Add color for results zscore ! Add package and doc html! Need to fill it

dridk · Apr 16, 2015 · 3e6130a · 3e6130a
1 parent f11fb91
commit 3e6130a
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Showing 5 changed files with 105 additions and 38 deletions.
diff --git a/IonWisecondor.py b/IonWisecondor.py
@@ -6,7 +6,7 @@
 import subprocess 
 from multiprocessing.pool import Pool
 import glob 
-
+import pickle
 from django.template import Context, Template
 from django.conf import settings
 settings.configure()
@@ -19,29 +19,18 @@ class IonWisecondor(IonPlugin):
 	envDict = dict(os.environ)
 
 
-
-
 	def launch(self, data=None):
 		print("Launch started...")
 
-		#For debugging... 
-		if "RESULTS_DIR" not in os.environ:
-			self.outputDir = "/home/ionadmin/result_dir"
-			self.rootDir="/home/ionadmin/root_dir"
-		else:
-			self.outputDir = os.environ["RESULTS_DIR"];  # The wisecondor results directory
-			self.analysisDir = os.environ["ANALYSIS_DIR"];
-			self.pluginDir = os.environ["PLUGIN_PATH"];
-			self.urlRoot = os.environ["URL_ROOT"]   # /output/Home/X/
-			self.urlPlugin = os.environ["TSP_URLPATH_PLUGIN_DIR"] # /output/Home/X/plugin_out/IonWisecondor
-
-
-
-			print(os.environ["PLUGINCONFIG__COUNT"])
-
-
-
-		#=================Set files dictionnary to send to html report template 
+
+		# ================ GET GLOBAL PATH
+		self.outputDir 		= os.environ["RESULTS_DIR"];  # The wisecondor results directory
+		self.analysisDir 	= os.environ["ANALYSIS_DIR"];
+		self.pluginDir		= os.environ["PLUGIN_PATH"];
+		self.urlRoot 		= os.environ["URL_ROOT"]   # /output/Home/X/
+		self.urlPlugin 		= os.environ["TSP_URLPATH_PLUGIN_DIR"] # /output/Home/X/plugin_out/IonWisecondor
+
+		# ================ GET INSTANCE PARAMETERS AND STORE THEM IN A LIST 
 		fileCount = int(os.environ["PLUGINCONFIG__COUNT"])
 		files = []
 		for i in range(fileCount):
@@ -55,39 +44,64 @@ def launch(self, data=None):
 			item["barcode"] = barcode
  			item["key"]  	= key
 			item["path"] 	= path 
-			# item["name"] = os.path.splitext(os.path.basename(path))[0]
 			item["pickle"] 	= self.urlPlugin + "/" + barcode +"_rawlib.pickle" 
 			item["gcc"] 	= self.urlPlugin + "/" + barcode +"_rawlib.gcc" 
 			item["tested"] 	= self.urlPlugin + "/" + barcode +"_rawlib.tested" 
 			item["pdf"] 	= self.urlPlugin + "/" + barcode +"_rawlib.pdf" 
 
  			files.append(item)
 
-		# ====================Start Computation 
-
+		# ================ LOOP ON EACH FILES AND START COMPUTATION 
 		for item in files:
+			# Launch run.sh 
 			cmd = self.pluginDir+"/run.sh %s %s %s" % (item["path"], self.outputDir, self.pluginDir)
-			print(cmd)
 			p1 = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
 			stdout, stderr = p1.communicate()
-
+			# Check error
 			if p1.returncode == 0:
+				# Compute average of zSmoothDict from barcode_rawlib.tested
+
+				filePath = os.environ["RESULTS_DIR"] + "/" + item["barcode"] + "_rawlib.tested" 
+
+				item["s21"] = self.scoreOf(filePath, "21")
+				item["s18"] = self.scoreOf(filePath, "18")
+				item["s13"] = self.scoreOf(filePath, "13")
+
 				print(stdout)
 			else:
 				raise Exception(stderr)
 
-		# ====================Generate HTML
+
+
+
+
+
+
+		# ================ GENERATE RESULTS HTML FROM DJANGO TEMPLATE SYSTEM
 
 		source = open(os.environ["RUNINFO__PLUGIN__PATH"] + "/block_template.html", "r").read()
 		t = Template(source)
+		# Pass files arguments to the template 
 		c = Context({'files': files})
 		html = t.render(c)
-
+		# Output html render 
 		f = open(self.outputDir+"/resultat_block.html","w")
 		f.write(html)
 		f.close()
 
 
+	def scoreOf(self, testedFile, chrom):
+		with open(testedFile) as file:
+			data 	= pickle.loads(file.read())
+			zScores = data["zSmoothDict"][chrom]
+			score   = -1
+			try:
+				score = sum(zScores) / len(zScores)
+			except :
+				score = -1
+
+		return round(score,2)
+
 
 
 

diff --git a/about.html b/about.html
@@ -0,0 +1,17 @@
+<!DOCTYPE html>
+<html>
+    <body>
+        <h2>Run Transfer Plugin</h2>
+This plugin transfers signal processing output files to another Torrent Server and launches a re-analysis
+of the dataset on that server.  The files that are transferred are Basecaller Input Files.
+<ul>
+    <li>1.wells
+    <li>analysis.bfmask.bin
+    <li>analysis.bfmask.stat
+    <li>average_nuke_trace*.txt
+    <li>Bead_density_*.png
+</ul>
+Proton datasets will transfer block-level files when the thumbnail option is unchecked.  When thumbnail option is checked,
+only the thumbnail files will be transferred.
+    </body>
+</html>
diff --git a/block_template.html b/block_template.html
@@ -5,21 +5,48 @@
 	<link href="/site_media/resources/kendo/styles/kendo.common.min.css" rel="stylesheet">
 	<link href="/site_media/resources/less/kendo.tb.min.css" rel="stylesheet">
 	<link type="text/css" rel="stylesheet" href="/site_media/resources/styles/tb-styles.min.css">
+	<script type="text/javascript" src="/site_media/jquery/js/jquery-1.7.2.min.js"></script>
 
 	<style type="text/css">
 		p, ul{font-family: "Lucida Sans Unicode", "Lucida Grande", Sans-Serif;}
-		.zebra {  background-color: #E1EFFA;}
-		.table_hover{    color: #009;    background-color: #6DBCEE;}
+		.zebra 			{  background-color: #E1EFFA;}
+		.table_hover 	{color: #009;background-color: #6DBCEE;}
+		.k-grid td  	{text-align: center;}
+
+		.green 	{color:#39B54A;}
+		.orange	{color:#F7941D;}
+		.red	{color:#ED1C24;}
 
-		.k-grid td {
-			text-align: center;
-		}
 
 	</style>
 </head>
 
 <body style="background:white">
 
+	<script>
+	$( document ).ready(function() {
+
+	$('.zscore').each(function() {
+	var zscore =parseFloat($(this).text()) ;
+	console.debug(zscore);
+
+	if (zscore < 1.96) 
+		$(this).addClass('green');
+
+	if (zscore >= 1.96 && zscore < 1.96 * 2) 
+		$(this).addClass('orange');
+
+	if (zscore >= 1.96*2) 
+		$(this).addClass('red');
+
+});
+
+	});
+
+
+
+	</script>
+
 
 	<table>
 		<tr><td>Wisecondor version 0.1</td>	<td>0.1</td></tr>
@@ -44,7 +71,10 @@
 				<tr>
 					<th><span class="help" title="Sample name">Barcode Name</span></th>
 					<th><span class="help" title="Number of called variants">Sample</span></th>
-					<th><span class="help" title="Results">Results</span></th>
+					<th><span class="help" title="Chrom21">chrom 21</span></th>
+					<th><span class="help" title="Chrom18">chrom 18</span></th>
+					<th><span class="help" title="Chrom13">chrom 13</span></th>
+
 					<th><span class="help" title="Download links">Download Links</span></th>
 
 				</tr>
@@ -59,7 +89,9 @@
 
 				<td>{{i.sample}}</td>
 
-				<td>sdfsdfsdfsdf</td>
+				<td class="zscore">{{i.s21}}</td>
+				<td class="zscore">{{i.s18}}</td>
+				<td class="zscore">{{i.s13}}</td>
 
 				<td style="text-align:center"><a class="btn" href="{{ i.pickle }}">PICKLE</a>
 					<a class="btn" href="{{ i.tested }}">TESTED</a>

diff --git a/package.json b/package.json
@@ -0,0 +1,2 @@
+{"icon":"etc/icon.png","documentation":"etc/IonWisecondor.pdf","screenshot":"etc/screenshot.png"}
+
diff --git a/run.sh b/run.sh
@@ -1,7 +1,9 @@
 #!/bin/bash
-file_path=$1
-dest_path=$2
-plugin_path=$3
+
+
+file_path=$1									# BAM file path which you want to test 
+dest_path=$2									# Destination folder where results will be stored
+plugin_path=$3									# wisecondor parent PATH to run script from anywhere
 filename=`basename $file_path`
 basename=${filename%.*}