gbs_svfusions_gene_list_selection"] = "";
+			$_SESSION["gbs_gbs_gene_list_selection"] = "";
 		}
 
 		// Store the manual entry gene list submitted
@@ -236,14 +236,14 @@
 		}
 
 		// If no gene list was selected and no genes were typed into the manual entry box
-		if ($_SESSION["gbs_svfusions_gene_list_selection"] == "" && $_SESSION["gbs_svfusions_gene_list"] == "") {
+		if ($_SESSION["gbs_gbs_gene_list_selection"] == "" && $_SESSION["gbs_svfusions_gene_list"] == "") {
 			// Empty array of genes to search (means all will be searched)
 			$gene_list_to_search = array();
 		// If at least one gene list was selected or genes were typed into the manual entry box
 		} else {
 			// If at least one gene list was selected
-			if (isset($_POST["svfusions_gene_list_selection"])) {
+			if (isset($_POST["gbs_gene_list_selection"])) {
-				$gene_list_to_search = determine_gene_list($_POST["svfusions_gene_list_selection"], $_SESSION["gbs_svfusions_gene_list"]);
+				$gene_list_to_search = determine_gene_list($_POST["gbs_gene_list_selection"], $_SESSION["gbs_svfusions_gene_list"]);
 			// Otherwise just parse the manual entry list
 			} else {
 				$gene_list_to_search = determine_gene_list("", $_SESSION["gbs_svfusions_gene_list"]);

diff --git a/config.ini b/config.ini
@@ -32,6 +32,8 @@ default_minimum_variant_quality=0
 default_exclude_failed_variants=true
 default_gbs_cnlessthan=1.5
 default_gbs_cngreaterthan=2.5
+default_gbs_minblocksize=0
+default_gbs_exclude_failed_variants=true
 
 [query_databases]
 ; Setting any option below to true implies you adhere to the terms of use of the respective data source (e.g. for research use only)

diff --git a/functions/gene_list_functions.php b/functions/gene_list_functions.php
@@ -11,7 +11,8 @@ function fetch_gene_lists() {
 		$sql .= "list_name, ";
 		$sql .= "(SELECT COUNT(*) FROM KCCG_GENE_LISTS.genes_in_lists WHERE list_id = gene_lists.list_id) AS num_genes ";
 	$sql .= "FROM ";
-		$sql .= "KCCG_GENE_LISTS.gene_lists";
+		$sql .= "KCCG_GENE_LISTS.gene_lists ";
+	$sql .= "ORDER BY list_name";
 	$sql .= ";";
 
 	$statement = $GLOBALS["mysql_connection"]->prepare($sql);
@@ -22,12 +23,46 @@ function fetch_gene_lists() {
 		$gene_list[$list["list_name"]] = $list["num_genes"];
 	}
 
-	// If more than 1 gene list was found, sort them naturally
+	return $gene_list;
-	if (count($gene_list) > 1) {
+}
-		array_multisort(array_keys($gene_list), SORT_NATURAL, $gene_list); // Natural sort by gene list name
+
+#############################################
+# FETCH GENOMICS ENGLAND PANELAPP GENE COUNTS
+#############################################
+
+function fetch_panel_counts_ge_panelapp() {
+	$ge_panelapp_panels = array();
+
+	$sql = "SELECT ";
+		$sql .= "panels.name, ";
+		$sql .= "genes_in_panels.confidence_level, ";
+		$sql .= "COUNT(*) AS num_genes ";
+	$sql .= "FROM ";
+		$sql .= "GEPANELAPP.genes_in_panels ";
+	$sql .= "LEFT JOIN GEPANELAPP.panels ON GEPANELAPP.genes_in_panels.panel_id = GEPANELAPP.panels.id ";
+	$sql .= "GROUP BY panels.name, genes_in_panels.confidence_level ";
+	$sql .= "ORDER BY panels.name";
+	$sql .= ";";
+
+	$statement = $GLOBALS["mysql_connection"]->prepare($sql);
+
+	$statement->execute();
+
+	while ($panels = $statement->fetch()) {
+		$ge_panelapp_panels[$panels["name"]][$panels["confidence_level"]] = $panels["num_genes"];
+	}
+	// Format: $ge_panelapp_panels[<panel name>][<confidence level>] = number of genes
+
+	// Go through each panel
+	foreach (array_keys($ge_panelapp_panels) as $ge_panelapp_panel) {
+		// If the current panel has both high and moderate evidence genes
+		if (isset($ge_panelapp_panels[$ge_panelapp_panel]["HighEvidence"], $ge_panelapp_panels[$ge_panelapp_panel]["ModerateEvidence"])) {
+			// Inject in a new evidence level which combines the high and moderate counts
+			$ge_panelapp_panels[$ge_panelapp_panel]["HighModerateEvidence"] = $ge_panelapp_panels[$ge_panelapp_panel]["HighEvidence"] + $ge_panelapp_panels[$ge_panelapp_panel]["ModerateEvidence"];
+		}
 	}
 
-	return $gene_list;
+	return $ge_panelapp_panels;
 }
 
 #############################################

diff --git a/functions/session_variable_functions.php b/functions/session_variable_functions.php
@@ -20,9 +20,8 @@ function clean_session($logout = NULL) {
 	$_SESSION["gbs_family"] = "";
 	$_SESSION["gbs_analysis_type"] = "";
 	$_SESSION["gbs_regions"] = ""; // For the genomic coordinates analysis type
-	$_SESSION["gbs_gene_list_selection"] = ""; // For the gene list(s) analysis type
+	$_SESSION["gbs_gene_list_selection"] = ""; // For the GBS gene list selection (regardless of analysis type)
 	$_SESSION["gbs_gene_list"] = ""; // For the gene list(s) analysis type
-	$_SESSION["gbs_svfusions_gene_list_selection"] = ""; // For the SV Fusions analysis type
 	$_SESSION["gbs_svfusions_gene_list"] = ""; // For the SV Fusions analysis type
 	$_SESSION["gbs_cnlessthan"] = ""; // For most the the analysis types
 	$_SESSION["gbs_cngreaterthan"] = ""; // For most the the analysis types