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