From fa0043bebbe796e9ae1b7551a8abebf3068c6e7d Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Mon, 11 Jun 2012 14:34:04 -0700 Subject: [PATCH] Return a gerald version number as a number and not a cvs string. (Also my emacs configuration cleared excess spaces after on several lines) --- htsworkflow/pipelines/gerald.py | 151 ++++++++++-------- htsworkflow/pipelines/runfolder.py | 4 +- .../pipelines/test/test_runfolder026.py | 49 +++--- .../pipelines/test/test_runfolder030.py | 55 ++++--- .../pipelines/test/test_runfolder110.py | 17 +- .../pipelines/test/test_runfolder_ipar100.py | 17 +- .../pipelines/test/test_runfolder_ipar130.py | 17 +- .../pipelines/test/test_runfolder_pair.py | 19 ++- .../pipelines/test/test_runfolder_rta.py | 17 +- .../pipelines/test/test_runfolder_rta160.py | 19 ++- .../pipelines/test/test_runfolder_rta180.py | 19 ++- 11 files changed, 201 insertions(+), 183 deletions(-) diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py index 087edd4..12d8302 100644 --- a/htsworkflow/pipelines/gerald.py +++ b/htsworkflow/pipelines/gerald.py @@ -4,6 +4,7 @@ Provide access to information stored in the GERALD directory. from datetime import datetime, date import logging import os +import re import stat import time @@ -19,18 +20,17 @@ from htsworkflow.util.ethelp import indent, flatten LOGGER = logging.getLogger(__name__) -class Gerald(object): +class Alignment(object): """ Capture meaning out of the GERALD directory """ XML_VERSION = 1 - GERALD='Gerald' RUN_PARAMETERS='RunParameters' SUMMARY='Summary' - def __init__(self, xml=None): - self.pathname = None - self.tree = None + def __init__(self, xml=None, pathname=None, tree=None): + self.pathname = pathname + self.tree = tree # parse lane parameters out of the config.xml file self.lanes = LaneSpecificRunParameters(self) @@ -41,6 +41,56 @@ class Gerald(object): if xml is not None: self.set_elements(xml) + def _get_time(self): + return time.mktime(self.date.timetuple()) + time = property(_get_time, doc='return run time as seconds since epoch') + + def _get_chip_attribute(self, value): + return self.tree.findtext('ChipWideRunParameters/%s' % (value,)) + + def dump(self): + """ + Debugging function, report current object + """ + print 'Software:'. self.__class__.__name__ + print 'Alignment version:', self.version + print 'Run date:', self.date + print 'config.xml:', self.tree + self.summary.dump() + + def get_elements(self): + if self.tree is None or self.summary is None: + return None + + gerald = ElementTree.Element(Gerald.GERALD, + {'version': unicode(Gerald.XML_VERSION)}) + gerald.append(self.tree) + gerald.append(self.summary.get_elements()) + if self.eland_results: + gerald.append(self.eland_results.get_elements()) + return gerald + + def set_elements(self, tree): + if tree.tag != self.__class__.GERALD: + raise ValueError('expected GERALD') + xml_version = int(tree.attrib.get('version', 0)) + if xml_version > Gerald.XML_VERSION: + LOGGER.warn('XML tree is a higher version than this class') + self.eland_results = ELAND() + for element in list(tree): + tag = element.tag.lower() + if tag == Gerald.RUN_PARAMETERS.lower(): + self.tree = element + elif tag == Gerald.SUMMARY.lower(): + self.summary = Summary(xml=element) + elif tag == ELAND.ELAND.lower(): + self.eland_results = ELAND(xml=element) + else: + LOGGER.warn("Unrecognized tag %s" % (element.tag,)) + +class Gerald(Alignment): + GERALD='Gerald' + def _get_date(self): if self.tree is None: return datetime.today() @@ -54,10 +104,6 @@ class Gerald(object): return datetime.today() date = property(_get_date) - def _get_time(self): - 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 @@ -69,13 +115,8 @@ class Gerald(object): expt_root = os.path.normpath(self._get_experiment_root()) chip_expt_dir = self.tree.findtext('ChipWideRunParameters/EXPT_DIR') - # hiseqs renamed the experiment dir location - defaults_expt_dir = self.tree.findtext('Defaults/EXPT_DIR') - experiment_dir = None - if defaults_expt_dir is not None: - _, experiment_dir = os.path.split(defaults_expt_dir) - elif expt_root is not None and chip_expt_dir is not None: + if expt_root is not None and chip_expt_dir is not None: experiment_dir = chip_expt_dir.replace(expt_root+os.path.sep, '') experiment_dir = experiment_dir.split(os.path.sep)[0] @@ -91,54 +132,37 @@ class Gerald(object): ga_version = self.tree.findtext( 'ChipWideRunParameters/SOFTWARE_VERSION') if ga_version is not None: + match = re.match("@.*GERALD.pl,v (?P\d+(\.\d+)+)", + ga_version) + if match: + return match.group('version') return ga_version - hiseq_software_node = self.tree.find('Software') - hiseq_version = hiseq_software_node.attrib['Version'] - return hiseq_version - version = property(_get_version) - def _get_chip_attribute(self, value): - return self.tree.findtext('ChipWideRunParameters/%s' % (value,)) +class CASAVA(Alignment): + GERALD='Casava' - def dump(self): - """ - Debugging function, report current object - """ - print 'Gerald version:', self.version - print 'Gerald run date:', self.date - print 'Gerald config.xml:', self.tree - self.summary.dump() + def _get_runfolder_name(self): + if self.tree is None: + return None - def get_elements(self): - if self.tree is None or self.summary is None: + # hiseqs renamed the experiment dir location + defaults_expt_dir = self.tree.findtext('Defaults/EXPT_DIR') + _, experiment_dir = os.path.split(defaults_expt_dir) + + if experiment_dir is None or len(experiment_dir) == 0: return None + return experiment_dir - gerald = ElementTree.Element(Gerald.GERALD, - {'version': unicode(Gerald.XML_VERSION)}) - gerald.append(self.tree) - gerald.append(self.summary.get_elements()) - if self.eland_results: - gerald.append(self.eland_results.get_elements()) - return gerald + runfolder_name = property(_get_runfolder_name) - def set_elements(self, tree): - if tree.tag != Gerald.GERALD: - raise ValueError('exptected GERALD') - xml_version = int(tree.attrib.get('version', 0)) - if xml_version > Gerald.XML_VERSION: - LOGGER.warn('XML tree is a higher version than this class') - self.eland_results = ELAND() - for element in list(tree): - tag = element.tag.lower() - if tag == Gerald.RUN_PARAMETERS.lower(): - self.tree = element - elif tag == Gerald.SUMMARY.lower(): - self.summary = Summary(xml=element) - elif tag == ELAND.ELAND.lower(): - self.eland_results = ELAND(xml=element) - else: - LOGGER.warn("Unrecognized tag %s" % (element.tag,)) + def _get_version(self): + if self.tree is None: + return None + hiseq_software_node = self.tree.find('Software') + hiseq_version = hiseq_software_node.attrib['Version'] + return hiseq_version + version = property(_get_version) class LaneParameters(object): @@ -321,27 +345,28 @@ class LaneSpecificRunParameters(object): def gerald(pathname): - g = Gerald() - g.pathname = os.path.expanduser(pathname) - path, name = os.path.split(g.pathname) LOGGER.info("Parsing gerald config.xml") - config_pathname = os.path.join(g.pathname, 'config.xml') - g.tree = ElementTree.parse(config_pathname).getroot() + pathname = os.path.expanduser(pathname) + config_pathname = os.path.join(pathname, 'config.xml') + config_tree = ElementTree.parse(config_pathname).getroot() # parse Summary.htm file - summary_xml = os.path.join(g.pathname, 'Summary.xml') - summary_htm = os.path.join(g.pathname, 'Summary.htm') - report_summary = os.path.join(g.pathname, '..', 'Data', + summary_xml = os.path.join(pathname, 'Summary.xml') + summary_htm = os.path.join(pathname, 'Summary.htm') + report_summary = os.path.join(pathname, '..', 'Data', 'reports', 'Summary', ) if os.path.exists(summary_xml): + g = Gerald(pathname = pathname, tree=config_tree) LOGGER.info("Parsing Summary.xml") g.summary = SummaryGA(summary_xml) g.eland_results = eland(g.pathname, g) elif os.path.exists(summary_htm): + g = Gerald(pathname=pathname, tree=config_tree) LOGGER.info("Parsing Summary.htm") g.summary = SummaryGA(summary_htm) g.eland_results = eland(g.pathname, g) elif os.path.isdir(report_summary): + g = CASAVA(pathname=pathname, tree=config_tree) LOGGER.info("Parsing %s" % (report_summary,)) g.summary = SummaryHiSeq(report_summary) diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py index 9edba31..04c1377 100644 --- a/htsworkflow/pipelines/runfolder.py +++ b/htsworkflow/pipelines/runfolder.py @@ -123,6 +123,8 @@ class PipelineRun(object): self.bustard = bustard.Bustard(xml=element) elif tag == gerald.Gerald.GERALD.lower(): self.gerald = gerald.Gerald(xml=element) + elif tag == gerald.CASAVA.GERALD.lower(): + self.gerald = gerald.CASAVA(xml=element) else: LOGGER.warn('PipelineRun unrecognized tag %s' % (tag,)) @@ -212,7 +214,7 @@ def get_runs(runfolder, flowcell_id=None): for aligned in glob(aligned_glob): LOGGER.info("Found aligned directory %s" % (aligned,)) try: - g = gerald.gerald(aligned) + g = gerald.HiSeq(aligned) p = PipelineRun(runfolder, flowcell_id) p.datadir = datadir p.image_analysis = image_analysis diff --git a/htsworkflow/pipelines/test/test_runfolder026.py b/htsworkflow/pipelines/test/test_runfolder026.py index f8160ed..9ab1722 100644 --- a/htsworkflow/pipelines/test/test_runfolder026.py +++ b/htsworkflow/pipelines/test/test_runfolder026.py @@ -222,12 +222,12 @@ def make_eland_results(gerald_dir): >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 Lambda.fa 8796855 R DD 24T """ for i in range(1,9): - pathname = os.path.join(gerald_dir, + pathname = os.path.join(gerald_dir, 's_%d_eland_result.txt' % (i,)) f = open(pathname, 'w') f.write(eland_result) f.close() - + class RunfolderTests(unittest.TestCase): """ Test components of the runfolder processing code @@ -237,14 +237,14 @@ class RunfolderTests(unittest.TestCase): # make a fake runfolder directory self.temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_') - self.runfolder_dir = os.path.join(self.temp_dir, + self.runfolder_dir = os.path.join(self.temp_dir, '080102_HWI-EAS229_0010_207BTAAXX') os.mkdir(self.runfolder_dir) self.data_dir = os.path.join(self.runfolder_dir, 'Data') os.mkdir(self.data_dir) - self.firecrest_dir = os.path.join(self.data_dir, + self.firecrest_dir = os.path.join(self.data_dir, 'C1-33_Firecrest1.8.28_12-04-2008_diane' ) os.mkdir(self.firecrest_dir) @@ -253,11 +253,11 @@ class RunfolderTests(unittest.TestCase): matrix_filename = os.path.join(self.matrix_dir, 's_matrix') make_matrix(matrix_filename) - self.bustard_dir = os.path.join(self.firecrest_dir, + self.bustard_dir = os.path.join(self.firecrest_dir, 'Bustard1.8.28_12-04-2008_diane') os.mkdir(self.bustard_dir) make_phasing_params(self.bustard_dir) - + self.gerald_dir = os.path.join(self.bustard_dir, 'GERALD_12-04-2008_diane') os.mkdir(self.gerald_dir) @@ -300,7 +300,7 @@ class RunfolderTests(unittest.TestCase): self.failUnlessEqual(b.user, 'diane') self.failUnlessEqual(len(b.phasing), 8) self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099) - + xml = b.get_elements() b2 = bustard.Bustard(xml=xml) self.failUnlessEqual(b.version, b2.version) @@ -308,25 +308,24 @@ class RunfolderTests(unittest.TestCase): self.failUnlessEqual(b.user, b2.user) self.failUnlessEqual(len(b.phasing), len(b2.phasing)) for key in b.phasing.keys(): - self.failUnlessEqual(b.phasing[key].lane, + self.failUnlessEqual(b.phasing[key].lane, b2.phasing[key].lane) - self.failUnlessEqual(b.phasing[key].phasing, + self.failUnlessEqual(b.phasing[key].phasing, b2.phasing[key].phasing) - self.failUnlessEqual(b.phasing[key].prephasing, + self.failUnlessEqual(b.phasing[key].prephasing, b2.phasing[key].prephasing) def test_gerald(self): # need to update gerald and make tests for it - g = gerald.gerald(self.gerald_dir) + g = gerald.gerald(self.gerald_dir) - self.failUnlessEqual(g.version, - '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp') + self.failUnlessEqual(g.version, '1.68.2.2') self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30)) self.failUnlessEqual(len(g.lanes), len(g.lanes.keys())) self.failUnlessEqual(len(g.lanes), len(g.lanes.items())) - - # list of genomes, matches what was defined up in + + # list of genomes, matches what was defined up in # make_gerald_config. # the first None is to offset the genomes list to be 1..9 # instead of pythons default 0..8 @@ -342,7 +341,7 @@ class RunfolderTests(unittest.TestCase): self.failUnlessEqual(cur_lane.use_bases, 'Y'*32) # test data extracted from summary file - clusters = [None, + clusters = [None, (17421, 2139), (20311, 2402), (20193, 2399), (15537, 2531), (32047, 3356), (32946, 4753), (39504, 4171), (37998, 3792)] @@ -385,15 +384,15 @@ class RunfolderTests(unittest.TestCase): for lane in g_eland.results[0].keys(): g_results = g_eland.results[0][lane] g2_results = g2_eland.results[0][lane] - self.failUnlessEqual(g_results.reads, + self.failUnlessEqual(g_results.reads, g2_results.reads) - self.failUnlessEqual(len(g_results.mapped_reads), + self.failUnlessEqual(len(g_results.mapped_reads), len(g2_results.mapped_reads)) for k in g_results.mapped_reads.keys(): self.failUnlessEqual(g_results.mapped_reads[k], g2_results.mapped_reads[k]) - self.failUnlessEqual(len(g_results.match_codes), + self.failUnlessEqual(len(g_results.match_codes), len(g2_results.match_codes)) for k in g_results.match_codes.keys(): self.failUnlessEqual(g_results.match_codes[k], @@ -407,7 +406,7 @@ class RunfolderTests(unittest.TestCase): genome_maps = { 1:dm3_map, 2:dm3_map, 3:dm3_map, 4:dm3_map, 5:dm3_map, 6:dm3_map, 7:dm3_map, 8:dm3_map } eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps) - + for i in range(1,9): lane = eland.results[0][i] self.failUnlessEqual(lane.reads, 4) @@ -439,12 +438,12 @@ class RunfolderTests(unittest.TestCase): self.failUnlessEqual(len(l1.match_codes), 9) self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes)) for k in l1.match_codes.keys(): - self.failUnlessEqual(l1.match_codes[k], + self.failUnlessEqual(l1.match_codes[k], l2.match_codes[k]) def test_runfolder(self): runs = runfolder.get_runs(self.runfolder_dir) - + # do we get the flowcell id from the filename? self.failUnlessEqual(len(runs), 1) self.failUnlessEqual(runs[0].name, 'run_207BTAAXX_2008-04-19.xml') @@ -454,7 +453,7 @@ class RunfolderTests(unittest.TestCase): runs = runfolder.get_runs(self.runfolder_dir) self.failUnlessEqual(len(runs), 1) self.failUnlessEqual(runs[0].name, 'run_207BTAAXY_2008-04-19.xml') - + r1 = runs[0] xml = r1.get_elements() xml_str = ElementTree.tostring(xml) @@ -464,11 +463,11 @@ class RunfolderTests(unittest.TestCase): self.failIfEqual(r2.image_analysis, None) self.failIfEqual(r2.bustard, None) self.failIfEqual(r2.gerald, None) - + def suite(): return unittest.makeSuite(RunfolderTests,'test') if __name__ == "__main__": unittest.main(defaultTest="suite") - + diff --git a/htsworkflow/pipelines/test/test_runfolder030.py b/htsworkflow/pipelines/test/test_runfolder030.py index 0691308..a995c39 100644 --- a/htsworkflow/pipelines/test/test_runfolder030.py +++ b/htsworkflow/pipelines/test/test_runfolder030.py @@ -14,7 +14,7 @@ from htsworkflow.pipelines.runfolder import ElementTree from htsworkflow.pipelines.test.simulate_runfolder import * - + def make_summary_htm(gerald_dir): summary_htm=""" @@ -627,7 +627,7 @@ def make_eland_results(gerald_dir): >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 Lambda.fa 8796855 R DD 24T """ for i in range(1,9): - pathname = os.path.join(gerald_dir, + pathname = os.path.join(gerald_dir, 's_%d_eland_result.txt' % (i,)) f = open(pathname, 'w') f.write(eland_result) @@ -640,14 +640,14 @@ def make_runfolder(obj=None): # make a fake runfolder directory temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_') - runfolder_dir = os.path.join(temp_dir, + runfolder_dir = os.path.join(temp_dir, '080102_HWI-EAS229_0010_207BTAAXX') os.mkdir(runfolder_dir) data_dir = os.path.join(runfolder_dir, 'Data') os.mkdir(data_dir) - firecrest_dir = os.path.join(data_dir, + firecrest_dir = os.path.join(data_dir, 'C1-33_Firecrest1.8.28_12-04-2008_diane' ) os.mkdir(firecrest_dir) @@ -656,7 +656,7 @@ def make_runfolder(obj=None): matrix_filename = os.path.join(matrix_dir, 's_matrix.txt') make_matrix(matrix_filename) - bustard_dir = os.path.join(firecrest_dir, + bustard_dir = os.path.join(firecrest_dir, 'Bustard1.8.28_12-04-2008_diane') os.mkdir(bustard_dir) make_phasing_params(bustard_dir) @@ -676,8 +676,8 @@ def make_runfolder(obj=None): obj.matrix_dir = matrix_dir obj.bustard_dir = bustard_dir obj.gerald_dir = gerald_dir - - + + class RunfolderTests(unittest.TestCase): """ Test components of the runfolder processing code @@ -722,7 +722,7 @@ class RunfolderTests(unittest.TestCase): self.failUnlessEqual(b.user, 'diane') self.failUnlessEqual(len(b.phasing), 8) self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099) - + xml = b.get_elements() b2 = bustard.Bustard(xml=xml) self.failUnlessEqual(b.version, b2.version) @@ -730,25 +730,24 @@ class RunfolderTests(unittest.TestCase): self.failUnlessEqual(b.user, b2.user) self.failUnlessEqual(len(b.phasing), len(b2.phasing)) for key in b.phasing.keys(): - self.failUnlessEqual(b.phasing[key].lane, + self.failUnlessEqual(b.phasing[key].lane, b2.phasing[key].lane) - self.failUnlessEqual(b.phasing[key].phasing, + self.failUnlessEqual(b.phasing[key].phasing, b2.phasing[key].phasing) - self.failUnlessEqual(b.phasing[key].prephasing, + self.failUnlessEqual(b.phasing[key].prephasing, b2.phasing[key].prephasing) def test_gerald(self): # need to update gerald and make tests for it - g = gerald.gerald(self.gerald_dir) + g = gerald.gerald(self.gerald_dir) - self.failUnlessEqual(g.version, - '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp') + self.failUnlessEqual(g.version, '1.68.2.2') self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30)) self.failUnlessEqual(len(g.lanes), len(g.lanes.keys())) self.failUnlessEqual(len(g.lanes), len(g.lanes.items())) - - # list of genomes, matches what was defined up in + + # list of genomes, matches what was defined up in # make_gerald_config. # the first None is to offset the genomes list to be 1..9 # instead of pythons default 0..8 @@ -764,9 +763,9 @@ class RunfolderTests(unittest.TestCase): self.failUnlessEqual(cur_lane.use_bases, 'Y'*32) # test data extracted from summary file - clusters = [None, - (96483, 9074), (133738, 7938), - (152142, 10002), (15784, 2162), + clusters = [None, + (96483, 9074), (133738, 7938), + (152142, 10002), (15784, 2162), (119735, 8465), (152177, 8146), (84649, 7325), (54622, 4812),] @@ -809,15 +808,15 @@ class RunfolderTests(unittest.TestCase): for lane in g_eland.results[0].keys(): g_results = g_eland.results[0][lane] g2_results = g2_eland.results[0][lane] - self.failUnlessEqual(g_results.reads, + self.failUnlessEqual(g_results.reads, g2_results.reads) - self.failUnlessEqual(len(g_results.mapped_reads), + self.failUnlessEqual(len(g_results.mapped_reads), len(g2_results.mapped_reads)) for k in g_results.mapped_reads.keys(): self.failUnlessEqual(g_results.mapped_reads[k], g2_results.mapped_reads[k]) - self.failUnlessEqual(len(g_results.match_codes), + self.failUnlessEqual(len(g_results.match_codes), len(g2_results.match_codes)) for k in g_results.match_codes.keys(): self.failUnlessEqual(g_results.match_codes[k], @@ -831,7 +830,7 @@ class RunfolderTests(unittest.TestCase): genome_maps = { 1:dm3_map, 2:dm3_map, 3:dm3_map, 4:dm3_map, 5:dm3_map, 6:dm3_map, 7:dm3_map, 8:dm3_map } eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps) - + for i in range(1,9): lane = eland.results[0][i] self.failUnlessEqual(lane.reads, 4) @@ -863,12 +862,12 @@ class RunfolderTests(unittest.TestCase): self.failUnlessEqual(len(l1.match_codes), 9) self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes)) for k in l1.match_codes.keys(): - self.failUnlessEqual(l1.match_codes[k], + self.failUnlessEqual(l1.match_codes[k], l2.match_codes[k]) def test_runfolder(self): runs = runfolder.get_runs(self.runfolder_dir) - + # do we get the flowcell id from the filename? self.failUnlessEqual(len(runs), 1) self.failUnlessEqual(runs[0].name, 'run_207BTAAXX_2008-04-19.xml') @@ -878,7 +877,7 @@ class RunfolderTests(unittest.TestCase): runs = runfolder.get_runs(self.runfolder_dir) self.failUnlessEqual(len(runs), 1) self.failUnlessEqual(runs[0].name, 'run_207BTAAXY_2008-04-19.xml') - + r1 = runs[0] xml = r1.get_elements() xml_str = ElementTree.tostring(xml) @@ -888,11 +887,11 @@ class RunfolderTests(unittest.TestCase): self.failIfEqual(r2.image_analysis, None) self.failIfEqual(r2.bustard, None) self.failIfEqual(r2.gerald, None) - + def suite(): return unittest.makeSuite(RunfolderTests,'test') if __name__ == "__main__": unittest.main(defaultTest="suite") - + diff --git a/htsworkflow/pipelines/test/test_runfolder110.py b/htsworkflow/pipelines/test/test_runfolder110.py index fc91ce4..d9c57a0 100644 --- a/htsworkflow/pipelines/test/test_runfolder110.py +++ b/htsworkflow/pipelines/test/test_runfolder110.py @@ -120,8 +120,7 @@ class RunfolderTests(unittest.TestCase): # need to update gerald and make tests for it g = gerald.gerald(self.gerald_dir) - self.failUnlessEqual(g.version, - '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp') + self.failUnlessEqual(g.version, '1.171') self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59)) self.failUnlessEqual(len(g.lanes), len(g.lanes.keys())) self.failUnlessEqual(len(g.lanes), len(g.lanes.items())) @@ -131,14 +130,14 @@ class RunfolderTests(unittest.TestCase): # make_gerald_config. # the first None is to offset the genomes list to be 1..9 # instead of pythons default 0..8 - genomes = [None, - '/g/mm9', - '/g/mm9', - '/g/elegans190', + genomes = [None, + '/g/mm9', + '/g/mm9', + '/g/elegans190', '/g/arabidopsis01222004', - '/g/mm9', - '/g/mm9', - '/g/mm9', + '/g/mm9', + '/g/mm9', + '/g/mm9', '/g/mm9', ] # test lane specific parameters from gerald config file diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar100.py b/htsworkflow/pipelines/test/test_runfolder_ipar100.py index d58a70d..ec647b8 100644 --- a/htsworkflow/pipelines/test/test_runfolder_ipar100.py +++ b/htsworkflow/pipelines/test/test_runfolder_ipar100.py @@ -119,8 +119,7 @@ class RunfolderTests(unittest.TestCase): # need to update gerald and make tests for it g = gerald.gerald(self.gerald_dir) - self.failUnlessEqual(g.version, - '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp') + self.failUnlessEqual(g.version, '1.171') self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59)) self.failUnlessEqual(len(g.lanes), len(g.lanes.keys())) self.failUnlessEqual(len(g.lanes), len(g.lanes.items())) @@ -130,14 +129,14 @@ class RunfolderTests(unittest.TestCase): # make_gerald_config. # the first None is to offset the genomes list to be 1..9 # instead of pythons default 0..8 - genomes = [None, - '/g/mm9', - '/g/mm9', - '/g/elegans190', + genomes = [None, + '/g/mm9', + '/g/mm9', + '/g/elegans190', '/g/arabidopsis01222004', - '/g/mm9', - '/g/mm9', - '/g/mm9', + '/g/mm9', + '/g/mm9', + '/g/mm9', '/g/mm9', ] # test lane specific parameters from gerald config file diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar130.py b/htsworkflow/pipelines/test/test_runfolder_ipar130.py index 13011ba..46a26f0 100644 --- a/htsworkflow/pipelines/test/test_runfolder_ipar130.py +++ b/htsworkflow/pipelines/test/test_runfolder_ipar130.py @@ -141,8 +141,7 @@ class RunfolderTests(unittest.TestCase): # need to update gerald and make tests for it g = gerald.gerald(self.gerald_dir) - self.failUnlessEqual(g.version, - '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp') + self.failUnlessEqual(g.version, '1.171') self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59)) self.failUnlessEqual(len(g.lanes), len(g.lanes.keys())) self.failUnlessEqual(len(g.lanes), len(g.lanes.items())) @@ -152,14 +151,14 @@ class RunfolderTests(unittest.TestCase): # make_gerald_config. # the first None is to offset the genomes list to be 1..9 # instead of pythons default 0..8 - genomes = [None, - '/g/mm9', - '/g/mm9', - '/g/elegans190', + genomes = [None, + '/g/mm9', + '/g/mm9', + '/g/elegans190', '/g/arabidopsis01222004', - '/g/mm9', - '/g/mm9', - '/g/mm9', + '/g/mm9', + '/g/mm9', + '/g/mm9', '/g/mm9', ] # test lane specific parameters from gerald config file diff --git a/htsworkflow/pipelines/test/test_runfolder_pair.py b/htsworkflow/pipelines/test/test_runfolder_pair.py index c0fb684..1ef2797 100644 --- a/htsworkflow/pipelines/test/test_runfolder_pair.py +++ b/htsworkflow/pipelines/test/test_runfolder_pair.py @@ -79,7 +79,7 @@ class RunfolderTests(unittest.TestCase): self.failUnlessEqual(f.start, 1) self.failUnlessEqual(f.stop, 152) self.failUnlessEqual(f.user, 'diane') - # As of 2008-12-8, the date was being set in + # As of 2008-12-8, the date was being set in # simulate_runfolder.make_firecrest_dir self.failUnlessEqual(f.date, date(2008,4,12)) @@ -122,8 +122,7 @@ class RunfolderTests(unittest.TestCase): # need to update gerald and make tests for it g = gerald.gerald(self.gerald_dir) - self.failUnlessEqual(g.version, - '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp') + self.failUnlessEqual(g.version, '1.171') self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59)) self.failUnlessEqual(len(g.lanes), len(g.lanes.keys())) self.failUnlessEqual(len(g.lanes), len(g.lanes.items())) @@ -133,14 +132,14 @@ class RunfolderTests(unittest.TestCase): # make_gerald_config. # the first None is to offset the genomes list to be 1..9 # instead of pythons default 0..8 - genomes = [None, - '/g/mm9', - '/g/mm9', - '/g/elegans190', + genomes = [None, + '/g/mm9', + '/g/mm9', + '/g/elegans190', '/g/arabidopsis01222004', - '/g/mm9', - '/g/mm9', - '/g/mm9', + '/g/mm9', + '/g/mm9', + '/g/mm9', '/g/mm9', ] # test lane specific parameters from gerald config file diff --git a/htsworkflow/pipelines/test/test_runfolder_rta.py b/htsworkflow/pipelines/test/test_runfolder_rta.py index 08db8e2..02b8e44 100644 --- a/htsworkflow/pipelines/test/test_runfolder_rta.py +++ b/htsworkflow/pipelines/test/test_runfolder_rta.py @@ -106,8 +106,7 @@ class RunfolderTests(unittest.TestCase): # need to update gerald and make tests for it g = gerald.gerald(self.gerald_dir) - self.failUnlessEqual(g.version, - '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp') + self.failUnlessEqual(g.version, '1.171') self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59)) self.failUnlessEqual(len(g.lanes), len(g.lanes.keys())) self.failUnlessEqual(len(g.lanes), len(g.lanes.items())) @@ -117,14 +116,14 @@ class RunfolderTests(unittest.TestCase): # make_gerald_config. # the first None is to offset the genomes list to be 1..9 # instead of pythons default 0..8 - genomes = [None, - '/g/mm9', - '/g/mm9', - '/g/elegans190', + genomes = [None, + '/g/mm9', + '/g/mm9', + '/g/elegans190', '/g/arabidopsis01222004', - '/g/mm9', - '/g/mm9', - '/g/mm9', + '/g/mm9', + '/g/mm9', + '/g/mm9', '/g/mm9', ] # test lane specific parameters from gerald config file diff --git a/htsworkflow/pipelines/test/test_runfolder_rta160.py b/htsworkflow/pipelines/test/test_runfolder_rta160.py index d446e49..75ca37e 100644 --- a/htsworkflow/pipelines/test/test_runfolder_rta160.py +++ b/htsworkflow/pipelines/test/test_runfolder_rta160.py @@ -70,13 +70,12 @@ class RunfolderTests(unittest.TestCase): # The only thing different from the previous RTA version is # I'm processing the Summary.xml file - + def test_gerald(self): # need to update gerald and make tests for it g = gerald.gerald(self.gerald_dir) - self.failUnlessEqual(g.version, - '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp') + self.failUnlessEqual(g.version, '1.171') self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59)) self.failUnlessEqual(len(g.lanes), len(g.lanes.keys())) self.failUnlessEqual(len(g.lanes), len(g.lanes.items())) @@ -86,14 +85,14 @@ class RunfolderTests(unittest.TestCase): # make_gerald_config. # the first None is to offset the genomes list to be 1..9 # instead of pythons default 0..8 - genomes = [None, - '/g/mm9', - '/g/mm9', - '/g/elegans190', + genomes = [None, + '/g/mm9', + '/g/mm9', + '/g/elegans190', '/g/arabidopsis01222004', - '/g/mm9', - '/g/mm9', - '/g/mm9', + '/g/mm9', + '/g/mm9', + '/g/mm9', '/g/mm9', ] # test lane specific parameters from gerald config file diff --git a/htsworkflow/pipelines/test/test_runfolder_rta180.py b/htsworkflow/pipelines/test/test_runfolder_rta180.py index 7475b36..5cb2822 100644 --- a/htsworkflow/pipelines/test/test_runfolder_rta180.py +++ b/htsworkflow/pipelines/test/test_runfolder_rta180.py @@ -78,13 +78,12 @@ class RunfolderTests(unittest.TestCase): self.failUnlessEqual(b.version, b2.version) self.failUnlessEqual(b.date, b2.date ) self.failUnlessEqual(b.user, b2.user) - + def test_gerald(self): # need to update gerald and make tests for it g = gerald.gerald(self.gerald_dir) - self.failUnlessEqual(g.version, - '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp') + self.failUnlessEqual(g.version, '1.171') self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59)) self.failUnlessEqual(len(g.lanes), len(g.lanes.keys())) self.failUnlessEqual(len(g.lanes), len(g.lanes.items())) @@ -94,14 +93,14 @@ class RunfolderTests(unittest.TestCase): # make_gerald_config. # the first None is to offset the genomes list to be 1..9 # instead of pythons default 0..8 - genomes = [None, - '/g/mm9', - '/g/mm9', - '/g/elegans190', + genomes = [None, + '/g/mm9', + '/g/mm9', + '/g/elegans190', '/g/arabidopsis01222004', - '/g/mm9', - '/g/mm9', - '/g/mm9', + '/g/mm9', + '/g/mm9', + '/g/mm9', '/g/mm9', ] # test lane specific parameters from gerald config file -- 2.30.2