htsworkflow/pipelines/test/test_run_xml.py

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