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Commit 4ab149d7 authored by Hanna JULIENNE's avatar Hanna JULIENNE
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Merge branch 'staging' into 'master' 

Update requirement, change default behaviour

See merge request !28
parents 483323f5 9dc76727
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jass/__main__.py
+ 31
− 31
View file @ 4ab149d7
......@@ -32,32 +32,32 @@ def absolute_path_of_the_file(fileName, output_file = False):
if (Directory_path_exist == False):
# Test the path using the Jass data directory
absoluteFilePath = os.path.normpath(os.path.join(config["DATA_DIR"], fileName))
Directory_path_exist = os.path.exists(os.path.dirname(absoluteFilePath))
if (Directory_path_exist == False):
Message = "The directory of the file {} does not exist".format(fileName)
raise NameError(Message)
else:
# Test if the file path exist
File_path_exist = os.path.exists(absoluteFilePath)
if (File_path_exist == False):
# Test the path using the Jass data directory
absoluteFilePath = os.path.normpath(os.path.join(config["DATA_DIR"], fileName))
File_path_exist = os.path.exists(absoluteFilePath)
if (File_path_exist == False):
Message = "The file {} does not exist".format(fileName)
raise NameError(Message)
# Test if it is realy a file
Is_a_file = os.path.isfile(absoluteFilePath)
if (not Is_a_file) :
Message = "{} is not a file".format(fileName)
raise NameError(Message)
return absoluteFilePath
......@@ -72,17 +72,17 @@ def w_list_phenotypes(args):
def compute_worktable(args):
csv_file_path = args.csv_file_path
if (csv_file_path is not None):
csv_file_path = absolute_path_of_the_file(csv_file_path, True)
init_table_path = absolute_path_of_the_file(args.init_table_path)
worktable_path = absolute_path_of_the_file(args.worktable_path, True)
selected_phenotypes = args.phenotypes
remove_nan = not (args.keep_nans)
remove_nan = (args.remove_nans)
significance_treshold = float(args.significance_treshold)
post_filtering = bool(args.post_filtering)
custom_loadings = args.custom_loadings
custom_loadings = args.custom_loadings
chromosome = args.chromosome_number
pos_Start = args.start_position
pos_End = args.end_position
......@@ -99,10 +99,10 @@ def compute_worktable(args):
strategy = args.strategy
create_worktable_file(
phenotype_ids = selected_phenotypes,
init_file_path = init_table_path,
phenotype_ids = selected_phenotypes,
init_file_path = init_table_path,
project_hdf_path = worktable_path,
remove_nan = remove_nan,
remove_nan = remove_nan,
stat = strategy,
optim_na = True,
csv_file = csv_file_path,
......@@ -125,8 +125,8 @@ def w_create_project_data(args):
manhattan_plot_path = absolute_path_of_the_file(args.manhattan_plot_path, True)
quadrant_plot_path = absolute_path_of_the_file(args.quadrant_plot_path, True)
create_global_plot(worktable_path, manhattan_plot_path)
create_quadrant_plot(worktable_path,
quadrant_plot_path,
create_quadrant_plot(worktable_path,
quadrant_plot_path,
significance_treshold = float(args.significance_treshold))
......@@ -136,7 +136,7 @@ def w_create_inittable(args):
regions_map_path = absolute_path_of_the_file(args.regions_map_path)
description_file_path = absolute_path_of_the_file(args.description_file_path)
init_table_path = absolute_path_of_the_file(args.init_table_path, True)
create_inittable_file(
input_data_path,
regions_map_path,
......@@ -155,8 +155,8 @@ def w_plot_quadrant(args):
worktable_path = absolute_path_of_the_file(args.worktable_path)
plot_path = absolute_path_of_the_file(args.plot_path)
significance_treshold = float(args.significance_treshold)
create_quadrant_plot(worktable_path,
plot_path,
create_quadrant_plot(worktable_path,
plot_path,
significance_treshold=significance_treshold)
......@@ -197,7 +197,7 @@ def get_parser():
parser_create_pd.add_argument(
"--worktable-path", required=True, help="path to the worktable file to generate"
)
parser_create_pd.add_argument("--keep-nans", action="store_true", default=False)
parser_create_pd.add_argument("--remove-nans", action="store_true", default=False)
parser_create_pd.add_argument(
"--manhattan-plot-path",
required=True,
......@@ -237,7 +237,7 @@ def get_parser():
required=False,
help="path to the results file in csv format"
)
parser_create_pd.add_argument(
"--chromosome-number",
required=False,
......@@ -255,7 +255,7 @@ def get_parser():
required=False,
help="option used only for local analysis: end position of the region studied"
)
strategies = parser_create_pd.add_mutually_exclusive_group()
strategies.add_argument("--omnibus", action="store_true", default=True)
strategies.add_argument("--sumz", action="store_true", default=False)
......@@ -336,15 +336,15 @@ def get_parser():
required=False,
help="path to the results file in csv format"
)
parser_create_wt.add_argument(
"--chunk-size",
required=False,
default=50,
help="Number of region to load in memory at once",
)
parser_create_wt.add_argument("--keep-nans", action="store_true", default=False)
parser_create_wt.add_argument("--remove-nans", action="store_true", default=False)
parser_create_wt.add_argument(
"--chromosome-number",
......@@ -363,14 +363,14 @@ def get_parser():
required=False,
help="option used only for local analysis: end position of the region studied"
)
strategies = parser_create_wt.add_mutually_exclusive_group()
strategies.add_argument("--omnibus", action="store_true", default=True)
strategies.add_argument("--sumz", action="store_true", default=False)
strategies.add_argument("--fisher_test", action="store_true", default=False)
strategies.add_argument("--meta_analysis", action="store_true", default=False)
strategies.add_argument("--strategy")
parser_create_wt.set_defaults(func=w_create_worktable)
# ------- plot-manhattan -------
......@@ -385,8 +385,8 @@ def get_parser():
help="path to the worktable file containing the data",
)
parser_create_mp.add_argument(
"--plot-path",
required=True,
"--plot-path",
required=True,
help="path to the manhattan plot file to generate"
)
parser_create_mp.set_defaults(func=w_plot_manhattan)
......@@ -402,8 +402,8 @@ def get_parser():
help="path to the worktable file containing the data",
)
parser_create_mp.add_argument(
"--plot-path",
required=True,
"--plot-path",
required=True,
help="path to the quadrant plot file to generate"
)
parser_create_mp.add_argument(
......@@ -412,7 +412,7 @@ def get_parser():
help="threshold at which a p-value is considered significant"
)
parser_create_mp.set_defaults(func=w_plot_quadrant)
return parser
......
jass/static/chromo_heatmap_manhattan.html
+ 2
− 10
View file @ 4ab149d7
......@@ -28,12 +28,9 @@
<!-- Plotly.js -->
<script src="js/plotly-latest.min.js"></script> <!--https://cdn.plot.ly/plotly-latest.min.js-->
<!--<script src="js/jquery.min.js"></script> http://ajax.googleapis.com/ajax/libs/
jquery/1.8.1/jquery.min.js-->
<script src="js/plotly-latest.min.js"></script>
<script src="https://code.jquery.com/jquery-3.3.1.js"></script>
<script src="js/jquery-ui.js"></script> <!--https://code.jquery.com/ui/1.12.1/jquery-ui.js-->
<script src="js/jquery-ui.js"></script>
<script src="js/snap.svg-min.js"></script>
<script src="js/Chromosome.js"></script>
......@@ -49,7 +46,6 @@
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/js/bootstrap.min.js" ></script>
<!--<script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" ></script>-->
<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script>
<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap.min.js"></script>
<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/select/1.3.0/js/dataTables.select.min.js"></script>
......@@ -63,10 +59,6 @@
<script src="https://cdn.datatables.net/buttons/1.3.1/js/dataTables.buttons.min.js"></script>
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/buttons/1.3.1/css/buttons.dataTables.min.css">
<script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.flash.min.js"></script>
<script src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-MML-AM_CHTML" type="text/javascript"></script>
<!--<script defer language="javascript" src="js/create_genome_full_csv.js" type="text/javascript"> </script>-->
<style>
......
jass/static/directLink.html
+ 156
− 93
View file @ 4ab149d7
<html>
<script src="https://code.jquery.com/jquery-3.2.1.min.js"></script>
<script src="http://malsup.github.io/jquery.blockUI.js"></script>
<script>
function directLink() {
//var phe = ["z_DIAGRAM_T2D", "z_GLG_HDL", "z_GLG_LDL", "z_GLG_TC", "z_GLG_TG"];
//http://jass.pasteur.fr/directLink.html?z_DIAGRAM_T2D,%20z_GLG_HDL,%20z_GLG_LDL,%20z_GLG_TC,%20z_GLG_TG
var phes = extractUrlParam();
//phes ="z_PGC_BIP,z_GIANT_BMI";
//phes ="z_DIAGRAM_T2D,z_GLG_HDL,z_GLG_LDL,z_GLG_TC,z_GLG_TG";
//console.log("!!!!!!!"+phes);
//console.log(phes[0])
var phe = {};
phe['phenotypeID'] =phes;
//var phes = extractUrlParams();
//phes +="";
//var phenotypes = phes.split(',');
//var phenotypes = ["z_C4D_CHD","z_CARDIOGRAM_CHD","z_ICBP_DBP"];
//var monobjet_json = JSON.stringify(phenotypes);
//console.log(monobjet_json);
//sessionStorage.setItem("phenotypes",monobjet_json);
//location.href = 'http://hub17.hosting.pasteur.fr/getVar.html';
//var test =extractUrlParams();
//console.log(test);
//console.log(extractUrlParams());
//location.href = 'chromo_heatmap_manhattan.html';
$.blockUI({ css: {
border: 'none',
padding: '15px',
backgroundColor: '#000',
'-webkit-border-radius': '10px',
'-moz-border-radius': '10px',
opacity: .5,
color: '#fff'} });
var status="-1";
var getProjectStatus = function(){
//$.post( "/api/projects",{'phenotypeID':"z_DIAGRAM_T2D,z_GLG_HDL,z_GLG_LDL,z_GLG_TC,z_GLG_TG"}).done(function( data ) {
$.post( "/api/projects",phe).done(function( data ) {
status = data.status.worktable;
console.log("!! status "+status);
if(status =="READY"){
$.unblockUI();
console.log( data );
sessionStorage.setItem("id",data.id);
console.log(data.phenotypes);
//var monobjet_json = JSON.stringify(data.phenotypes[0]);
var monobjet_json = JSON.stringify(data.phenotypes);
sessionStorage.setItem("phenotypes",monobjet_json);
console.log(data.phenotypes[0]["cohort"]);
//location.href = 'http://hub17.hosting.pasteur.fr/getVar.html';
location.href = 'chromo_heatmap_manhattan.html';
}
else if(status =="CREATING"){
console.log("CREATING");
setTimeout(getProjectStatus, 10000);
}
});
};
getProjectStatus();
}
function extractUrlParam(){
var t = location.search.substring(1).split('=');
return t[1];
}
function extractUrlParams(){
console.log(location.search);
var t = location.search.substring(1).split('&');
var f = [];
for (var i=0; i<t.length; i++){
var x = t[ i ].split('=');
f[x[0]]=x[1];
}
return f;
}
</script>
<body onload="directLink()">
</body>
</html>
<html>
<style>
div.blockMe { padding: 30px; margin: 30px; border: 10px solid #ccc; background-color: #ffd }
#question { background-color: #ffc; padding: 10px; }
#question input { width: 4em ; }
</style>
<script src="https://code.jquery.com/jquery-3.2.1.min.js"></script>
<script src="https://malsup.github.io/jquery.blockUI.js"></script>
<script>
function avancement() {
var ava = document.getElementById("avancement");
var prc = document.getElementById("pourcentage");
prc.innerHTML = ava.value + "%";
}
function modif(val) {
var ava = document.getElementById("avancement");
if((ava.value+val)<=ava.max && (ava.value+val)>0) {
ava.value += val;
}
avancement();
}
function directLink() {
var toApply = 1;
var phe = {};
var url = new URL(window.location.toString());
var search_params = new URLSearchParams(url.search);
if (search_params.has("phenotypes")) {
var phes = search_params.get("phenotypes");
phe['phenotypeID'] = phes;
if (phes == '') {
selectedNumber = 0;
}
else {
selectedNumber = (phes.split(",")).length;
}
console.log("phes='"+phes+"'");
console.log("selectedNumber="+selectedNumber);
if (selectedNumber == 0){
// WARNING: No phenotype is selected !
var User_Message = "𝐖𝐀𝐑𝐍𝐈𝐍𝐆: 𝐏𝐥𝐞𝐚𝐬𝐞 𝐜𝐡𝐨𝐨𝐬𝐞 𝐚𝐧 𝐚𝐫𝐫𝐚𝐲 𝐨𝐟 𝐏𝐡𝐞𝐧𝐨𝐭𝐲𝐩𝐞𝐬..."
alert(User_Message);
toApply = 0;
}
else if (selectedNumber == 1){
// A confirmation window is displayed
var User_Message = "𝐖𝐀𝐑𝐍𝐈𝐍𝐆: 𝐲𝐨𝐮 𝐡𝐚𝐯𝐞 𝐬𝐞𝐥𝐞𝐜𝐭𝐞𝐝 𝐨𝐧𝐥𝐲 𝐨𝐧𝐞 𝐩𝐡𝐞𝐧𝐨𝐭𝐲𝐩𝐞!" +
"\nIt isn't the way JASS normally works.\nDo you want to continue?";
var r = confirm(User_Message);
if (r == true) { // Button OK is selected
toApply = 1;
} else { // Button CANCEL is selected
toApply = 0;
}
}
else if ((selectedNumber > 20) && (selectedNumber <= 64)){
// A confirmation window is displayed
var User_Message = "𝐖𝐀𝐑𝐍𝐈𝐍𝐆: 𝐲𝐨𝐮 𝐡𝐚𝐯𝐞 𝐬𝐞𝐥𝐞𝐜𝐭𝐞𝐝 " +
selectedNumber +
" 𝐩𝐡𝐞𝐧𝐨𝐭𝐲𝐩𝐞𝐬!\nThe computation will be very long. \nDo you want to continue?";
var g = confirm(User_Message);
if (g == true) { // Button OK is selected
toApply = 1;
} else { // Button CANCEL is selected
toApply = 0;
}
}
else if (selectedNumber > 64) {
// ERROR: More than 64 Phenotypes have been selected !
var User_Message = "𝐄𝐑𝐑𝐎𝐑: 𝐲𝐨𝐮 𝐡𝐚𝐯𝐞 𝐬𝐞𝐥𝐞𝐜𝐭𝐞𝐝 " +
selectedNumber +
" 𝐩𝐡𝐞𝐧𝐨𝐭𝐲𝐩𝐞𝐬!\nThe current implementation of JASS cannot analyze more than 64 phenotypes.";
alert(User_Message);
toApply = 0;
}
}
else {
// WARNING: No phenotype is selected !
var User_Message = "𝐖𝐀𝐑𝐍𝐈𝐍𝐆: 𝐏𝐥𝐞𝐚𝐬𝐞 𝐜𝐡𝐨𝐨𝐬𝐞 𝐚𝐧 𝐚𝐫𝐫𝐚𝐲 𝐨𝐟 𝐏𝐡𝐞𝐧𝐨𝐭𝐲𝐩𝐞𝐬..."
alert(User_Message);
toApply = 0;
}
if (toApply == 1){
if (search_params.has("chromosome")) {
var chromosome = search_params.get("chromosome");
// Local analysis
var User_Message =
"Local analysis is not yet implemented in this version of JASS." +
"\nDo not specify a chromosome number and start and end positions";
alert(User_Message);
toApply = 0;
// var Page_to_display = "chromo_heatmap_manhattan_by_region.html"
}
else {
// Whole genome analysis
var Page_to_display = "chromo_heatmap_manhattan.html"
}
if(search_params.has("start")) {
var start = search_params.get("start");
}
if(search_params.has("end")) {
var end = search_params.get("end");
}
}
if (toApply == 1){
$.blockUI({ message: $('#question'), css: { width: '275px' }});
avancement(); //Initialisation
var status = "-1";
var JASS_progress = 0;
var Old_progress = 0;
var getProjectStatus = function(){
$.post( "/api/projects",phe).done(function( data ) {
status = data.status.worktable;
JASS_progress = data.progress;
var deltaProgress = JASS_progress - Old_progress;
Old_progress = JASS_progress;
modif(deltaProgress);
if(status == "READY"){
$.unblockUI();
sessionStorage.setItem("id",data.id);
var monobjet_json = JSON.stringify(data.phenotypes);
sessionStorage.setItem("phenotypes",monobjet_json);
location.href = Page_to_display;
}
else if(status == "CREATING"){
setTimeout(getProjectStatus, 10000);
}
});
};
getProjectStatus();
}
}
</script>
<body onload="directLink()">
<div id="question" style="display:none; cursor: default">
<H3>Analysis in progress ...</H3>
<progress id="avancement" value="0" max="100"></progress>
<span id="pourcentage"></span>
</div>
</body>
</html>
jass/static/export.html
+ 171
− 201
View file @ 4ab149d7
<html>
<head>
<script src="js/jquery.min.js"></script> <!--https://cdn.plot.ly/plotly-latest.min.js-->
<script src="https://cdn.plot.ly/plotly-latest.min.js"></script> <!--https://cdn.plot.ly/plotly-latest.min.js-->
<!--<script src="http://tablesorter.com/addons/pager/jquery.tablesorter.pager.js"></script>-->
<!-- <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/1.10.15/css/jquery.dataTables.css"> -->
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.15/css/jquery.dataTables.min.css">
<script type="text/javascript" charset="utf8" src="//cdn.datatables.net/1.10.15/js/jquery.dataTables.js"></script>
<!-- datatables buttons pdf csv copy -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"></script>
<script src="js/pdfmake.min.js"></script>
<script src="js/vfs_fonts.js"></script>
<script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.html5.min.js"></script>
<script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.print.min.js"></script>
<script src="https://cdn.datatables.net/buttons/1.3.1/js/dataTables.buttons.min.js"></script>
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/buttons/1.3.1/css/buttons.dataTables.min.css">
<script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.flash.min.js"></script>
<script src="http://malsup.github.io/jquery.blockUI.js"></script>
<link rel="stylesheet" href="http://ajax.googleapis.com/ajax/libs/jqueryui/1/themes/smoothness/jquery-ui.css">
<link rel="stylesheet" href="https://research.pasteur.fr/wp-content/themes/biologyx2/style.css" type="text/css" >
<style>
.header {
margin:0 0 30px 0;
padding: 5px 0 0 0 ;
height:50;
background-image: url('/static/img/bkg_part2_wthLabel.jpg');
background-color: transparent;
background-size:contain;
object-fit: contain;
background-repeat:no-repeat;
}
#image-top {height:80!important}
</style>
<script>
var selected = [];
//goToURL();
var typeExport = sessionStorage.getItem("typeExport");
var idProject = sessionStorage.getItem("id");
console.log(idProject);
var selectedRegion = sessionStorage.getItem("selectedRegion");
var selectedChr = sessionStorage.getItem("selectedChr");
console.log(selectedRegion);
console.log(selectedChr);
if(typeExport =="localStat"){
Plotly.d3.csv("/api/projects/"+idProject+"/manhattan/"+selectedChr+"/"+selectedRegion, function(data){ processExportJASSPVAL(data) } );
}
else if (typeExport =="globalStat"){
Plotly.d3.csv("/api/projects/"+idProject+"/genome",
function(data){ processExportGJASSPVAL(data)});
}
else if(typeExport =="heatmap"){
Plotly.d3.csv("/api/projects/"+idProject+"/heatmap/"+selectedChr+"/"+selectedRegion,
function(data){ processExportHeatmap(data) } );
}
function processExportGJASSPVAL(rows) {
console.log("processExportGJASSPVAL rows.length "+rows.length);
console.log(rows[0]);
var columns =["CHR","JOSTmin","MiddlePosition","PVALmin","Region","snp_ids"]
tabulate(rows,columns);
}
function processExportHeatmap(rows) {
console.log("processExportHeatmap rows.length "+rows.length);
var columns =["Region","CHR","position","snp_ids","JASS_PVAL"];
tabulate(rows,columns);
}
function processExportJASSPVAL(rows) {
console.log("processExportJASSPVAL rows.length "+rows.length);
var columns =["Region","CHR","position","snp_ids","JASS_PVAL"];
tabulate(rows,columns);
}
function tabulate(data, columns) {
console.log(data);
//var table = document.createElement("table");
var table = $('#pheTable');
//table.id="pheTable";
var thead = document.createElement("thead");
var tr = document.createElement("tr");
for (var i=0; i<columns.length; i++) {
if ((columns[i] != "ID")&&(columns[i] != "linkRef")){
var th = document.createElement("th");
th.innerHTML =columns[i];
tr.appendChild(th);
}
}
//var th = document.createElement("th");
//th.innerHTML ="Select";
//thead.appendChild(th);
thead.appendChild(tr);
table.append(thead);
//console.log(table);
//var idCounter=1;
var tbody = document.createElement("tbody");
for (var i=0; i<data.length; i++) {
//for (var j=0; j<columns.length; j++) {
//console.log(data[i]);
//console.log("id "+data[i]['ID']);
//}
var tr = document.createElement("tr");
//var val = data[i]['ID'];
//var linkRef = data[i]['linkRef'];
for (var j=0; j<columns.length; j++) {
var td = document.createElement("td");
td.innerHTML=data[i][columns[j]];
tr.append(td);
}
//var td = document.createElement("td");
//td.innerHTML='-';
//var val = data[i]['ID'];
// td.innerHTML= "<input id='chk_" + idCounter + "' name ='type' type='checkbox' value='" + val + "' />";
// idCounter ++;
//tr.append(td);
tbody.appendChild(tr);
}
table.append(tbody);
//header1.setAttribute("class", "header1" );
//return table;
var tmpArray =new Array();
for (var j=0; j<columns.length; j++) {
tmpArray.push({});
}
var table = $('#pheTable').dataTable( {
aoColumns: tmpArray,
dom: 'Bfrtip',
buttons: [
'copy', 'csv', 'pdf'
]
} );
//'copy', 'csv', 'excel', 'pdf'
/*new $.fn.dataTable.Buttons( table, {
buttons: [
{
text: 'Button 2',
action: function ( e, dt, node, conf ) {
alert( 'Button 2 clicked on' );
}
},
{
text: 'Button 3',
action: function ( e, dt, node, conf ) {
alert( 'Button 3 clicked on' );
}
}
]
} );*/
}
</script>
</head>
<body>
<div class="header" > </div>
<h2>Data Table Export</h2>
<div id='divContainer' width ="400px">
<table id ="pheTable" style="width :500px" class="display dataTable"></table>
</div>
<!-- <button id="btn1">Export</button> -->
</body>
</html>
<html>
<head>
<script src="js/jquery.min.js"></script>
<script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.15/css/jquery.dataTables.min.css">
<script type="text/javascript" charset="utf8" src="//cdn.datatables.net/1.10.15/js/jquery.dataTables.js"></script>
<!-- datatables buttons pdf csv copy -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"></script>
<script src="js/pdfmake.min.js"></script>
<script src="js/vfs_fonts.js"></script>
<script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.html5.min.js"></script>
<script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.print.min.js"></script>
<script src="https://cdn.datatables.net/buttons/1.3.1/js/dataTables.buttons.min.js"></script>
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/buttons/1.3.1/css/buttons.dataTables.min.css">
<script src="https://cdn.datatables.net/buttons/1.3.1/js/buttons.flash.min.js"></script>
<script src="https://malsup.github.io/jquery.blockUI.js"></script>
<link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1/themes/smoothness/jquery-ui.css">
<link rel="stylesheet" href="https://research.pasteur.fr/wp-content/themes/biologyx2/style.css" type="text/css" >
<style>
.header {
margin:0 0 30px 0;
padding: 5px 0 0 0 ;
height:50;
background-image: url('/static/img/bkg_part2_wthLabel.jpg');
background-color: transparent;
background-size:contain;
object-fit: contain;
background-repeat:no-repeat;
}
#image-top {height:80!important}
</style>
<script>
var selected = [];
var typeExport = sessionStorage.getItem("typeExport");
var idProject = sessionStorage.getItem("id");
console.log(idProject);
var selectedRegion = sessionStorage.getItem("selectedRegion");
var selectedChr = sessionStorage.getItem("selectedChr");
console.log(selectedRegion);
console.log(selectedChr);
if(typeExport =="localStat"){
Plotly.d3.csv("/api/projects/"+idProject+"/manhattan/"+selectedChr+"/"+selectedRegion, function(data){ processExportJASSPVAL(data) } );
}
else if (typeExport =="globalStat"){
Plotly.d3.csv("/api/projects/"+idProject+"/genome",
function(data){ processExportGJASSPVAL(data)});
}
else if(typeExport =="heatmap"){
Plotly.d3.csv("/api/projects/"+idProject+"/heatmap/"+selectedChr+"/"+selectedRegion,
function(data){ processExportHeatmap(data) } );
}
function processExportGJASSPVAL(rows) {
console.log("processExportGJASSPVAL rows.length "+rows.length);
console.log(rows[0]);
var columns =["CHR","JOSTmin","MiddlePosition","PVALmin","Region","snp_ids"]
tabulate(rows,columns);
}
function processExportHeatmap(rows) {
console.log("processExportHeatmap rows.length "+rows.length);
var columns =["Region","CHR","position","snp_ids","JASS_PVAL"];
tabulate(rows,columns);
}
function processExportJASSPVAL(rows) {
console.log("processExportJASSPVAL rows.length "+rows.length);
var columns =["Region","CHR","position","snp_ids","JASS_PVAL"];
tabulate(rows,columns);
}
function tabulate(data, columns) {
console.log(data);
var table = $('#pheTable');
var thead = document.createElement("thead");
var tr = document.createElement("tr");
for (var i=0; i<columns.length; i++) {
if ((columns[i] != "ID")&&(columns[i] != "linkRef")){
var th = document.createElement("th");
th.innerHTML =columns[i];
tr.appendChild(th);
}
}
thead.appendChild(tr);
table.append(thead);
var tbody = document.createElement("tbody");
for (var i=0; i<data.length; i++) {
var tr = document.createElement("tr");
for (var j=0; j<columns.length; j++) {
var td = document.createElement("td");
td.innerHTML=data[i][columns[j]];
tr.append(td);
}
tbody.appendChild(tr);
}
table.append(tbody);
var tmpArray =new Array();
for (var j=0; j<columns.length; j++) {
tmpArray.push({});
}
var table = $('#pheTable').dataTable( {
aoColumns: tmpArray,
dom: 'Bfrtip',
buttons: [ {
extend: 'csv',
text : 'Export to CSV',
filename: function(){
var d = new Date();
var n = d.getTime();
return 'Data_Table';
},
}]
} );
}
</script>
</head>
<body>
<div class="header" > </div>
<h2>Data Table Export</h2>
<div id='divContainer' width ="400px">
<table id ="pheTable" style="width :500px" class="display dataTable"></table>
</div>
</body>
</html>
jass/static/index.html
+ 3
− 3
View file @ 4ab149d7
......@@ -55,15 +55,15 @@
<div id="tabs-3">
<p><b>JASS: command line and web interface for the joint analysis of GWAS results</b><br />
Hanna Julienne, Pierre Lechat, Vincent Guillemot, Carla Lasry, Chunzi Yao, Robinson Araud, Vincent Laville, Bjarni Vilhjalmsson, Hervé Ménager, Hugues Aschard<br />
in: NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020, lqaa003, <a href="https://doi.org/10.1093/nargab/lqaa003"> <FONT color=#0000FF>https://doi.org/10.1093/nargab/lqaa003</FONT></a></p>
in: NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020, lqaa003, <a href="https://urldefense.com/v3/__https://doi.org/10.1093/nargab/lqaa003__;!!JFdNOqOXpB6UZW0!75infPACk5lQWcBTD-rE5FQb6Yk4WckKROxH7a5qa4ERTDyiliWfWLGe8-HIgjvh3Gk$"> <FONT color=#0000FF>https://doi.org/10.1093/nargab/lqaa003</FONT></a></p>
<p><b>Multitrait genetic-phenotype associations to connect disease variants and biological mechanisms</b><br />
Hanna Julienne, Vincent Laville, Zachary R. McCaw, Zihuai He, Vincent Guillemot, Carla Lasry, Andrey Ziyatdinov, Amaury Vaysse, Pierre Lechat, Hervé Ménager, Wilfried Le Goff, Marie-Pierre Dube, Peter Kraft, Iuliana Ionita-Laza, Bjarni J. Vilhjálmsson, Hugues Aschard<br />
preprint in: biorxiv, <a href=https://www.biorxiv.org/content/10.1101/2020.06.26.172999v1.full> <FONT color=#0000FF>https://www.biorxiv.org/content/10.1101/2020.06.26.172999v1.full</FONT></a></p>
preprint in: biorxiv, <a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2020.06.26.172999v1.full__;!!JFdNOqOXpB6UZW0!75infPACk5lQWcBTD-rE5FQb6Yk4WckKROxH7a5qa4ERTDyiliWfWLGe8-HIV8Z7Cco$"> <FONT color=#0000FF>https://www.biorxiv.org/content/10.1101/2020.06.26.172999v1.full</FONT></a></p>
</div>
</div>
</body>
<footer id="colophon" class="site-footer" role="contentinfo">
<a href="http://www.pasteur.fr/en" target="_blank"><div id="footlogo"></div></a>
<a href="https://www.pasteur.fr/en" target="_blank"><div id="footlogo"></div></a>
</footer>
</html>
jass/static/selectPhenotypes.html
+ 2
− 4
View file @ 4ab149d7
......@@ -7,7 +7,7 @@
<link rel="stylesheet" type="text/css" href="/css/jquery.dataTables.min.css">
<script type="text/javascript" charset="utf8" src="/js/jquery.dataTables.js"></script>
<script src="/js/jquery.blockUI.js"></script>
<link rel="stylesheet" href="http://ajax.googleapis.com/ajax/libs/jqueryui/1/themes/smoothness/jquery-ui.css">
<link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1/themes/smoothness/jquery-ui.css">
<link rel="stylesheet" href="https://research.pasteur.fr/wp-content/themes/biologyx2/style.css" type="text/css" >
<style>
.header {
......@@ -180,11 +180,9 @@
console.log( data );
sessionStorage.setItem("id",data.id);
console.log(data.phenotypes);
//var monobjet_json = JSON.stringify(data.phenotypes[0]);
var monobjet_json = JSON.stringify(data.phenotypes);
var monobjet_json = JSON.stringify(data.phenotypes);
sessionStorage.setItem("phenotypes",monobjet_json);
console.log(data.phenotypes[0]["cohort"]);
//location.href = 'http://hub17.hosting.pasteur.fr/getVar.html';
location.href = 'chromo_heatmap_manhattan.html';
}
else if(status =="CREATING"){
......
requirements.txt
+ 1
− 1
View file @ 4ab149d7
git+https://github.com/hmenager/connexion.git#egg=connexion[swagger-ui]
git+https://github.com/hmenager/connexion.git@master#egg=connexion[swagger-ui]
aiohttp
python_dateutil
setuptools
......
setup.py
+ 12
− 1
View file @ 4ab149d7
......@@ -10,7 +10,18 @@ SETUP_DIR = os.path.dirname(__file__)
README = os.path.join(SETUP_DIR, 'README.md')
readme = open(README).read()
REQUIRES = ["connexion", "python_dateutil", "setuptools", "pandas", "tables", "scipy", "matplotlib", "celery", "h5py", "aiohttp", "numpy"]
REQUIRES = [
"connexion[swagger-ui] @ git+https://github.com/hmenager/connexion.git@master#egg=connexion[swagger-ui]",
"aiohttp",
"python_dateutil",
"setuptools",
"numpy",
"pandas",
"tables",
"scipy",
"matplotlib",
"celery",
]
setup(
name=NAME,
......
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