Return a gerald version number as a number and not a cvs string.

[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 0691308229959889fac17ec1149e9b6044c34644..a995c39accf59b3116fe2533cad74851ef9a3e99 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder030.py
+++ b/htsworkflow/pipelines/test/test_runfolder030.py
@@ -14,7 +14,7 @@ from htsworkflow.pipelines.runfolder import ElementTree
 
 from htsworkflow.pipelines.test.simulate_runfolder import *
 
-    
+
 def make_summary_htm(gerald_dir):
     summary_htm="""<!--RUN_TIME Wed Jul  2 06:47:44 2008 -->
 <!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
@@ -627,7 +627,7 @@ def make_eland_results(gerald_dir):
 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA        U1      0       1       0       Lambda.fa        8796855 R       DD      24T
 """
     for i in range(1,9):
-        pathname = os.path.join(gerald_dir, 
+        pathname = os.path.join(gerald_dir,
                                 's_%d_eland_result.txt' % (i,))
         f = open(pathname, 'w')
         f.write(eland_result)
@@ -640,14 +640,14 @@ def make_runfolder(obj=None):
     # make a fake runfolder directory
     temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
 
-    runfolder_dir = os.path.join(temp_dir, 
+    runfolder_dir = os.path.join(temp_dir,
                                  '080102_HWI-EAS229_0010_207BTAAXX')
     os.mkdir(runfolder_dir)
 
     data_dir = os.path.join(runfolder_dir, 'Data')
     os.mkdir(data_dir)
 
-    firecrest_dir = os.path.join(data_dir, 
+    firecrest_dir = os.path.join(data_dir,
                                  'C1-33_Firecrest1.8.28_12-04-2008_diane'
                                  )
     os.mkdir(firecrest_dir)
@@ -656,7 +656,7 @@ def make_runfolder(obj=None):
     matrix_filename = os.path.join(matrix_dir, 's_matrix.txt')
     make_matrix(matrix_filename)
 
-    bustard_dir = os.path.join(firecrest_dir, 
+    bustard_dir = os.path.join(firecrest_dir,
                                'Bustard1.8.28_12-04-2008_diane')
     os.mkdir(bustard_dir)
     make_phasing_params(bustard_dir)
@@ -676,8 +676,8 @@ def make_runfolder(obj=None):
         obj.matrix_dir = matrix_dir
         obj.bustard_dir = bustard_dir
         obj.gerald_dir = gerald_dir
-        
-                     
+
+
 class RunfolderTests(unittest.TestCase):
     """
     Test components of the runfolder processing code
@@ -722,7 +722,7 @@ class RunfolderTests(unittest.TestCase):
         self.failUnlessEqual(b.user,    'diane')
         self.failUnlessEqual(len(b.phasing), 8)
         self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
-        
+
         xml = b.get_elements()
         b2 = bustard.Bustard(xml=xml)
         self.failUnlessEqual(b.version, b2.version)
@@ -730,25 +730,24 @@ class RunfolderTests(unittest.TestCase):
         self.failUnlessEqual(b.user,    b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
         for key in b.phasing.keys():
-            self.failUnlessEqual(b.phasing[key].lane, 
+            self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
-            self.failUnlessEqual(b.phasing[key].phasing, 
+            self.failUnlessEqual(b.phasing[key].phasing,
                                  b2.phasing[key].phasing)
-            self.failUnlessEqual(b.phasing[key].prephasing, 
+            self.failUnlessEqual(b.phasing[key].prephasing,
                                  b2.phasing[key].prephasing)
 
     def test_gerald(self):
         # need to update gerald and make tests for it
-        g = gerald.gerald(self.gerald_dir) 
+        g = gerald.gerald(self.gerald_dir)
 
-        self.failUnlessEqual(g.version, 
-            '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp')
+        self.failUnlessEqual(g.version, '1.68.2.2')
         self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
         self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
         self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
 
-        
-        # list of genomes, matches what was defined up in 
+
+        # list of genomes, matches what was defined up in
         # make_gerald_config.
         # the first None is to offset the genomes list to be 1..9
         # instead of pythons default 0..8
@@ -764,9 +763,9 @@ class RunfolderTests(unittest.TestCase):
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
 
         # test data extracted from summary file
-        clusters = [None, 
-                    (96483, 9074), (133738, 7938), 
-                    (152142, 10002), (15784, 2162), 
+        clusters = [None,
+                    (96483, 9074), (133738, 7938),
+                    (152142, 10002), (15784, 2162),
                     (119735, 8465), (152177, 8146),
                     (84649, 7325), (54622, 4812),]
 
@@ -809,15 +808,15 @@ class RunfolderTests(unittest.TestCase):
             for lane in g_eland.results[0].keys():
                 g_results = g_eland.results[0][lane]
                 g2_results = g2_eland.results[0][lane]
-                self.failUnlessEqual(g_results.reads, 
+                self.failUnlessEqual(g_results.reads,
                                      g2_results.reads)
-                self.failUnlessEqual(len(g_results.mapped_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), 
+                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],
@@ -831,7 +830,7 @@ class RunfolderTests(unittest.TestCase):
         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.results[0][i]
             self.failUnlessEqual(lane.reads, 4)
@@ -863,12 +862,12 @@ class RunfolderTests(unittest.TestCase):
             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], 
+                self.failUnlessEqual(l1.match_codes[k],
                                      l2.match_codes[k])
 
     def test_runfolder(self):
         runs = runfolder.get_runs(self.runfolder_dir)
-        
+
         # do we get the flowcell id from the filename?
         self.failUnlessEqual(len(runs), 1)
         self.failUnlessEqual(runs[0].name, 'run_207BTAAXX_2008-04-19.xml')
@@ -878,7 +877,7 @@ class RunfolderTests(unittest.TestCase):
         runs = runfolder.get_runs(self.runfolder_dir)
         self.failUnlessEqual(len(runs), 1)
         self.failUnlessEqual(runs[0].name, 'run_207BTAAXY_2008-04-19.xml')
-        
+
         r1 = runs[0]
         xml = r1.get_elements()
         xml_str = ElementTree.tostring(xml)
@@ -888,11 +887,11 @@ class RunfolderTests(unittest.TestCase):
         self.failIfEqual(r2.image_analysis, None)
         self.failIfEqual(r2.bustard, None)
         self.failIfEqual(r2.gerald, None)
-        
+
 
 def suite():
     return unittest.makeSuite(RunfolderTests,'test')
 
 if __name__ == "__main__":
     unittest.main(defaultTest="suite")
-    
+