htsworkflow/pipelines/test/test_run_xml.py

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