Massively rework eland file finding and indexing.

[htsworkflow.git] / htsworkflow / pipelines / test / test_runfolder_ipar130.py

diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar130.py b/htsworkflow/pipelines/test/test_runfolder_ipar130.py
index 011a993a484339d7eff1ca88876ca0af73b00f8b..eb018d87db908ba69e31c01f8e8e81b0361f6b96 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_ipar130.py
+++ b/htsworkflow/pipelines/test/test_runfolder_ipar130.py
@@ -224,9 +224,9 @@ class RunfolderTests(unittest.TestCase):
 
             g_eland = g.eland_results
             g2_eland = g2.eland_results
-            for lane in g_eland.results[0].keys():
-                g_results = g_eland.results[0][lane]
-                g2_results = g2_eland.results[0][lane]
+            for key in g_eland:
+                g_results = g_eland[key]
+                g2_results = g2_eland[key]
                 self.failUnlessEqual(g_results.reads,
                                      g2_results.reads)
                 if isinstance(g_results, eland.ElandLane):
@@ -255,44 +255,43 @@ class RunfolderTests(unittest.TestCase):
         eland_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
 
         # I added sequence lanes to the last 2 lanes of this test case
-        for i in range(1,7):
-            lane = eland_container.results[0][i]
-            self.failUnlessEqual(lane.reads, 6)
-            self.failUnlessEqual(lane.sample_name, "s")
-            self.failUnlessEqual(lane.lane_id, i)
-            self.failUnlessEqual(len(lane.mapped_reads), 17)
-            self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
-            self.failUnlessEqual(lane.match_codes['U0'], 3)
-            self.failUnlessEqual(lane.match_codes['R0'], 2)
-            self.failUnlessEqual(lane.match_codes['U1'], 1)
-            self.failUnlessEqual(lane.match_codes['R1'], 9)
-            self.failUnlessEqual(lane.match_codes['U2'], 0)
-            self.failUnlessEqual(lane.match_codes['R2'], 12)
-            self.failUnlessEqual(lane.match_codes['NM'], 1)
-            self.failUnlessEqual(lane.match_codes['QC'], 0)
-
-        # test scarf
-        lane = eland_container.results[0][7]
-        self.failUnlessEqual(lane.reads, 5)
-        self.failUnlessEqual(lane.sample_name, 's')
-        self.failUnlessEqual(lane.lane_id, 7)
-        self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.SCARF_TYPE)
-
-        # test fastq
-        lane = eland_container.results[0][8]
-        self.failUnlessEqual(lane.reads, 3)
-        self.failUnlessEqual(lane.sample_name, 's')
-        self.failUnlessEqual(lane.lane_id, 8)
-        self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.FASTQ_TYPE)
+        for key in eland_container:
+            lane = eland_container[key]
+            if key.lane in [1,2,3,4,5,6]:
+                self.failUnlessEqual(lane.reads, 6)
+                self.failUnlessEqual(lane.sample_name, "s")
+                self.failUnlessEqual(lane.lane_id, key.lane)
+                self.failUnlessEqual(len(lane.mapped_reads), 17)
+                self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
+                self.failUnlessEqual(lane.match_codes['U0'], 3)
+                self.failUnlessEqual(lane.match_codes['R0'], 2)
+                self.failUnlessEqual(lane.match_codes['U1'], 1)
+                self.failUnlessEqual(lane.match_codes['R1'], 9)
+                self.failUnlessEqual(lane.match_codes['U2'], 0)
+                self.failUnlessEqual(lane.match_codes['R2'], 12)
+                self.failUnlessEqual(lane.match_codes['NM'], 1)
+                self.failUnlessEqual(lane.match_codes['QC'], 0)
+            elif key.lane == 7:
+                self.failUnlessEqual(lane.reads, 5)
+                self.failUnlessEqual(lane.sample_name, 's')
+                self.failUnlessEqual(lane.lane_id, 7)
+                self.failUnlessEqual(lane.sequence_type,
+                                     eland.SequenceLane.SCARF_TYPE)
+            elif key.lane == 8:
+                self.failUnlessEqual(lane.reads, 3)
+                self.failUnlessEqual(lane.sample_name, 's')
+                self.failUnlessEqual(lane.lane_id, 8)
+                self.failUnlessEqual(lane.sequence_type,
+                                     eland.SequenceLane.FASTQ_TYPE)
 
         xml = eland_container.get_elements()
         # just make sure that element tree can serialize the tree
         xml_str = ElementTree.tostring(xml)
         e2 = gerald.ELAND(xml=xml)
 
-        for i in range(1,9):
-            l1 = eland_container.results[0][i]
-            l2 = e2.results[0][i]
+        for key in eland_container:
+            l1 = eland_container[key]
+            l2 = e2[key]
             self.failUnlessEqual(l1.reads, l2.reads)
             self.failUnlessEqual(l1.sample_name, l2.sample_name)
             self.failUnlessEqual(l1.lane_id, l2.lane_id)