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Merge pull request #6 from KCCG/ge-panelapp-integration
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GE PanelApp integration
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@drmjc
drmjc committed Apr 10, 2018
2 parents ef964c9 + 0b3cc8c commit 2324e70
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Showing 11 changed files with 542 additions and 250 deletions.
228 changes: 92 additions & 136 deletions actions/action_gbs_analysis.php
View file
Expand Up @@ -133,6 +133,97 @@
}
}

#############################################
# IF A GENE LIST WAS SUBMITTED FOR AN ANALYSIS TYPE THAT ALLOWS THEM
#############################################

if (in_array($_SESSION["gbs_analysis_type"], array("svfusions", "gene_lists"))) {
// Store the lists selected in the multi-select box so they can be restored on the query page (only used for this)
if (isset($_POST["gbs_gene_list_selection"])) {
$_SESSION["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_gene_list_selection"] = "";
}

// Store the manual entry gene list submitted
if (isset($_POST["genes"])) {
$_SESSION["gbs_gene_list"] = htmlspecialchars($_POST["genes"], ENT_QUOTES, 'UTF-8');
} else {
$_SESSION["gbs_gene_list"] = "";
}

// Store the PanelApp panel selected so it can be restored on the query page (only used for this)
if (isset($_POST["gbs_panelapp_panel_selection"]) && $_POST["gbs_panelapp_panel_selection"] != "None") {
$_SESSION["gbs_panelapp_panel_selection"] = $_POST["gbs_panelapp_panel_selection"];
// If no panel was selected reset to nothing (in case one was selected before)
} else {
$_SESSION["gbs_panelapp_panel_selection"] = "";
}

// If no gene lists to search were selected, no PanelApp panel was selected and nothing was typed in the manual entry box
if ($_SESSION["gbs_gene_list_selection"] == "" && $_SESSION["gbs_gene_list"] == "" && $_SESSION["gbs_panelapp_panel_selection"] == "") {;
if ($_SESSION["gbs_analysis_type"] == "svfusions") {
// Empty array of genes to search (means all will be searched)
$gene_list_to_search = array();
} elseif ($_SESSION["gbs_analysis_type"] == "gene_lists") {
gbs_query_page_redirect("no_genes_specified");
}
// If genes were specified
} else {
$gene_list_to_search = determine_gene_list($_POST["gbs_gene_list_selection"], $_SESSION["gbs_gene_list"], $_SESSION["gbs_panelapp_panel_selection"]);

if ($gene_list_to_search === false) {
gbs_query_page_redirect("cant_determine_gene_list");
}

// If no genes were parsed out of the gene lists selected and manual list submitted
if (count($gene_list_to_search) == 0) {
if ($_SESSION["gbs_analysis_type"] == "svfusions") {
log_results_page_error("No genes were extracted from the gene list(s) you specified. Returning results for all genes in the genome.");
} elseif ($_SESSION["gbs_analysis_type"] == "gene_lists") {
gbs_query_page_redirect("no_genes_specified");
}
} else {
// Determine which genes (if any) are not in the GBS gene name -> co-ordinate table, these are genes that will not be searched for
$missing_genes = validate_gene_list_gbs($gene_list_to_search);

if ($missing_genes === false) {
gbs_query_page_redirect("cant_determine_missing_genes");
}

// If missing genes were found
if (count($missing_genes) > 0) {
// Save any genes that were not found to a string to display to the user
log_results_page_error("Some genes do not have coordinates stored in the GBS for block searching, no blocks will be returned for these genes: ".implode(", ", $missing_genes)."\n");

// Subtract the missing genes from the genes to search
foreach ($gene_list_to_search as $gene) {
// If the gene is not in the GBS
if (array_search($gene, $missing_genes) !== false) { // array_search returns an ID which can evaluate to true/false, the function will return false when it doesn't find a match, check this with === or !==
// Delete it from the gene list to search
unset($gene_list_to_search[array_search($gene, $gene_list_to_search)]);
}
}

// Reindex the array
$gene_list_to_search = array_values($gene_list_to_search);

// Check that genes are remaining to search
if (count($gene_list_to_search) == 0) {
// Allow the query to go through with a warning for SV Fusions
if ($_SESSION["gbs_analysis_type"] == "svfusions") {
log_results_page_error("No valid genes were extracted from the gene list(s) you specified. Returning results for all genes in the genome.");
// Stop the query going through for Gene Lists as you need at least 1 gene
} elseif ($_SESSION["gbs_analysis_type"] == "gene_lists") {
gbs_query_page_redirect("no_genes_remaining_to_query");
}
}
}
}
}
}

#############################################
# ANALYSIS TYPE SAMPLE OVERLAPPING BLOCKS
#############################################
Expand Down Expand Up @@ -219,76 +310,7 @@
# ANALYSIS TYPE METHOD SV FUSIONS
#############################################

} 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"])) {
$_SESSION["gbs_svfusions_gene_list_selection"] = $_POST["svfusions_gene_list_selection"];
// If no list was selected reset to nothing (in case some were selected before)
} else {
$_SESSION["gbs_svfusions_gene_list_selection"] = "";
}

// Store the manual entry gene list submitted
if (isset($_POST["svfusions_genes"])) {
$_SESSION["gbs_svfusions_gene_list"] = htmlspecialchars($_POST["svfusions_genes"], ENT_QUOTES, 'UTF-8');
} else {
$_SESSION["gbs_svfusions_gene_list"] = "";
}

// 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"] == "") {
// 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"])) {
$gene_list_to_search = determine_gene_list($_POST["svfusions_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"]);
}

if ($gene_list_to_search === false) {
gbs_query_page_redirect("cant_determine_gene_list");
}

// If no genes were parsed out of the gene lists selected and manual list submitted
if (count($gene_list_to_search) == 0) {
log_results_page_error("No genes were extracted from the gene list(s) you specified. Returning results for all genes in the genome.");
} else {
// Determine which genes (if any) are not in the GBS gene name -> co-ordinate table, these are genes that will not be searched for
$missing_genes = validate_gene_list_gbs($gene_list_to_search);

if ($missing_genes === false) {
gbs_query_page_redirect("cant_determine_missing_genes");
}

// If missing genes were found
if (count($missing_genes) > 0) {
// Save any genes that were not found to a string to display to the user
log_results_page_error("Some genes do not have coordinates stored in the GBS for block searching, no blocks will be returned for these genes: ".implode(", ", $missing_genes)."\n");

// Subtract the missing genes from the genes to search
foreach ($gene_list_to_search as $gene) {
// If the gene is not in the GBS
if (array_search($gene, $missing_genes) !== false) { // array_search returns an ID which can evaluate to true/false, the function will return false when it doesn't find a match, check this with === or !==
// Delete it from the gene list to search
unset($gene_list_to_search[array_search($gene, $gene_list_to_search)]);
}
}

// Reindex the array
$gene_list_to_search = array_values($gene_list_to_search);

// Check that genes are remaining to search
if (count($gene_list_to_search) == 0) {
log_results_page_error("No valid genes were extracted from the gene list(s) you specified. Returning results for all genes in the genome.");
}
}
}
}

} elseif ($_SESSION["gbs_analysis_type"] == "svfusions") {
$svfusions_blocks = analysis_type_svfusions_gbs($svfusions_samples_to_query, $gene_list_to_search);

if ($svfusions_blocks === false) {
Expand All @@ -304,72 +326,6 @@
#############################################

} elseif ($_SESSION["gbs_analysis_type"] == "gene_lists") {
// Store the lists selected in the multi-select box so they can be restored on the query page (only used for this)
if (isset($_POST["gene_list_selection"])) {
$_SESSION["gbs_gene_list_selection"] = $_POST["gene_list_selection"];
// If no list was selected reset to nothing (in case some were selected before)
} else {
$_SESSION["gbs_gene_list_selection"] = "";
}

// Store the manual entry gene list submitted
if (isset($_POST["genes"])) {
$_SESSION["gbs_gene_list"] = htmlspecialchars($_POST["genes"], ENT_QUOTES, 'UTF-8');
} else {
$_SESSION["gbs_gene_list"] = "";
}

// If no gene list was selected and no genes were typed into the manual entry box
if ($_SESSION["gbs_gene_list_selection"] == "" && $_SESSION["gbs_gene_list"] == "") {
gbs_query_page_redirect("no_genes_specified");
}

// If gene lists were selected
if (isset($_POST["gene_list_selection"])) {
$gene_list_to_search = determine_gene_list($_POST["gene_list_selection"], $_SESSION["gbs_gene_list"]);
} else {
$gene_list_to_search = determine_gene_list("", $_SESSION["gbs_gene_list"]);
}

if ($gene_list_to_search === false) {
gbs_query_page_redirect("cant_determine_gene_list");
}

// If no genes were parsed out of the gene lists selected and manual list submitted
if (count($gene_list_to_search) == 0) {
gbs_query_page_redirect("no_genes_specified");
}

// Determine which genes (if any) are not in the GBS gene name -> co-ordinate table, these are genes that will not be searched for
$missing_genes = validate_gene_list_gbs($gene_list_to_search);

if ($missing_genes === false) {
gbs_query_page_redirect("cant_determine_missing_genes");
}

// If missing genes were found
if (count($missing_genes) > 0) {
// Save any genes that were not found to a string to display to the user
log_results_page_error("Some genes do not have coordinates stored in the GBS for block searching, no blocks will be returned for these genes: ".implode(", ", $missing_genes)."\n");

// Subtract the missing genes from the genes to search
foreach ($gene_list_to_search as $gene) {
// If the gene is not in the GBS
if (array_search($gene, $missing_genes) !== false) { // array_search returns an ID which can evaluate to true/false, the function will return false when it doesn't find a match, check this with === or !==
// Delete it from the gene list to search
unset($gene_list_to_search[array_search($gene, $gene_list_to_search)]);
}
}

// Reindex the array
$gene_list_to_search = array_values($gene_list_to_search);

// Check that genes are remaining to search
if (count($gene_list_to_search) == 0) {
gbs_query_page_redirect("no_genes_remaining_to_query");
}
}

// Run the analysis for blocks
$gene_lists_blocks_output = analysis_type_gene_lists_gbs($gene_list_to_search, $samples_to_query);

Expand Down
4 changes: 2 additions & 2 deletions actions/action_gene_list_administration.php
View file
Expand Up @@ -44,7 +44,7 @@
}

// Determine a list of genes to add while removing duplicates and invalid genes
$gene_list = determine_gene_list("", $_POST["genes_to_add"]); // Array of genes, will have 0 elements if no genes submitted
$gene_list = determine_gene_list("", $_POST["genes_to_add"], ""); // Array of genes, will have 0 elements if no genes submitted

// Only try to validate a gene list if query genes exist
if ($gene_list === false || count($gene_list) == 0) {
Expand Down Expand Up @@ -155,7 +155,7 @@
}

// Determine a list of genes to delete while removing duplicates and invalid genes
$gene_list = determine_gene_list("", $_POST["genes_to_delete"]); // Array of genes, will have 0 elements if no genes submitted
$gene_list = determine_gene_list("", $_POST["genes_to_delete"], ""); // Array of genes, will have 0 elements if no genes submitted

// Only try to validate a gene list if query genes exist
if ($gene_list === false || count($gene_list) == 0) {
Expand Down
75 changes: 34 additions & 41 deletions actions/action_run_query.php
View file
Expand Up @@ -36,15 +36,15 @@

######################

// Store the lists selected in the multi-select box so they can be restored on the query page (only used for this)
// Store the lists selected in the multi-select box so they can be restored on the query page
if (isset($_POST["gene_list_selection"])) {
$_SESSION["gene_list_selection"] = $_POST["gene_list_selection"];
// If no list was selected reset to nothing (in case some were selected before)
} else {
$_SESSION["gene_list_selection"] = "";
}

// Store the lists selected in the multi-select boxe so they can be restored on the query page (only used for this)
// Store the lists selected in the multi-select boxe so they can be restored on the query page
if (isset($_POST["gene_list_exclusion_selection"])) {
$_SESSION["gene_list_exclusion_selection"] = $_POST["gene_list_exclusion_selection"];
// If no list was selected reset to nothing (in case some were selected before)
Expand All @@ -56,31 +56,35 @@
$_SESSION["exclusion_gene_list"] = htmlspecialchars($_POST["exclude_genes"], ENT_QUOTES, 'UTF-8');
$_SESSION["gene_list"] = htmlspecialchars($_POST["genes"], ENT_QUOTES, 'UTF-8');

// Store the PanelApp panel selected so it can be restored on the query page (only used for this)
if (isset($_POST["panelapp_panel_selection"]) && $_POST["panelapp_panel_selection"] != "None") {
$_SESSION["panelapp_panel_selection"] = $_POST["panelapp_panel_selection"];
// If no panel was selected reset to nothing (in case one was selected before)
} else {
$_SESSION["panelapp_panel_selection"] = "";
}

// Store the PanelApp panel selected so it can be restored on the query page (only used for this)
if (isset($_POST["panelapp_panel_exclusion_selection"]) && $_POST["panelapp_panel_exclusion_selection"] != "None") {
$_SESSION["panelapp_panel_exclusion_selection"] = $_POST["panelapp_panel_exclusion_selection"];
// If no panel was selected reset to nothing (in case one was selected before)
} else {
$_SESSION["panelapp_panel_exclusion_selection"] = "";
}

######################

// If no gene lists to search were selected and nothing was typed in the manual entry box, set the gene list to search to an empty array
if (!isset($_POST["gene_list_selection"]) && $_SESSION["gene_list"] == "") {
// If no gene lists to search were selected, no PanelApp panel was selected and nothing was typed in the manual entry box, set the gene list to search to an empty array
if ($_SESSION["gene_list_selection"] == "" && $_SESSION["gene_list"] == "" && $_SESSION["panelapp_panel_selection"] == "") {;
$_SESSION["gene_list_to_search"] = array();
// If gene lists were selected or typed in the manual entry box
} else {
// If gene lists were selected
if (isset($_POST["gene_list_selection"])) {
$gene_list_result = determine_gene_list($_POST["gene_list_selection"], $_SESSION["gene_list"]);

if ($gene_list_result === false) {
results_page_redirect("cant_determine_gene_list");
} else {
$_SESSION["gene_list_to_search"] = $gene_list_result;
}
// If no gene lists were selected but something was typed in the manual entry box
$gene_list_result = determine_gene_list($_SESSION["gene_list_selection"], $_SESSION["gene_list"], $_SESSION["panelapp_panel_selection"]);

if ($gene_list_result === false) {
results_page_redirect("cant_determine_gene_list");
} else {
$gene_list_result = determine_gene_list("", $_SESSION["gene_list"]);

if ($gene_list_result === false) {
results_page_redirect("cant_determine_gene_list");
} else {
$_SESSION["gene_list_to_search"] = $gene_list_result;
}
$_SESSION["gene_list_to_search"] = $gene_list_result;
}

if (count($_SESSION["gene_list_to_search"]) > 0) { // Only try to validate a gene list if query genes exist
Expand All @@ -104,30 +108,18 @@
}

######################
// If no gene lists to search were selected and nothing was typed in the manual entry box, set the gene list to search to an empty array
if (!isset($_POST["gene_list_exclusion_selection"]) && $_SESSION["exclusion_gene_list"] == "") {

// If no gene lists to search were selected, no PanelApp panel was selected and nothing was typed in the manual entry box, set the gene list to search to an empty array
if ($_SESSION["gene_list_exclusion_selection"] == "" && $_SESSION["exclusion_gene_list"] == "" && $_SESSION["panelapp_panel_exclusion_selection"] == "") {
$_SESSION["gene_list_to_exclude"] = array();
// If gene lists were selected or typed in the manual entry box
} else {
// If gene lists were selected
if (isset($_POST["gene_list_exclusion_selection"])) {
$gene_list_result = determine_gene_list($_POST["gene_list_exclusion_selection"], $_SESSION["exclusion_gene_list"]);

if ($gene_list_result === false) {
results_page_redirect("cant_determine_exclusion_gene_list");
} else {
$_SESSION["gene_list_to_exclude"] = $gene_list_result;
}
// If no gene lists were selected but something was typed in the manual entry box
$gene_list_result = determine_gene_list($_SESSION["gene_list_exclusion_selection"], $_SESSION["exclusion_gene_list"], $_SESSION["panelapp_panel_exclusion_selection"]);

if ($gene_list_result === false) {
results_page_redirect("cant_determine_exclusion_gene_list");
} else {
$gene_list_result = determine_gene_list("", $_SESSION["exclusion_gene_list"]);

if ($gene_list_result === false) {
results_page_redirect("cant_determine_exclusion_gene_list");
} else {
$_SESSION["gene_list_to_exclude"] = $gene_list_result;
}
$_SESSION["gene_list_to_exclude"] = $gene_list_result;
}

if (count($_SESSION["gene_list_to_exclude"]) > 0) { // Only try to validate a gene list if query genes exist
Expand Down Expand Up @@ -713,6 +705,7 @@
array_push($column_order, "Orphanet Disorders");
array_push($column_order, "Is Orphanet AR");
array_push($column_order, "Is Orphanet AD");
array_push($column_order, "Genomics England PanelApp");
array_push($column_order, "ClinVar Variation ID");
array_push($column_order, "ClinVar Clinical Significance");
array_push($column_order, "ClinVar Trait");
Expand Down

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