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Helper to allow regrouping of incoming FASTQs
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‎SequenceAnalysis/resources/web/SequenceAnalysis/panel/SequenceImportPanel.js‎

Lines changed: 200 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1331,7 +1331,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
13311331
grid.getPlugin('cellediting').completeEdit( );
13321332
var s = grid.getSelectionModel().getSelection();
13331333

1334-
if (!s.length){
1334+
if (!s.length) {
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Ext4.Msg.hide();
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Ext4.Msg.alert('Error', 'No records selected');
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return;
@@ -1344,7 +1344,8 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
13441344
}
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13461346
var originals = [];
1347-
for (var i = 0, r; r = s[i]; i++){
1347+
for (var i = 0; i < s.length; i++){
1348+
var r = s[i];
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if (r.get('fileGroupId'))
13491350
originals.push(r.get('fileGroupId'));
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@@ -1392,13 +1393,209 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
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grid.getView().refresh();
13931394
}, this, null, defaultVal);
13941395
}
1396+
},{
1397+
text: 'Regroup By Regex (Advanced)',
1398+
scope: this,
1399+
handler: function (btn) {
1400+
var grid = btn.up('grid');
1401+
grid.getPlugin('cellediting').completeEdit();
1402+
var s = grid.getSelectionModel().getSelection();
1403+
if (!s.length){
1404+
Ext4.Msg.hide();
1405+
Ext4.Msg.alert('Error', 'No records selected');
1406+
return;
1407+
}
1408+
1409+
Ext4.create('Ext.window.Window', {
1410+
title: 'Regroup Selected Records By RegExp',
1411+
bodyStyle: 'padding: 10px;',
1412+
width: 500,
1413+
items: [{
1414+
html: 'This helper allows you to provide a regular expression to extract the file group, and a second expression to extract platformUnit. Any file pairs with the same group will be imported as a single readset. Any files with the same non-null platform unit will be merged. Specifying different platform units can be important for read groups, and downstream operations like MarkDuplicates. Regular expressions will be tested against the first filename in each pair only. For each regex, if not match is found, the original group or platformUnit values is retained.',
1415+
border: false
1416+
},{
1417+
xtype: 'textfield',
1418+
fieldLabel: 'Group RegEx',
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itemId: 'groupEx',
1420+
value: '(.*)_'
1421+
},{
1422+
xtype: 'ldk-integerfield',
1423+
fieldLabel: 'Group Index',
1424+
itemId: 'groupNum',
1425+
value: 1,
1426+
minValue: 0
1427+
},{
1428+
xtype: 'textfield',
1429+
fieldLabel: 'Platform Unit RegEx',
1430+
itemId: 'platformEx',
1431+
value: '(.*)_'
1432+
},{
1433+
xtype: 'ldk-integerfield',
1434+
fieldLabel: 'Platform Index',
1435+
itemId: 'platformNum',
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value: 2,
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minValue: 0
1438+
}],
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buttons: [{
1440+
text: 'Test',
1441+
scope: this,
1442+
handler: function (btn) {
1443+
var groupEx = btn.up('window').down('#groupEx').getValue();
1444+
var groupNum = btn.up('window').down('#groupNum').getValue();
1445+
1446+
var platformEx = btn.up('window').down('#platformEx').getValue();
1447+
var platformNum = btn.up('window').down('#platformNum').getValue();
1448+
1449+
if (groupEx) {
1450+
groupEx = new RegExp(groupEx);
1451+
}
1452+
1453+
if (platformEx) {
1454+
platformEx = new RegExp(platformEx);
1455+
}
1456+
1457+
var rows = [];
1458+
Ext4.Array.forEach(s, function(record){
1459+
var recId = record.get('fileRecord1');
1460+
var data = this.fileNameStore.snapshot || this.fileNameStore.data;
1461+
var fileDataRecIdx = data.findIndexBy(function(r){
1462+
return r.get('id') === recId;
1463+
});
1464+
var fileDataRec = data.getAt(fileDataRecIdx);
1465+
if (!fileDataRec) {
1466+
return;
1467+
}
1468+
1469+
var val = fileDataRec.get('fileName');
1470+
var row = [val, null, null, record];
1471+
if (groupEx) {
1472+
var m = val.match(groupEx);
1473+
if (m && m.length) {
1474+
if (groupNum && groupNum < m.length) {
1475+
row[1] = m[groupNum];
1476+
}
1477+
}
1478+
}
1479+
1480+
if (platformEx) {
1481+
var m = val.match(platformEx);
1482+
if (m && m.length) {
1483+
if (platformNum && platformNum < m.length) {
1484+
row[2] = m[platformNum];
1485+
}
1486+
}
1487+
}
1488+
1489+
rows.push(row);
1490+
}, this);
1491+
1492+
rows.sort(function(a, b){
1493+
if (a[1] > b[1]) return 1;
1494+
if (b[1] > a[1]) return -1;
1495+
1496+
return 0;
1497+
});
1498+
1499+
var dataItems = [{
1500+
html: 'File'
1501+
},{
1502+
html: 'Updated Group'
1503+
},{
1504+
html: 'Updated Platform Unit'
1505+
}];
1506+
1507+
Ext4.Array.forEach(rows, function(r){
1508+
dataItems.push({
1509+
html: r[0]
1510+
});
1511+
1512+
dataItems.push({
1513+
html: r[1] || ''
1514+
});
1515+
1516+
dataItems.push({
1517+
html: r[2] || ''
1518+
});
1519+
}, this);
1520+
Ext4.create('Ext.window.Window', {
1521+
title: 'Preview',
1522+
parentWindow: btn.up('window'),
1523+
width: 800,
1524+
bodyStyle: 'padding: 5px',
1525+
defaults: {
1526+
style: 'padding: 5px;',
1527+
border: false
1528+
},
1529+
layout: {
1530+
type: 'table',
1531+
columns: 3
1532+
},
1533+
items: dataItems,
1534+
buttons: [{
1535+
text: 'Make Changes',
1536+
scope: this,
1537+
handler: function (btn) {
1538+
var win = btn.up('window');
1539+
var parentWindow = win.parentWindow;
1540+
win.close();
1541+
1542+
Ext4.Array.forEach(rows, function(row){
1543+
if (row[2]) {
1544+
row[3].set('platformUnit', row[2]);
1545+
}
1546+
1547+
if (row[1]) {
1548+
row[3].set('fileGroupId', row[1]);
1549+
}
1550+
}, this);
1551+
1552+
//clear/populate readsetStore
1553+
var fileGroupIds = [];
1554+
this.readDataStore.each(function(r){
1555+
fileGroupIds.push(r.get('fileGroupId'));
1556+
}, this);
1557+
fileGroupIds = Ext4.unique(fileGroupIds);
1558+
1559+
this.readsetStore.removeAll();
1560+
1561+
if (fileGroupIds.length){
1562+
var toAdd = [];
1563+
Ext4.Array.forEach(fileGroupIds, function(id){
1564+
toAdd.push(this.readsetStore.createModel({
1565+
fileGroupId: id
1566+
}));
1567+
}, this);
1568+
1569+
this.readsetStore.add(toAdd);
1570+
}
1571+
1572+
parentWindow.close();
1573+
}
1574+
},{
1575+
text: 'Abort',
1576+
scope: this,
1577+
handler: function (btn) {
1578+
btn.up('window').close();
1579+
}
1580+
}]
1581+
1582+
}).show();
1583+
}
1584+
},{
1585+
text: 'Close',
1586+
scope: this,
1587+
handler: function (btn) {
1588+
btn.up('window').close();
1589+
}
1590+
}]
1591+
}).show();
1592+
}
13951593
},{
13961594
text: 'Add Missing Readsets',
13971595
scope: this,
13981596
handler : function(btn) {
13991597
var grid = btn.up('grid');
14001598

1401-
14021599
var fileGroupIds = [];
14031600
this.readDataStore.each(function(r){
14041601
fileGroupIds.push(r.get('fileGroupId'));

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