diff --git a/mutalyzer/templates/base/js/interface.js b/mutalyzer/templates/base/js/interface.js
index be42d8d761caf5f734d48df0d32559bf57c45c1f..fde632138f75e1711a4ea27a1ae588e2d84c412a 100644
--- a/mutalyzer/templates/base/js/interface.js
+++ b/mutalyzer/templates/base/js/interface.js
@@ -3,21 +3,25 @@ function updateVisibility() {
document.getElementById('url_label').style.display = "none";
document.getElementById('gene_label').style.display = "none";
document.getElementById('range_label').style.display = "none";
+ document.getElementById('chrname_label').style.display = "none";
for (i = 0; i < document.invoer.invoermethode.length; i++) {
if (document.invoer.invoermethode[i].checked) {
if (document.invoer.invoermethode[i].value == 'file') {
- file_label.style.display = "";
+ document.getElementById('file_label').style.display = "";
}
else if (document.invoer.invoermethode[i].value == 'url') {
- url_label.style.display = "";
+ document.getElementById('url_label').style.display = "";
}
else if (document.invoer.invoermethode[i].value == 'gene') {
- gene_label.style.display = "";
+ document.getElementById('gene_label').style.display = "";
}
else if (document.invoer.invoermethode[i].value == 'chr') {
- range_label.style.display = "";
- }
+ document.getElementById('range_label').style.display = "";
+ }
+ else if (document.invoer.invoermethode[i].value == 'chrname') {
+ document.getElementById('chrname_label').style.display = "";
+ }
}//if
}//for
}//updateVisibility
@@ -52,7 +56,7 @@ function onloadBatch() {
function getHTTPObject(){
if (window.ActiveXObject)
return new ActiveXObject("Microsoft.XMLHTTP");
- else if (window.XMLHttpRequest)
+ else if (window.XMLHttpRequest)
return new XMLHttpRequest();
else {
alert("Your browser does not support AJAX.");
diff --git a/mutalyzer/templates/gbupload.html b/mutalyzer/templates/gbupload.html
index aabd5efebaf6e6978f52ac0639d080468d7dab5e..67381d3edf0713fb315d19e4651a3f64a3bbfc66 100644
--- a/mutalyzer/templates/gbupload.html
+++ b/mutalyzer/templates/gbupload.html
@@ -36,7 +36,10 @@
Retrieve part of the reference genome for a (HGNC) gene symbol<br>
<input type="radio" name="invoermethode" value='chr'
onClick="updateVisibility();">
- Retrieve a range of a chromosome<br>
+ Retrieve a range of a chromosome by accession number<br>
+ <input type="radio" name="invoermethode" value='chrname'
+ onClick="updateVisibility();">
+ Retrieve a range of a chromosome by name<br>
</td>
</tr>
<tr height="20px"></tr>
@@ -80,21 +83,59 @@
and specify the range</i><br>
<table>
<tr>
- <td>Chromosome Accession Number</td>
+ <td>Chromosome accession number</td>
<td><input type='text' name="chracc"></td>
</tr>
<tr>
- <td>Start Position</td>
+ <td>Start position</td>
<td><input type='text' name="start"></td>
</tr>
<tr>
- <td>Stop Position</td>
+ <td>Stop position</td>
<td><input type='text' name="stop"></td>
</tr>
<tr>
<td>Orientation</td>
<td>
- <select name = "orientation">
+ <select name="orientation">
+ <option value="1">Forward</option>
+ <option value="2">Reverse</option>
+ </select>
+ </td>
+ </tr>
+ </table>
+ </span>
+ <span id="chrname_label">
+ <i>Please enter the name of the chromosome
+ and specify the range</i><br>
+ <table>
+ <tr>
+ <td>Assembly</td>
+ <td>
+ <select name="chrnameassembly">
+ <option tal:repeat = "i available_assemblies"
+ tal:content = "i"
+ tal:attributes = "value i">
+ </option>
+ </select>
+ </td>
+ </tr>
+ <tr>
+ <td>Chromosome name</td>
+ <td><input type='text' name="chrname"></td>
+ </tr>
+ <tr>
+ <td>Start position</td>
+ <td><input type='text' name="chrnamestart"></td>
+ </tr>
+ <tr>
+ <td>Stop position</td>
+ <td><input type='text' name="chrnamestop"></td>
+ </tr>
+ <tr>
+ <td>Orientation</td>
+ <td>
+ <select name="chrnameorientation">
<option value="1">Forward</option>
<option value="2">Reverse</option>
</select>
diff --git a/mutalyzer/templates/menu.html b/mutalyzer/templates/menu.html
index 54b7b39d0be1b824fd66bca3563799dd6521295e..38544d0ea6ef7e16e02de91157280af6dd760860 100644
--- a/mutalyzer/templates/menu.html
+++ b/mutalyzer/templates/menu.html
@@ -19,7 +19,7 @@
<script
type="text/javascript"
language="javascript"
- src="base/js/interface.js">
+ src="base/js/interface.js?20120511">
</script>
<script
type="text/javascript"
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index 2e70fba7648bc5dd78be13edbdc8172a4c6e157c..2c956243546e6475d8ede439cd7f9516b8edb84e 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -571,6 +571,7 @@ class PositionConverter:
'Received request positionConverter(%s, %s) from %s' % (
build, variant, IP))
+ # Todo: check for correct build.
converter = Converter(build, output)
#Convert chr accNo to NC number
@@ -1246,11 +1247,13 @@ class Uploader:
Render reference sequence uploader form.
"""
maxUploadSize = config.get('maxDldSize')
+ available_assemblies = config.get('dbNames')[::-1]
UD, errors = "", []
args = {
- "UD" : UD,
- "maxSize" : float(maxUploadSize) / 1048576,
- "errors" : errors
+ 'UD' : UD,
+ 'available_assemblies' : available_assemblies,
+ 'maxSize' : float(maxUploadSize) / 1048576,
+ 'errors' : errors
}
return render.gbupload(args)
#GET
@@ -1264,10 +1267,12 @@ class Uploader:
1. The reference sequence file is a local file.
2. The reference sequence file can be found at the following URL.
3. Retrieve part of the reference genome for a (HGNC) gene symbol.
- 4. Retrieve a range of a chromosome.
+ 4. Retrieve a range of a chromosome by accession number.
+ 5. Retrieve a range of a chromosome by name.
Parameters:
- - invoermethode: Input method. One of 'file', 'url', 'gene', 'chr'.
+ - invoermethode: Input method. One of 'file', 'url', 'gene', 'chr',
+ 'chrname'.
Depending on the input method, additional parameters are expected.
@@ -1288,8 +1293,16 @@ class Uploader:
- start: Start position.
- stop: Stop position.
- orientation: Orientation.
+
+ Parameters (method 'chrname'):
+ - chrnameassembly: Genome assembly (probably 'hg18' or 'hg19').
+ - chrname: Chromosome name.
+ - chrnamestart: Start position.
+ - chrnamestop: Stop position.
+ - chrnameorientation: Orientation.
"""
maxUploadSize = config.get('maxDldSize')
+ available_assemblies = config.get('dbNames')[::-1]
O = Output(__file__)
IP = web.ctx["ip"]
@@ -1300,13 +1313,16 @@ class Uploader:
i = web.input(invoermethode='', bestandsveld={}, urlveld='',
genesymbol='', organism='', fiveutr='', threeutr='',
- chracc='', start='', stop='', orientation='')
+ chracc='', start='', stop='', orientation='',
+ chrnameassembly='', chrname='', chrnamestart='',
+ chrnamestop='', chrnameorientation='')
O.addMessage(__file__, -1, 'INFO',
'Received request'
- ' upload(%s, %s, %s, %s, %s, %s, %s, %s, %s, %s) from %s' % (
+ ' upload(%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s) from %s' % (
i.invoermethode, i.urlveld, i.genesymbol, i.organism, i.fiveutr,
- i.threeutr, i.chracc, i.start, i.stop, i.orientation, IP))
+ i.threeutr, i.chracc, i.start, i.stop, i.orientation, i.chrnameassembly,
+ i.chrname, i.chrnamestart, i.chrnamestop, i.chrnameorientation, IP))
try:
if i.invoermethode == "file":
@@ -1347,6 +1363,27 @@ class Uploader:
stop = _checkInt(i.stop, "Stop position")
orientation = int(i.orientation)
UD = R.retrieveslice(accNo, start, stop, orientation)
+ elif i.invoermethode == "chrname":
+ build = i.chrnameassembly
+ name = i.chrname
+ start = _checkInt(i.chrnamestart, "Start position")
+ stop = _checkInt(i.chrnamestop, "Stop position")
+ orientation = int(i.chrnameorientation)
+
+ if build not in available_assemblies:
+ raise InputException('Assembly not available: %s' % build)
+
+ if not name.startswith('chr'):
+ name = 'chr%s' % name
+
+ database = Db.Mapping(build)
+ accession = database.chromAcc(name)
+
+ if not accession:
+ raise InputException('Chromosome not available for build %s: %s' %
+ (build, name))
+
+ UD = R.retrieveslice(accession, start, stop, orientation)
else:
#unknown "invoermethode"
raise InputException("Wrong method selected")
@@ -1361,15 +1398,17 @@ class Uploader:
errors.extend(map(lambda m: str(m), O.getMessages()))
args = {
- "UD" : UD,
- "maxSize" : float(maxUploadSize) / 1048576,
- "errors" : errors
+ "UD" : UD,
+ 'available_assemblies' : available_assemblies,
+ "maxSize" : float(maxUploadSize) / 1048576,
+ "errors" : errors
}
O.addMessage(__file__, -1, 'INFO',
- 'Finished request upload(%s, %s, %s, %s, %s, %s, %s, %s, %s, %s)' \
+ 'Finished request upload(%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s)' \
% (i.invoermethode, i.urlveld, i.genesymbol, i.organism,
- i.fiveutr, i.threeutr, i.chracc, i.start, i.stop, i.orientation))
+ i.fiveutr, i.threeutr, i.chracc, i.start, i.stop, i.orientation,
+ i.chrnameassembly, i.chrname, i.chrnamestart, i.chrnamestop, i.chrnameorientation))
return render.gbupload(args)
#POST