Handle paired-end eland files.

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

diff --git a/htsworkflow/pipelines/test/test_runfolder_pair.py b/htsworkflow/pipelines/test/test_runfolder_pair.py
index 783a5af7ece93c0accd70093503bd9178d120f34..9d8530e6e33f46c018b51b8d8363302231f51a2f 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_pair.py
+++ b/htsworkflow/pipelines/test/test_runfolder_pair.py
@@ -45,7 +45,7 @@ def make_runfolder(obj=None):
     os.mkdir(gerald_dir)
     make_gerald_config(gerald_dir)
     make_summary_paired_htm(gerald_dir)
-    make_eland_multi(gerald_dir)
+    make_eland_multi(gerald_dir, paired=True)
 
     if obj is not None:
         obj.temp_dir = temp_dir
@@ -197,20 +197,22 @@ class RunfolderTests(unittest.TestCase):
 
                 g_eland = g.eland_results
                 g2_eland = g2.eland_results
-                for lane in g_eland.keys():
-                    self.failUnlessEqual(g_eland[lane].reads,
-                                         g2_eland[lane].reads)
-                    self.failUnlessEqual(len(g_eland[lane].mapped_reads),
-                                         len(g2_eland[lane].mapped_reads))
-                    for k in g_eland[lane].mapped_reads.keys():
-                        self.failUnlessEqual(g_eland[lane].mapped_reads[k],
-                                             g2_eland[lane].mapped_reads[k])
-
-                    self.failUnlessEqual(len(g_eland[lane].match_codes),
-                                         len(g2_eland[lane].match_codes))
-                    for k in g_eland[lane].match_codes.keys():
-                        self.failUnlessEqual(g_eland[lane].match_codes[k],
-                                             g2_eland[lane].match_codes[k])
+                for lane in g_eland.results[end].keys():
+                    g_results = g_eland.results[end][lane]
+                    g2_results = g_eland.results[end][lane]
+                    self.failUnlessEqual(g_results.reads,
+                                         g2_results.reads)
+                    self.failUnlessEqual(len(g_results.mapped_reads),
+                                         len(g2_results.mapped_reads))
+                    for k in g_results.mapped_reads.keys():
+                        self.failUnlessEqual(g_results.mapped_reads[k],
+                                             g2_results.mapped_reads[k])
+
+                    self.failUnlessEqual(len(g_results.match_codes),
+                                         len(g2_results.match_codes))
+                    for k in g_results.match_codes.keys():
+                        self.failUnlessEqual(g_results.match_codes[k],
+                                             g2_results.match_codes[k])
 
 
     def test_eland(self):
@@ -224,8 +226,9 @@ class RunfolderTests(unittest.TestCase):
                         5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
         eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
 
+        # check first end
         for i in range(1,9):
-            lane = eland[i]
+            lane = eland.results[0][i]
             self.failUnlessEqual(lane.reads, 4)
             self.failUnlessEqual(lane.sample_name, "s")
             self.failUnlessEqual(lane.lane_id, i)
@@ -240,28 +243,46 @@ class RunfolderTests(unittest.TestCase):
             self.failUnlessEqual(lane.match_codes['NM'], 1)
             self.failUnlessEqual(lane.match_codes['QC'], 0)
 
+        # check second end
+        for i in range(1,9):
+            lane = eland.results[1][i]
+            self.failUnlessEqual(lane.reads, 5)
+            self.failUnlessEqual(lane.sample_name, "s")
+            self.failUnlessEqual(lane.lane_id, i)
+            self.failUnlessEqual(len(lane.mapped_reads), 15)
+            self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
+            self.failUnlessEqual(lane.match_codes['U0'], 1)
+            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'], 1)
+
         xml = eland.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[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)
-            self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
-            self.failUnlessEqual(len(l1.mapped_reads), 15)
-            for k in l1.mapped_reads.keys():
-                self.failUnlessEqual(l1.mapped_reads[k],
-                                     l2.mapped_reads[k])
-
-            self.failUnlessEqual(len(l1.match_codes), 9)
-            self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
-            for k in l1.match_codes.keys():
-                self.failUnlessEqual(l1.match_codes[k],
-                                     l2.match_codes[k])
+        for end in [0, 1]:
+            for i in range(1,9):
+                l1 = eland.results[end][i]
+                l2 = e2.results[end][i]
+                self.failUnlessEqual(l1.reads, l2.reads)
+                self.failUnlessEqual(l1.sample_name, l2.sample_name)
+                self.failUnlessEqual(l1.lane_id, l2.lane_id)
+                self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
+                self.failUnlessEqual(len(l1.mapped_reads), 15)
+                for k in l1.mapped_reads.keys():
+                    self.failUnlessEqual(l1.mapped_reads[k],
+                                         l2.mapped_reads[k])
+
+                self.failUnlessEqual(len(l1.match_codes), 9)
+                self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
+                for k in l1.match_codes.keys():
+                    self.failUnlessEqual(l1.match_codes[k],
+                                         l2.match_codes[k])
 
     def test_runfolder(self):
         runs = runfolder.get_runs(self.runfolder_dir)