htsworkflow/pipelines/test/test_runfolder_ipar130.py

   1 #!/usr/bin/env python
   2
   3 from datetime import datetime, date
   4 import os
   5 import tempfile
   6 import shutil
   7 import unittest
   8
   9 from htsworkflow.pipelines import ipar
  10 from htsworkflow.pipelines import bustard
  11 from htsworkflow.pipelines import gerald
  12 from htsworkflow.pipelines import runfolder
  13 from htsworkflow.pipelines.runfolder import ElementTree
  14
  15 from htsworkflow.pipelines.test.simulate_runfolder import *
  16
  17
  18 def make_runfolder(obj=None):
  19     """
  20     Make a fake runfolder, attach all the directories to obj if defined
  21     """
  22     # make a fake runfolder directory
  23     temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
  24
  25     runfolder_dir = os.path.join(temp_dir,
  26                                  '090313_HWI-EAS229_0101_3021JAAXX')
  27     os.mkdir(runfolder_dir)
  28
  29     data_dir = os.path.join(runfolder_dir, 'Data')
  30     os.mkdir(data_dir)
  31
  32     ipar_dir = make_ipar_dir(data_dir, '1.30')
  33
  34     bustard_dir = os.path.join(ipar_dir,
  35                                'Bustard1.3.2_15-03-2008_diane')
  36     os.mkdir(bustard_dir)
  37     make_phasing_params(bustard_dir)
  38     make_bustard_config132(bustard_dir)
  39
  40     gerald_dir = os.path.join(bustard_dir,
  41                               'GERALD_15-03-2008_diane')
  42     os.mkdir(gerald_dir)
  43     make_gerald_config_100(gerald_dir)
  44     make_summary_ipar130_htm(gerald_dir)
  45     make_eland_multi(gerald_dir)
  46
  47     if obj is not None:
  48         obj.temp_dir = temp_dir
  49         obj.runfolder_dir = runfolder_dir
  50         obj.data_dir = data_dir
  51         obj.image_analysis_dir = ipar_dir
  52         obj.bustard_dir = bustard_dir
  53         obj.gerald_dir = gerald_dir
  54
  55
  56 class RunfolderTests(unittest.TestCase):
  57     """
  58     Test components of the runfolder processing code
  59     which includes firecrest, bustard, and gerald
  60     """
  61     def setUp(self):
  62         # attaches all the directories to the object passed in
  63         make_runfolder(self)
  64
  65     def tearDown(self):
  66         shutil.rmtree(self.temp_dir)
  67
  68     def test_ipar(self):
  69         """
  70         Construct a firecrest object
  71         """
  72         i = ipar.ipar(self.image_analysis_dir)
  73         self.failUnlessEqual(i.version, '2.01.192.0')
  74         self.failUnlessEqual(i.start, 1)
  75         self.failUnlessEqual(i.stop, 37)
  76
  77         xml = i.get_elements()
  78         # just make sure that element tree can serialize the tree
  79         xml_str = ElementTree.tostring(xml)
  80
  81         i2 = ipar.IPAR(xml=xml)
  82         self.failUnlessEqual(i.version, i2.version)
  83         self.failUnlessEqual(i.start,   i2.start)
  84         self.failUnlessEqual(i.stop,    i2.stop)
  85         self.failUnlessEqual(i.date,    i2.date)
  86         self.failUnlessEqual(i.file_list(), i2.file_list())
  87
  88     def test_bustard(self):
  89         """
  90         construct a bustard object
  91         """
  92         b = bustard.bustard(self.bustard_dir)
  93         self.failUnlessEqual(b.version, '1.3.2')
  94         self.failUnlessEqual(b.date,    date(2008,3,15))
  95         self.failUnlessEqual(b.user,    'diane')
  96         self.failUnlessEqual(len(b.phasing), 8)
  97         self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
  98         self.failUnlessEqual(b.crosstalk.base.keys(), ['A','C','T','G'])
  99
 100         self.failUnlessAlmostEqual(b.crosstalk.base['A'][0],  1.27)
 101         self.failUnlessAlmostEqual(b.crosstalk.base['A'][1],  0.20999999999999)
 102         self.failUnlessAlmostEqual(b.crosstalk.base['A'][2], -0.02)
 103         self.failUnlessAlmostEqual(b.crosstalk.base['A'][3], -0.03)
 104
 105         self.failUnlessAlmostEqual(b.crosstalk.base['C'][0],  0.57)
 106         self.failUnlessAlmostEqual(b.crosstalk.base['C'][1],  0.58)
 107         self.failUnlessAlmostEqual(b.crosstalk.base['C'][2], -0.01)
 108         self.failUnlessAlmostEqual(b.crosstalk.base['C'][3], -0.01)
 109
 110         self.failUnlessAlmostEqual(b.crosstalk.base['T'][0], -0.02)
 111         self.failUnlessAlmostEqual(b.crosstalk.base['T'][1], -0.02)
 112         self.failUnlessAlmostEqual(b.crosstalk.base['T'][2],  0.80)
 113         self.failUnlessAlmostEqual(b.crosstalk.base['T'][3],  1.07)
 114
 115         self.failUnlessAlmostEqual(b.crosstalk.base['G'][0], -0.03)
 116         self.failUnlessAlmostEqual(b.crosstalk.base['G'][1], -0.04)
 117         self.failUnlessAlmostEqual(b.crosstalk.base['G'][2],  1.51)
 118         self.failUnlessAlmostEqual(b.crosstalk.base['G'][3], -0.02)
 119
 120         xml = b.get_elements()
 121         b2 = bustard.Bustard(xml=xml)
 122         self.failUnlessEqual(b.version, b2.version)
 123         self.failUnlessEqual(b.date,    b2.date )
 124         self.failUnlessEqual(b.user,    b2.user)
 125         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
 126         for key in b.phasing.keys():
 127             self.failUnlessEqual(b.phasing[key].lane,
 128                                  b2.phasing[key].lane)
 129             self.failUnlessEqual(b.phasing[key].phasing,
 130                                  b2.phasing[key].phasing)
 131             self.failUnlessEqual(b.phasing[key].prephasing,
 132                                  b2.phasing[key].prephasing)
 133
 134     def test_gerald(self):
 135         # need to update gerald and make tests for it
 136         g = gerald.gerald(self.gerald_dir)
 137
 138         self.failUnlessEqual(g.version,
 139             '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
 140         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
 141         self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
 142         self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
 143
 144
 145         # list of genomes, matches what was defined up in
 146         # make_gerald_config.
 147         # the first None is to offset the genomes list to be 1..9
 148         # instead of pythons default 0..8
 149         genomes = [None,
 150                    '/g/mm9',
 151                    '/g/mm9',
 152                    '/g/elegans190',
 153                    '/g/arabidopsis01222004',
 154                    '/g/mm9',
 155                    '/g/mm9',
 156                    '/g/mm9',
 157                    '/g/mm9', ]
 158
 159         # test lane specific parameters from gerald config file
 160         for i in range(1,9):
 161             cur_lane = g.lanes[i]
 162             self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
 163             self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
 164             self.failUnlessEqual(cur_lane.read_length, '37')
 165             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 166
 167         # I want to be able to use a simple iterator
 168         for l in g.lanes.values():
 169           self.failUnlessEqual(l.analysis, 'eland_extended')
 170           self.failUnlessEqual(l.read_length, '37')
 171           self.failUnlessEqual(l.use_bases, 'Y'*37)
 172
 173         # test data extracted from summary file
 174         clusters = [None,
 175                     (126910, 4300), (165739, 6792),
 176                     (196565, 8216), (153897, 8501),
 177                     (135536, 3908), (154083, 9315),
 178                     (159991, 9292), (198479, 17671),]
 179
 180         self.failUnlessEqual(len(g.summary), 1)
 181         for i in range(1,9):
 182             summary_lane = g.summary[0][i]
 183             self.failUnlessEqual(summary_lane.cluster, clusters[i])
 184             self.failUnlessEqual(summary_lane.lane, i)
 185
 186         xml = g.get_elements()
 187         # just make sure that element tree can serialize the tree
 188         xml_str = ElementTree.tostring(xml)
 189         g2 = gerald.Gerald(xml=xml)
 190
 191         # do it all again after extracting from the xml file
 192         self.failUnlessEqual(g.version, g2.version)
 193         self.failUnlessEqual(g.date, g2.date)
 194         self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
 195         self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
 196
 197         # test lane specific parameters from gerald config file
 198         for i in range(1,9):
 199             g_lane = g.lanes[i]
 200             g2_lane = g2.lanes[i]
 201             self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
 202             self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
 203             self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
 204             self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
 205
 206         # test (some) summary elements
 207         self.failUnlessEqual(len(g.summary), 1)
 208         for i in range(1,9):
 209             g_summary = g.summary[0][i]
 210             g2_summary = g2.summary[0][i]
 211             self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
 212             self.failUnlessEqual(g_summary.lane, g2_summary.lane)
 213
 214             g_eland = g.eland_results
 215             g2_eland = g2.eland_results
 216             for lane in g_eland.results[0].keys():
 217                 g_results = g_eland.results[0][lane]
 218                 g2_results = g2_eland.results[0][lane]
 219                 self.failUnlessEqual(g_results.reads,
 220                                      g2_results.reads)
 221                 self.failUnlessEqual(len(g_results.mapped_reads),
 222                                      len(g2_results.mapped_reads))
 223                 for k in g_results.mapped_reads.keys():
 224                     self.failUnlessEqual(g_results.mapped_reads[k],
 225                                          g2_results.mapped_reads[k])
 226
 227                 self.failUnlessEqual(len(g_results.match_codes),
 228                                      len(g2_results.match_codes))
 229                 for k in g_results.match_codes.keys():
 230                     self.failUnlessEqual(g_results.match_codes[k],
 231                                          g2_results.match_codes[k])
 232
 233
 234     def test_eland(self):
 235         hg_map = {'Lambda.fa': 'Lambda.fa'}
 236         for i in range(1,22):
 237           short_name = 'chr%d.fa' % (i,)
 238           long_name = 'hg18/chr%d.fa' % (i,)
 239           hg_map[short_name] = long_name
 240
 241         genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
 242                         5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
 243         eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
 244
 245         for i in range(1,9):
 246             lane = eland.results[0][i]
 247             self.failUnlessEqual(lane.reads, 6)
 248             self.failUnlessEqual(lane.sample_name, "s")
 249             self.failUnlessEqual(lane.lane_id, i)
 250             self.failUnlessEqual(len(lane.mapped_reads), 17)
 251             self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
 252             self.failUnlessEqual(lane.match_codes['U0'], 3)
 253             self.failUnlessEqual(lane.match_codes['R0'], 2)
 254             self.failUnlessEqual(lane.match_codes['U1'], 1)
 255             self.failUnlessEqual(lane.match_codes['R1'], 9)
 256             self.failUnlessEqual(lane.match_codes['U2'], 0)
 257             self.failUnlessEqual(lane.match_codes['R2'], 12)
 258             self.failUnlessEqual(lane.match_codes['NM'], 1)
 259             self.failUnlessEqual(lane.match_codes['QC'], 0)
 260
 261         xml = eland.get_elements()
 262         # just make sure that element tree can serialize the tree
 263         xml_str = ElementTree.tostring(xml)
 264         e2 = gerald.ELAND(xml=xml)
 265
 266         for i in range(1,9):
 267             l1 = eland.results[0][i]
 268             l2 = e2.results[0][i]
 269             self.failUnlessEqual(l1.reads, l2.reads)
 270             self.failUnlessEqual(l1.sample_name, l2.sample_name)
 271             self.failUnlessEqual(l1.lane_id, l2.lane_id)
 272             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
 273             self.failUnlessEqual(len(l1.mapped_reads), 17)
 274             for k in l1.mapped_reads.keys():
 275                 self.failUnlessEqual(l1.mapped_reads[k],
 276                                      l2.mapped_reads[k])
 277
 278             self.failUnlessEqual(len(l1.match_codes), 9)
 279             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
 280             for k in l1.match_codes.keys():
 281                 self.failUnlessEqual(l1.match_codes[k],
 282                                      l2.match_codes[k])
 283
 284     def test_runfolder(self):
 285         runs = runfolder.get_runs(self.runfolder_dir)
 286
 287         # do we get the flowcell id from the filename?
 288         self.failUnlessEqual(len(runs), 1)
 289         name = 'run_3021JAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
 290         self.failUnlessEqual(runs[0].name, name)
 291
 292         # do we get the flowcell id from the FlowcellId.xml file
 293         make_flowcell_id(self.runfolder_dir, '207BTAAXY')
 294         runs = runfolder.get_runs(self.runfolder_dir)
 295         self.failUnlessEqual(len(runs), 1)
 296         name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
 297         self.failUnlessEqual(runs[0].name, name)
 298
 299         r1 = runs[0]
 300         xml = r1.get_elements()
 301         xml_str = ElementTree.tostring(xml)
 302
 303         r2 = runfolder.PipelineRun(xml=xml)
 304         self.failUnlessEqual(r1.name, r2.name)
 305         self.failIfEqual(r2.image_analysis, None)
 306         self.failIfEqual(r2.bustard, None)
 307         self.failIfEqual(r2.gerald, None)
 308
 309
 310 def suite():
 311     return unittest.makeSuite(RunfolderTests,'test')
 312
 313 if __name__ == "__main__":
 314     unittest.main(defaultTest="suite")
 315