Return a gerald version number as a number and not a cvs string.

(Also my emacs configuration cleared excess spaces after on several lines)

diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py
index 087edd43a167a7ef8a9de585bfbfce72de42785b..12d83029be6cc1e8deb717f1f06f3abbfc2c0c60 100644 (file)
--- 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<version>\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 9edba3113b1a8d097993d2795a83b9c56acc1ae2..04c1377821b33833ddd8ff4261f661cd7422481e 100644 (file)
--- 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 f8160ed51b3df985be2598a8296bbfd1cd043143..9ab17225a28949331616beee30457d917bfed395 100644 (file)
--- 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 0691308229959889fac17ec1149e9b6044c34644..a995c39accf59b3116fe2533cad74851ef9a3e99 100644 (file)
--- 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="""<!--RUN_TIME Wed Jul  2 06:47:44 2008 -->
 <!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
@@ -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 fc91ce43ee3e32e23db57a0dae650cb66f15c438..d9c57a0ebe5fe5995ebd12426275db911306ca23 100644 (file)
--- 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 d58a70d991f0b9d384693b65edb9c811f074762f..ec647b83e8523c0cf57713ad7770a8edbd26b03a 100644 (file)
--- 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 13011bacf4916b9ef14cd2dc9b848c0188d82483..46a26f01892983a8f3fc2adc4177323f75433335 100644 (file)
--- 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 c0fb6842071c794389145bb36326f9b67b400a56..1ef2797ee901b24fe5c1c2dc57dd747c2c48e6b1 100644 (file)
--- 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 08db8e26db740e1c2e67e8cc5ec93e2acc0de89b..02b8e4424354b30bbe509be4df1caef392213ec2 100644 (file)
--- 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 d446e49065c3ebea72f6eba1eb75fe5d6784efc2..75ca37e9ab42e7a10f927c11edd9584b0de44705 100644 (file)
--- 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 7475b3662786fc9c2edeb29210985fddbc40a4c4..5cb282276d65c08d2bb08f94c5a5229e4e3dee7f 100644 (file)
--- 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