htsworkflow/pipelines/test/test_run_xml.py

   1 import os
   2 from unittest import TestCase
   3 from StringIO import StringIO
   4
   5 from simulate_runfolder import TESTDATA_DIR
   6 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
   7
   8 from htsworkflow.pipelines.eland import SampleKey
   9
  10
  11 class testLoadRunXML(TestCase):
  12     def _check_run_xml(self, run_xml_name, results, eland_results=8):
  13         run_xml_path = os.path.join(TESTDATA_DIR, run_xml_name)
  14         run = load_pipeline_run_xml(run_xml_path)
  15
  16         self.failUnlessEqual(run.image_analysis.start, results['cycle_start'])
  17         self.failUnlessEqual(run.image_analysis.stop, results['cycle_stop'])
  18
  19         query = SampleKey(read=1)
  20         eland_summary_by_lane = run.gerald.eland_results.find_keys(query)
  21         self.failUnlessEqual(len(list(eland_summary_by_lane)), eland_results)
  22
  23         runfolder_name = results['runfolder_name']
  24         self.failUnlessEqual(run.runfolder_name, runfolder_name)
  25         self.failUnlessEqual(run.gerald.runfolder_name, runfolder_name)
  26
  27         for (end, lane), lane_results in results['lane_results'].items():
  28             for name, test_value in lane_results.items():
  29                 xml_value = getattr(run.gerald.summary[end][lane], name)
  30
  31                 self.failUnlessEqual(xml_value, test_value,
  32                     "%s[%s][%s]: %s %s != %s" % (run_xml_name, end, lane, name, xml_value, test_value))
  33
  34     def testVersion0(self):
  35         run_xml_name = 'run_FC12150_2007-09-27.xml'
  36         results = {'runfolder_name': '070924_USI-EAS44_0022_FC12150',
  37                    'cycle_start': 1,
  38                    'cycle_stop': 36,
  39                    'lane_results': {
  40                        # end, lane
  41                        (0, 1): {
  42                            'average_alignment_score': (12116.63, 596.07),
  43                            'average_first_cycle_intensity': (500,36),
  44                            'cluster': (31261, 6010),
  45                            'cluster_pass_filter': None,
  46                            'percent_error_rate': (2.07, 0.38),
  47                            'percent_intensity_after_20_cycles': (74.74, 3.78),
  48                            'percent_pass_filter_align': None,
  49                            'percent_pass_filter_clusters': (27.38, 7.31),
  50                            }
  51                        }
  52                    }
  53         self._check_run_xml(run_xml_name, results, eland_results=0)
  54
  55     def testVersion1(self):
  56
  57         run_xml_name = 'run_207B2AAXX_2008-04-12.xml'
  58         results = {'runfolder_name': '080408_HWI-EAS229_0023_207B2AAXX',
  59                    'cycle_start': 1,
  60                    'cycle_stop': 33,
  61                    'lane_results': {
  62                        # end, lane
  63                        }
  64                    }
  65         self._check_run_xml(run_xml_name, results, eland_results=8)
  66
  67     def testVersion2(self):
  68         run_xml_name = 'run_62DJMAAXX_2011-01-09.xml'
  69         results = {'runfolder_name': '101229_ILLUMINA-EC5D15_00026_62DJMAAXX',
  70                    'cycle_start': 1,
  71                    'cycle_stop': 152,
  72                    'lane_results': {
  73                        # end, lane
  74                        (0, 2): {
  75                            'average_alignment_score': (171.98, 1.4),
  76                            'average_first_cycle_intensity': (381, 5),
  77                            'cluster': (443170, 10241),
  78                            'cluster_pass_filter': (362709, 8335),
  79                            'percent_error_rate': (4.13, 0.14),
  80                            'percent_intensity_after_20_cycles': (85.89, 3.26),
  81                            'percent_pass_filter_align': (79.73, 0.23),
  82                            'percent_pass_filter_clusters': (81.85, 0.8),
  83                            },
  84                        (0, 5): {
  85                            'average_alignment_score': None,
  86                            'average_first_cycle_intensity': (362, 4),
  87                            'cluster': (310619, 15946),
  88                            'cluster_pass_filter': (277584, 13858),
  89                            'percent_error_rate': None,
  90                            'percent_intensity_after_20_cycles': (90.35, 1.12),
  91                            'percent_pass_filter_align': None,
  92                            'percent_pass_filter_clusters': (89.37, 0.25),
  93                            }
  94                        }
  95                    }
  96         self._check_run_xml(run_xml_name, results, eland_results=8)
  97
  98
  99 def suite():
 100     from unittest import TestSuite, defaultTestLoader
 101     suite = TestSuite()
 102     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testLoadRunXML))
 103     return suite
 104
 105
 106 if __name__ == "__main__":
 107     from unittest import main
 108     main(defaultTest="suite")