htsworkflow/pipelines/test/test_runfolder_rta160.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 eland
  10 from htsworkflow.pipelines import ipar
  11 from htsworkflow.pipelines import bustard
  12 from htsworkflow.pipelines import gerald
  13 from htsworkflow.pipelines import runfolder
  14 from htsworkflow.pipelines.runfolder import ElementTree
  15
  16 from htsworkflow.pipelines.test.simulate_runfolder import *
  17
  18
  19 def make_runfolder(obj=None):
  20     """
  21     Make a fake runfolder, attach all the directories to obj if defined
  22     """
  23     # make a fake runfolder directory
  24     temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
  25
  26     runfolder_dir = os.path.join(temp_dir,
  27                                  '090608_HWI-EAS229_0117_4286GAAXX')
  28     os.mkdir(runfolder_dir)
  29
  30     data_dir = os.path.join(runfolder_dir, 'Data')
  31     os.mkdir(data_dir)
  32
  33     intensities_dir = make_rta_intensities_1460(data_dir)
  34
  35     basecalls_dir = make_rta_basecalls_1460(intensities_dir)
  36
  37     #make_phasing_params(bustard_dir)
  38     #make_bustard_config132(bustard_dir)
  39
  40     gerald_dir = os.path.join(basecalls_dir,
  41                               'GERALD_16-06-2009_diane')
  42     os.mkdir(gerald_dir)
  43     make_gerald_config_100(gerald_dir)
  44     make_summary_rta160_xml(gerald_dir)
  45     make_eland_multi(gerald_dir, lane_list=[1,2,3,4,5,6,])
  46     make_scarf(gerald_dir, lane_list=[7,])
  47     make_fastq(gerald_dir, lane_list=[8,])
  48
  49     if obj is not None:
  50         obj.temp_dir = temp_dir
  51         obj.runfolder_dir = runfolder_dir
  52         obj.data_dir = data_dir
  53         obj.image_analysis_dir = intensities_dir
  54         obj.bustard_dir = basecalls_dir
  55         obj.gerald_dir = gerald_dir
  56
  57
  58 class RunfolderTests(unittest.TestCase):
  59     """
  60     Test components of the runfolder processing code
  61     which includes firecrest, bustard, and gerald
  62     """
  63     def setUp(self):
  64         # attaches all the directories to the object passed in
  65         make_runfolder(self)
  66
  67     def tearDown(self):
  68         shutil.rmtree(self.temp_dir)
  69
  70     # The only thing different from the previous RTA version is
  71     # I'm processing the Summary.xml file
  72
  73
  74     def test_gerald(self):
  75         # need to update gerald and make tests for it
  76         g = gerald.gerald(self.gerald_dir)
  77
  78         self.failUnlessEqual(g.software, 'GERALD')
  79         self.failUnlessEqual(g.version, '1.171')
  80         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
  81         self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
  82         self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
  83
  84
  85         # list of genomes, matches what was defined up in
  86         # make_gerald_config.
  87         # the first None is to offset the genomes list to be 1..9
  88         # instead of pythons default 0..8
  89         genomes = [None,
  90                    '/g/mm9',
  91                    '/g/mm9',
  92                    '/g/elegans190',
  93                    '/g/arabidopsis01222004',
  94                    '/g/mm9',
  95                    '/g/mm9',
  96                    '/g/mm9',
  97                    '/g/mm9', ]
  98
  99         # test lane specific parameters from gerald config file
 100         for i in range(1,9):
 101             cur_lane = g.lanes[i]
 102             self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
 103             self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
 104             self.failUnlessEqual(cur_lane.read_length, '37')
 105             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 106
 107         # I want to be able to use a simple iterator
 108         for l in g.lanes.values():
 109           self.failUnlessEqual(l.analysis, 'eland_extended')
 110           self.failUnlessEqual(l.read_length, '37')
 111           self.failUnlessEqual(l.use_bases, 'Y'*37)
 112
 113         # test data extracted from summary file
 114         clusters = [None,
 115                     (281331, 11169), (203841, 13513),
 116                     (220889, 15653), (137294, 14666),
 117                     (129388, 14525), (262092, 10751),
 118                     (185754, 13503), (233765, 9537),]
 119
 120         self.failUnlessEqual(len(g.summary), 1)
 121         for i in range(1,9):
 122             summary_lane = g.summary[0][i]
 123             self.failUnlessEqual(summary_lane.cluster, clusters[i])
 124             self.failUnlessEqual(summary_lane.lane, i)
 125
 126         xml = g.get_elements()
 127         # just make sure that element tree can serialize the tree
 128         xml_str = ElementTree.tostring(xml)
 129         g2 = gerald.Gerald(xml=xml)
 130         return
 131
 132         # do it all again after extracting from the xml file
 133         self.failUnlessEqual(g.software, g2.software)
 134         self.failUnlessEqual(g.version, g2.version)
 135         self.failUnlessEqual(g.date, g2.date)
 136         self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
 137         self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
 138
 139         # test lane specific parameters from gerald config file
 140         for i in range(1,9):
 141             g_lane = g.lanes[i]
 142             g2_lane = g2.lanes[i]
 143             self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
 144             self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
 145             self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
 146             self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
 147
 148         # test (some) summary elements
 149         self.failUnlessEqual(len(g.summary), 1)
 150         for i in range(1,9):
 151             g_summary = g.summary[0][i]
 152             g2_summary = g2.summary[0][i]
 153             self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
 154             self.failUnlessEqual(g_summary.lane, g2_summary.lane)
 155
 156             g_eland = g.eland_results
 157             g2_eland = g2.eland_results
 158             for lane in g_eland.results[0].keys():
 159                 g_results = g_eland.results[0][lane]
 160                 g2_results = g2_eland.results[0][lane]
 161                 self.failUnlessEqual(g_results.reads,
 162                                      g2_results.reads)
 163                 if isinstance(g_results, eland.ElandLane):
 164                   self.failUnlessEqual(len(g_results.mapped_reads),
 165                                        len(g2_results.mapped_reads))
 166                   for k in g_results.mapped_reads.keys():
 167                       self.failUnlessEqual(g_results.mapped_reads[k],
 168                                            g2_results.mapped_reads[k])
 169
 170                   self.failUnlessEqual(len(g_results.match_codes),
 171                                        len(g2_results.match_codes))
 172                   for k in g_results.match_codes.keys():
 173                       self.failUnlessEqual(g_results.match_codes[k],
 174                                            g2_results.match_codes[k])
 175
 176
 177     def test_eland(self):
 178         return
 179         hg_map = {'Lambda.fa': 'Lambda.fa'}
 180         for i in range(1,22):
 181           short_name = 'chr%d.fa' % (i,)
 182           long_name = 'hg18/chr%d.fa' % (i,)
 183           hg_map[short_name] = long_name
 184
 185         genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
 186                         5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
 187         eland_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
 188
 189         # I added sequence lanes to the last 2 lanes of this test case
 190         for i in range(1,7):
 191             lane = eland_container.results[0][i]
 192             self.failUnlessEqual(lane.reads, 6)
 193             self.failUnlessEqual(lane.sample_name, "s")
 194             self.failUnlessEqual(lane.lane_id, i)
 195             self.failUnlessEqual(len(lane.mapped_reads), 17)
 196             self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
 197             self.failUnlessEqual(lane.match_codes['U0'], 3)
 198             self.failUnlessEqual(lane.match_codes['R0'], 2)
 199             self.failUnlessEqual(lane.match_codes['U1'], 1)
 200             self.failUnlessEqual(lane.match_codes['R1'], 9)
 201             self.failUnlessEqual(lane.match_codes['U2'], 0)
 202             self.failUnlessEqual(lane.match_codes['R2'], 12)
 203             self.failUnlessEqual(lane.match_codes['NM'], 1)
 204             self.failUnlessEqual(lane.match_codes['QC'], 0)
 205
 206         # test scarf
 207         lane = eland_container.results[0][7]
 208         self.failUnlessEqual(lane.reads, 5)
 209         self.failUnlessEqual(lane.sample_name, 's')
 210         self.failUnlessEqual(lane.lane_id, 7)
 211         self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.SCARF_TYPE)
 212
 213         # test fastq
 214         lane = eland_container.results[0][8]
 215         self.failUnlessEqual(lane.reads, 3)
 216         self.failUnlessEqual(lane.sample_name, 's')
 217         self.failUnlessEqual(lane.lane_id, 8)
 218         self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.FASTQ_TYPE)
 219
 220         xml = eland_container.get_elements()
 221         # just make sure that element tree can serialize the tree
 222         xml_str = ElementTree.tostring(xml)
 223         e2 = gerald.ELAND(xml=xml)
 224
 225         for i in range(1,9):
 226             l1 = eland_container.results[0][i]
 227             l2 = e2.results[0][i]
 228             self.failUnlessEqual(l1.reads, l2.reads)
 229             self.failUnlessEqual(l1.sample_name, l2.sample_name)
 230             self.failUnlessEqual(l1.lane_id, l2.lane_id)
 231             if isinstance(l1, eland.ElandLane):
 232               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
 233               self.failUnlessEqual(len(l1.mapped_reads), 17)
 234               for k in l1.mapped_reads.keys():
 235                   self.failUnlessEqual(l1.mapped_reads[k],
 236                                        l2.mapped_reads[k])
 237
 238               self.failUnlessEqual(len(l1.match_codes), 9)
 239               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
 240               for k in l1.match_codes.keys():
 241                   self.failUnlessEqual(l1.match_codes[k],
 242                                        l2.match_codes[k])
 243             elif isinstance(l1, eland.SequenceLane):
 244                 self.failUnlessEqual(l1.sequence_type, l2.sequence_type)
 245
 246     def test_runfolder(self):
 247         return
 248         runs = runfolder.get_runs(self.runfolder_dir)
 249
 250         # do we get the flowcell id from the filename?
 251         self.failUnlessEqual(len(runs), 1)
 252         name = 'run_4286GAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
 253         self.failUnlessEqual(runs[0].name, name)
 254
 255         # do we get the flowcell id from the FlowcellId.xml file
 256         make_flowcell_id(self.runfolder_dir, '207BTAAXY')
 257         runs = runfolder.get_runs(self.runfolder_dir)
 258         self.failUnlessEqual(len(runs), 1)
 259         name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
 260         self.failUnlessEqual(runs[0].name, name)
 261
 262         r1 = runs[0]
 263         xml = r1.get_elements()
 264         xml_str = ElementTree.tostring(xml)
 265
 266         r2 = runfolder.PipelineRun(xml=xml)
 267         self.failUnlessEqual(r1.name, r2.name)
 268         self.failIfEqual(r2.image_analysis, None)
 269         self.failIfEqual(r2.bustard, None)
 270         self.failIfEqual(r2.gerald, None)
 271
 272
 273 def suite():
 274     return unittest.makeSuite(RunfolderTests,'test')
 275
 276 if __name__ == "__main__":
 277     unittest.main(defaultTest="suite")
 278