From: Diane Trout Date: Thu, 9 Jun 2011 22:38:05 +0000 (-0700) Subject: Add a method to return the runfolder name. X-Git-Tag: 0.5.2~31 X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=6a605ef9924e495094f4e06a8699f97a189cae15 Add a method to return the runfolder name. Add a newer version of the run_*.xml file format for testing Also make sure that the various versions of the run xml file have the same "api". (Its not particularly obvious to use). --- diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py index 35bc037..58f3081 100644 --- a/htsworkflow/pipelines/gerald.py +++ b/htsworkflow/pipelines/gerald.py @@ -140,6 +140,32 @@ class Gerald(object): return time.mktime(self.date.timetuple()) time = property(_get_time, doc='return run time as seconds since epoch') + def _get_experiment_root(self): + if self.tree is None: + return None + return self.tree.findtext('ChipWideRunParameters/EXPT_DIR_ROOT') + + def _get_runfolder_name(self): + if self.tree is None: + return None + + root = self._get_experiment_root() + if root is None: + root = '' + else: + root = os.path.join(root,'') + + experiment_dir = self.tree.findtext('ChipWideRunParameters/EXPT_DIR') + if experiment_dir is None: + return None + experiment_dir = experiment_dir.replace(root, '') + if len(experiment_dir) == 0: + return None + + dirnames = experiment_dir.split(os.path.sep) + return dirnames[0] + runfolder_name = property(_get_runfolder_name) + def _get_version(self): if self.tree is None: return None diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py index 016ae87..78705e5 100644 --- a/htsworkflow/pipelines/runfolder.py +++ b/htsworkflow/pipelines/runfolder.py @@ -75,6 +75,13 @@ class PipelineRun(object): return self._flowcell_id flowcell_id = property(_get_flowcell_id) + def _get_runfolder_name(self): + if self.gerald is None: + return None + else: + return self.gerald.runfolder_name + runfolder_name = property(_get_runfolder_name) + def get_elements(self): """ make one master xml file from all of our sub-components. diff --git a/htsworkflow/pipelines/test/test_load_run_xml.py b/htsworkflow/pipelines/test/test_load_run_xml.py deleted file mode 100644 index 3a8713b..0000000 --- a/htsworkflow/pipelines/test/test_load_run_xml.py +++ /dev/null @@ -1,25 +0,0 @@ -import os -import unittest -from StringIO import StringIO - -from simulate_runfolder import TESTDATA_DIR -from htsworkflow.pipelines.runfolder import load_pipeline_run_xml - -class testLoadRunXML(unittest.TestCase): - def testVerson0(self): - runxml_path = os.path.join(TESTDATA_DIR, 'run_FC12150_2007-09-27.xml') - run = load_pipeline_run_xml(runxml_path) - eland_summary_by_lane = run.gerald.eland_results.results[0] - assert len(eland_summary_by_lane) == 8 - - def testVerson1(self): - runxml_path = os.path.join(TESTDATA_DIR, 'run_207B2AAXX_2008-04-12.xml') - run = load_pipeline_run_xml(runxml_path) - eland_summary_by_lane = run.gerald.eland_results.results[0] - assert len(eland_summary_by_lane) == 8 - -def suite(): - return unittest.makeSuite(testLoadRunXML,'test') - -if __name__ == "__main__": - unittest.main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/test_run_xml.py b/htsworkflow/pipelines/test/test_run_xml.py new file mode 100644 index 0000000..a694ed4 --- /dev/null +++ b/htsworkflow/pipelines/test/test_run_xml.py @@ -0,0 +1,99 @@ +import os +import unittest +from StringIO import StringIO + +from simulate_runfolder import TESTDATA_DIR +from htsworkflow.pipelines.runfolder import load_pipeline_run_xml + +class testLoadRunXML(unittest.TestCase): + + def _check_run_xml(self, run_xml_name, results): + run_xml_path = os.path.join(TESTDATA_DIR, run_xml_name) + run = load_pipeline_run_xml(run_xml_path) + + self.failUnlessEqual(run.image_analysis.start, results['cycle_start']) + self.failUnlessEqual(run.image_analysis.stop, results['cycle_stop']) + + eland_summary_by_lane = run.gerald.eland_results.results[0] + self.failUnlessEqual(len(eland_summary_by_lane), 8) + + runfolder_name = results['runfolder_name'] + self.failUnlessEqual(run.runfolder_name, runfolder_name) + self.failUnlessEqual(run.gerald.runfolder_name, runfolder_name) + + for (end, lane), lane_results in results['lane_results'].items(): + for name, test_value in lane_results.items(): + xml_value = getattr(run.gerald.summary[end][lane], name) + + self.failUnlessEqual(xml_value, test_value, + "%s[%s][%s]: %s %s != %s" % (run_xml_name, end, lane, name, xml_value, test_value)) + + def testVersion0(self): + run_xml_name = 'run_FC12150_2007-09-27.xml' + results = {'runfolder_name': '070924_USI-EAS44_0022_FC12150', + 'cycle_start': 1, + 'cycle_stop': 36, + 'lane_results': { + # end, lane + (0, 1): { + 'average_alignment_score': (12116.63, 596.07), + 'average_first_cycle_intensity': (500,36), + 'cluster': (31261, 6010), + 'cluster_pass_filter': None, + 'percent_error_rate': (2.07, 0.38), + 'percent_intensity_after_20_cycles': (74.74, 3.78), + 'percent_pass_filter_align': None, + 'percent_pass_filter_clusters': (27.38, 7.31), + } + } + } + self._check_run_xml(run_xml_name, results) + + def testVersion1(self): + + run_xml_name = 'run_207B2AAXX_2008-04-12.xml' + results = {'runfolder_name': '080408_HWI-EAS229_0023_207B2AAXX', + 'cycle_start': 1, + 'cycle_stop': 33, + 'lane_results': { + # end, lane + } + } + self._check_run_xml(run_xml_name, results) + + def testVersion2(self): + run_xml_name = 'run_62DJMAAXX_2011-01-09.xml' + results = {'runfolder_name': '101229_ILLUMINA-EC5D15_00026_62DJMAAXX', + 'cycle_start': 1, + 'cycle_stop': 152, + 'lane_results': { + # end, lane + (0, 2): { + 'average_alignment_score': (171.98, 1.4), + 'average_first_cycle_intensity': (381, 5), + 'cluster': (443170, 10241), + 'cluster_pass_filter': (362709, 8335), + 'percent_error_rate': (4.13, 0.14), + 'percent_intensity_after_20_cycles': (85.89, 3.26), + 'percent_pass_filter_align': (79.73, 0.23), + 'percent_pass_filter_clusters': (81.85, 0.8), + }, + (0, 5): { + 'average_alignment_score': None, + 'average_first_cycle_intensity': (362, 4), + 'cluster': (310619, 15946), + 'cluster_pass_filter': (277584, 13858), + 'percent_error_rate': None, + 'percent_intensity_after_20_cycles': (90.35, 1.12), + 'percent_pass_filter_align': None, + 'percent_pass_filter_clusters': (89.37, 0.25), + } + } + } + self._check_run_xml(run_xml_name, results) + +def suite(): + return unittest.makeSuite(testLoadRunXML,'test') + +if __name__ == "__main__": + unittest.main(defaultTest="suite") diff --git a/htsworkflow/pipelines/test/testdata/run_62DJMAAXX_2011-01-09.xml b/htsworkflow/pipelines/test/testdata/run_62DJMAAXX_2011-01-09.xml new file mode 100644 index 0000000..e45cc05 --- /dev/null +++ b/htsworkflow/pipelines/test/testdata/run_62DJMAAXX_2011-01-09.xml @@ -0,0 +1,4297 @@ + + 62DJMAAXX + + 1294547631 + + + + 0 + 0 + 0 + 0 + 0 + + + 0 + 0 + 0 + 0 + 0 + + 1 + 76 + 101229_ILLUMINA-EC5D15_00026_62DJMAAXX + + + 77 + 152 + 101229_ILLUMINA-EC5D15_00026_62DJMAAXX + + ILLUMINA-EC5D15 + 0 + 0 + 0 + 0 + + 1 + 76 + 101229_ILLUMINA-EC5D15_00026_62DJMAAXX + + + 77 + 152 + 101229_ILLUMINA-EC5D15_00026_62DJMAAXX + + 101229_ILLUMINA-EC5D15_00026_62DJMAAXX + 101229 + 00026 + PL14 + + + + + s + 1 + 4 + 7 + 10 + 3 + 2 + 13 + 6 + 5 + 16 + 9 + 8 + 19 + 12 + 11 + 22 + 15 + 14 + 25 + 18 + 17 + 28 + 21 + 20 + 31 + 24 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