The summary parsing code now seems to handle paired end runs

[htsworkflow.git] / htsworkflow / pipelines / test / test_runfolder030.py

diff --git a/htsworkflow/pipelines/test/test_runfolder030.py b/htsworkflow/pipelines/test/test_runfolder030.py
index 69227644947635b2e8c1bf870324bc290cc5ad62..6e97ec63eaca3b40574c4162b88a3f62df649915 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder030.py
+++ b/htsworkflow/pipelines/test/test_runfolder030.py
@@ -756,7 +756,7 @@ class RunfolderTests(unittest.TestCase):
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
-            cur_lane = g.lanes[str(i)]
+            cur_lane = g.lanes[i]
             self.failUnlessEqual(cur_lane.analysis, 'eland')
             self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
             self.failUnlessEqual(cur_lane.read_length, '32')
@@ -769,10 +769,11 @@ class RunfolderTests(unittest.TestCase):
                     (119735, 8465), (152177, 8146),
                     (84649, 7325), (54622, 4812),]
 
+        self.failUnlessEqual(len(g.summary), 1)
         for i in range(1,9):
-            summary_lane = g.summary[str(i)]
+            summary_lane = g.summary[0][i]
             self.failUnlessEqual(summary_lane.cluster, clusters[i])
-            self.failUnlessEqual(summary_lane.lane, str(i))
+            self.failUnlessEqual(summary_lane.lane, i)
 
         xml = g.get_elements()
         # just make sure that element tree can serialize the tree
@@ -787,17 +788,18 @@ class RunfolderTests(unittest.TestCase):
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
-            g_lane = g.lanes[str(i)]
-            g2_lane = g2.lanes[str(i)]
+            g_lane = g.lanes[i]
+            g2_lane = g2.lanes[i]
             self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
             self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
             self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
             self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
 
         # test (some) summary elements
+        self.failUnlessEqual(len(g.summary), 1)
         for i in range(1,9):
-            g_summary = g.summary[str(i)]
-            g2_summary = g2.summary[str(i)]
+            g_summary = g.summary[0][i]
+            g2_summary = g2.summary[0][i]
             self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
             self.failUnlessEqual(g_summary.lane, g2_summary.lane)
 
@@ -823,15 +825,15 @@ class RunfolderTests(unittest.TestCase):
         dm3_map = { 'chrUextra.fa' : 'dm3/chrUextra.fa',
                     'chr2L.fa': 'dm3/chr2L.fa',
                     'Lambda.fa': 'Lambda.fa'}
-        genome_maps = { '1':dm3_map, '2':dm3_map, '3':dm3_map, '4':dm3_map,
-                        '5':dm3_map, '6':dm3_map, '7':dm3_map, '8':dm3_map }
+        genome_maps = { 1:dm3_map, 2:dm3_map, 3:dm3_map, 4:dm3_map,
+                        5:dm3_map, 6:dm3_map, 7:dm3_map, 8:dm3_map }
         eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
         
         for i in range(1,9):
-            lane = eland[str(i)]
+            lane = eland[i]
             self.failUnlessEqual(lane.reads, 4)
             self.failUnlessEqual(lane.sample_name, "s")
-            self.failUnlessEqual(lane.lane_id, unicode(i))
+            self.failUnlessEqual(lane.lane_id, i)
             self.failUnlessEqual(len(lane.mapped_reads), 3)
             self.failUnlessEqual(lane.mapped_reads['Lambda.fa'], 1)
             self.failUnlessEqual(lane.mapped_reads['dm3/chr2L.fa'], 1)
@@ -844,8 +846,8 @@ class RunfolderTests(unittest.TestCase):
         e2 = gerald.ELAND(xml=xml)
 
         for i in range(1,9):
-            l1 = eland[str(i)]
-            l2 = e2[str(i)]
+            l1 = eland[i]
+            l2 = e2[i]
             self.failUnlessEqual(l1.reads, l2.reads)
             self.failUnlessEqual(l1.sample_name, l2.sample_name)
             self.failUnlessEqual(l1.lane_id, l2.lane_id)