Add unit test to check that the crosstalk matrix was being saved and reloaded

Aparently if your unit test fails to check something there's no guarantee
that it happens.
Also actually add an implementation for saving the matrix.

diff --git a/htsworkflow/pipelines/bustard.py b/htsworkflow/pipelines/bustard.py
index a8eb4c7b7b3d3b6875b2013a5c6737cf40477f83..91929ec2b07caf99029c709a415e9648e81f3e55 100644 (file)
--- a/htsworkflow/pipelines/bustard.py
+++ b/htsworkflow/pipelines/bustard.py
@@ -189,7 +189,7 @@ class Bustard(object):
         self.date = date.today()
         self.user = None
         self.phasing = {}
-        self.crosstalk = {}
+        self.crosstalk = None
         self.pathname = None
         self.bustard_config = None
 
@@ -215,10 +215,15 @@ class Bustard(object):
         user.text = self.user
         params = ElementTree.SubElement(root, Bustard.PARAMETERS)
 
+        # add phasing parameters
         for lane in LANE_LIST:
             params.append(self.phasing[lane].get_elements())
-            #params.append(self.crosstalk[lane].get_elements())
-        
+
+        # add crosstalk matrix if it exists
+        if self.crosstalk is not None:
+            root.append(self.crosstalk.get_elements())
+       
+        # add bustard config if it exists
         if self.bustard_config is not None:
             root.append(self.bustard_config)
         return root
@@ -240,6 +245,8 @@ class Bustard(object):
                 for param in element:
                     p = Phasing(xml=param)
                     self.phasing[p.lane] = p
+            elif element.tag == CrosstalkMatrix.CROSSTALK:
+                self.crosstalk = CrosstalkMatrix(xml=element)
             elif element.tag == Bustard.BUSTARD_CONFIG:
                 self.bustard_config = element
             else:

diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar130.py b/htsworkflow/pipelines/test/test_runfolder_ipar130.py
index efa6fe1e97409947d251ba6bed110684793f2742..c782e4f642920f01ee0cdeac830cb99f6c140101 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_ipar130.py
+++ b/htsworkflow/pipelines/test/test_runfolder_ipar130.py
@@ -89,6 +89,27 @@ class RunfolderTests(unittest.TestCase):
         """
         construct a bustard object
         """
+        def check_crosstalk(crosstalk):
+            self.failUnlessAlmostEqual(crosstalk.base['A'][0],  1.27)
+            self.failUnlessAlmostEqual(crosstalk.base['A'][1],  0.20999999999999)
+            self.failUnlessAlmostEqual(crosstalk.base['A'][2], -0.02)
+            self.failUnlessAlmostEqual(crosstalk.base['A'][3], -0.03)
+
+            self.failUnlessAlmostEqual(crosstalk.base['C'][0],  0.57)
+            self.failUnlessAlmostEqual(crosstalk.base['C'][1],  0.58)
+            self.failUnlessAlmostEqual(crosstalk.base['C'][2], -0.01)
+            self.failUnlessAlmostEqual(crosstalk.base['C'][3], -0.01)
+
+            self.failUnlessAlmostEqual(crosstalk.base['T'][0], -0.02)
+            self.failUnlessAlmostEqual(crosstalk.base['T'][1], -0.02)
+            self.failUnlessAlmostEqual(crosstalk.base['T'][2],  0.80)
+            self.failUnlessAlmostEqual(crosstalk.base['T'][3],  1.07)
+
+            self.failUnlessAlmostEqual(crosstalk.base['G'][0], -0.03)
+            self.failUnlessAlmostEqual(crosstalk.base['G'][1], -0.04)
+            self.failUnlessAlmostEqual(crosstalk.base['G'][2],  1.51)
+            self.failUnlessAlmostEqual(crosstalk.base['G'][3], -0.02)
+
         b = bustard.bustard(self.bustard_dir)
         self.failUnlessEqual(b.version, '1.3.2')
         self.failUnlessEqual(b.date,    date(2008,3,15))
@@ -96,28 +117,10 @@ class RunfolderTests(unittest.TestCase):
         self.failUnlessEqual(len(b.phasing), 8)
         self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
         self.failUnlessEqual(b.crosstalk.base.keys(), ['A','C','T','G'])
-
-        self.failUnlessAlmostEqual(b.crosstalk.base['A'][0],  1.27)
-        self.failUnlessAlmostEqual(b.crosstalk.base['A'][1],  0.20999999999999)
-        self.failUnlessAlmostEqual(b.crosstalk.base['A'][2], -0.02)
-        self.failUnlessAlmostEqual(b.crosstalk.base['A'][3], -0.03)
-
-        self.failUnlessAlmostEqual(b.crosstalk.base['C'][0],  0.57)
-        self.failUnlessAlmostEqual(b.crosstalk.base['C'][1],  0.58)
-        self.failUnlessAlmostEqual(b.crosstalk.base['C'][2], -0.01)
-        self.failUnlessAlmostEqual(b.crosstalk.base['C'][3], -0.01)
-
-        self.failUnlessAlmostEqual(b.crosstalk.base['T'][0], -0.02)
-        self.failUnlessAlmostEqual(b.crosstalk.base['T'][1], -0.02)
-        self.failUnlessAlmostEqual(b.crosstalk.base['T'][2],  0.80)
-        self.failUnlessAlmostEqual(b.crosstalk.base['T'][3],  1.07)
-
-        self.failUnlessAlmostEqual(b.crosstalk.base['G'][0], -0.03)
-        self.failUnlessAlmostEqual(b.crosstalk.base['G'][1], -0.04)
-        self.failUnlessAlmostEqual(b.crosstalk.base['G'][2],  1.51)
-        self.failUnlessAlmostEqual(b.crosstalk.base['G'][3], -0.02)
+        check_crosstalk(b.crosstalk)
 
         xml = b.get_elements()
+        print ElementTree.dump(xml)
         b2 = bustard.Bustard(xml=xml)
         self.failUnlessEqual(b.version, b2.version)
         self.failUnlessEqual(b.date,    b2.date )
@@ -130,6 +133,7 @@ class RunfolderTests(unittest.TestCase):
                                  b2.phasing[key].phasing)
             self.failUnlessEqual(b.phasing[key].prephasing,
                                  b2.phasing[key].prephasing)
+        check_crosstalk(b2.crosstalk)
 
     def test_gerald(self):
         # need to update gerald and make tests for it