htsworkflow/pipelines/test/test_runfolder110.py

   1 #!/usr/bin/env python
   2 from __future__ import absolute_import
   3
   4 from datetime import datetime, date
   5 import os
   6 import tempfile
   7 import shutil
   8 from unittest import TestCase
   9
  10 from htsworkflow.pipelines import firecrest
  11 from htsworkflow.pipelines import bustard
  12 from htsworkflow.pipelines import gerald
  13 from htsworkflow.pipelines import runfolder
  14 from htsworkflow.pipelines import ElementTree
  15
  16 from .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                                  '081017_HWI-EAS229_0062_30J55AAXX')
  28     os.mkdir(runfolder_dir)
  29
  30     data_dir = os.path.join(runfolder_dir, 'Data')
  31     os.mkdir(data_dir)
  32
  33     firecrest_dir = os.path.join(data_dir,
  34                                  'C1-37_Firecrest1.9.6_20-10-2008_diane')
  35     os.mkdir(firecrest_dir)
  36
  37     bustard_dir = os.path.join(firecrest_dir,
  38                                'Bustard1.9.6_20-10-2008_diane')
  39     os.mkdir(bustard_dir)
  40     make_phasing_params(bustard_dir)
  41
  42     matrix_name = os.path.join(bustard_dir, 'matrix1.txt')
  43     make_matrix(matrix_name)
  44
  45
  46     gerald_dir = os.path.join(bustard_dir,
  47                               'GERALD_20-10-2008_diane')
  48     os.mkdir(gerald_dir)
  49     make_gerald_config_100(gerald_dir)
  50     make_summary_htm_110(gerald_dir)
  51     make_eland_multi(gerald_dir)
  52
  53     if obj is not None:
  54         obj.temp_dir = temp_dir
  55         obj.runfolder_dir = runfolder_dir
  56         obj.data_dir = data_dir
  57         obj.image_analysis_dir = firecrest_dir
  58         obj.bustard_dir = bustard_dir
  59         obj.gerald_dir = gerald_dir
  60
  61
  62 class RunfolderTests(TestCase):
  63     """
  64     Test components of the runfolder processing code
  65     which includes firecrest, bustard, and gerald
  66     """
  67     def setUp(self):
  68         # attaches all the directories to the object passed in
  69         make_runfolder(self)
  70
  71     def tearDown(self):
  72         shutil.rmtree(self.temp_dir)
  73
  74     def test_firecrest(self):
  75         """
  76         Construct a firecrest object
  77         """
  78         f = firecrest.firecrest(self.image_analysis_dir)
  79         self.failUnlessEqual(f.software, 'Firecrest')
  80         self.failUnlessEqual(f.version, '1.9.6')
  81         self.failUnlessEqual(f.start, 1)
  82         self.failUnlessEqual(f.stop, 37)
  83         self.failUnlessEqual(f.user, 'diane')
  84         self.failUnlessEqual(f.date, date(2008,10,20))
  85
  86         xml = f.get_elements()
  87         # just make sure that element tree can serialize the tree
  88         xml_str = ElementTree.tostring(xml)
  89
  90         f2 = firecrest.Firecrest(xml=xml)
  91         self.failUnlessEqual(f.software, f2.software)
  92         self.failUnlessEqual(f.version, f2.version)
  93         self.failUnlessEqual(f.start,   f2.start)
  94         self.failUnlessEqual(f.stop,    f2.stop)
  95         self.failUnlessEqual(f.user,    f2.user)
  96
  97     def test_bustard(self):
  98         """
  99         construct a bustard object
 100         """
 101         b = bustard.bustard(self.bustard_dir)
 102         self.failUnlessEqual(b.software, 'Bustard')
 103         self.failUnlessEqual(b.version, '1.9.6')
 104         self.failUnlessEqual(b.date,    date(2008,10,20))
 105         self.failUnlessEqual(b.user,    'diane')
 106         self.failUnlessEqual(len(b.phasing), 8)
 107         self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
 108
 109         xml = b.get_elements()
 110         b2 = bustard.Bustard(xml=xml)
 111         self.failUnlessEqual(b.software, b2.software)
 112         self.failUnlessEqual(b.version, b2.version)
 113         self.failUnlessEqual(b.date,    b2.date )
 114         self.failUnlessEqual(b.user,    b2.user)
 115         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
 116         for key in b.phasing.keys():
 117             self.failUnlessEqual(b.phasing[key].lane,
 118                                  b2.phasing[key].lane)
 119             self.failUnlessEqual(b.phasing[key].phasing,
 120                                  b2.phasing[key].phasing)
 121             self.failUnlessEqual(b.phasing[key].prephasing,
 122                                  b2.phasing[key].prephasing)
 123
 124     def test_gerald(self):
 125         # need to update gerald and make tests for it
 126         g = gerald.gerald(self.gerald_dir)
 127
 128         self.failUnlessEqual(g.software, 'GERALD')
 129         self.failUnlessEqual(g.version, '1.171')
 130         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
 131         self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
 132         self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
 133
 134
 135         # list of genomes, matches what was defined up in
 136         # make_gerald_config.
 137         # the first None is to offset the genomes list to be 1..9
 138         # instead of pythons default 0..8
 139         genomes = [None,
 140                    '/g/mm9',
 141                    '/g/mm9',
 142                    '/g/elegans190',
 143                    '/g/arabidopsis01222004',
 144                    '/g/mm9',
 145                    '/g/mm9',
 146                    '/g/mm9',
 147                    '/g/mm9', ]
 148
 149         # test lane specific parameters from gerald config file
 150         for i in range(1,9):
 151             cur_lane = g.lanes[i]
 152             self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
 153             self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
 154             self.failUnlessEqual(cur_lane.read_length, '37')
 155             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 156
 157         # I want to be able to use a simple iterator
 158         for l in g.lanes.values():
 159           self.failUnlessEqual(l.analysis, 'eland_extended')
 160           self.failUnlessEqual(l.read_length, '37')
 161           self.failUnlessEqual(l.use_bases, 'Y'*37)
 162
 163         # raw cluster numbers extracted from summary file
 164         # its the first +/- value in the lane results summary
 165         # section
 166         clusters = [None,
 167                     (190220, 15118), (190560, 14399),
 168                     (187597, 12369), (204142, 16877),
 169                     (247308, 11600), (204298, 15640),
 170                     (202707, 15404), (198075, 14702),]
 171
 172         self.failUnlessEqual(len(g.summary), 1)
 173         for i in range(1,9):
 174             summary_lane = g.summary[0][i]
 175             self.failUnlessEqual(summary_lane.cluster, clusters[i])
 176             self.failUnlessEqual(summary_lane.lane, i)
 177
 178         xml = g.get_elements()
 179         # just make sure that element tree can serialize the tree
 180         xml_str = ElementTree.tostring(xml)
 181         g2 = gerald.Gerald(xml=xml)
 182
 183         # do it all again after extracting from the xml file
 184         self.failUnlessEqual(g.software, g2.software)
 185         self.failUnlessEqual(g.version, g2.version)
 186         self.failUnlessEqual(g.date, g2.date)
 187         self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
 188         self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
 189
 190         # test lane specific parameters from gerald config file
 191         for i in range(1,9):
 192             g_lane = g.lanes[i]
 193             g2_lane = g2.lanes[i]
 194             self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
 195             self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
 196             self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
 197             self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
 198
 199         self.failUnlessEqual(len(g.summary), 1)
 200         # test (some) summary elements
 201         for i in range(1,9):
 202             g_summary = g.summary[0][i]
 203             g2_summary = g2.summary[0][i]
 204             self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
 205             self.failUnlessEqual(g_summary.lane, g2_summary.lane)
 206
 207             g_eland = g.eland_results
 208             g2_eland = g2.eland_results
 209             for key in g_eland:
 210                 g_results = g_eland[key]
 211                 g2_results = g2_eland[key]
 212                 self.failUnlessEqual(g_results.reads,
 213                                      g2_results.reads)
 214                 self.failUnlessEqual(len(g_results.mapped_reads),
 215                                      len(g2_results.mapped_reads))
 216                 for k in g_results.mapped_reads.keys():
 217                     self.failUnlessEqual(g_results.mapped_reads[k],
 218                                          g2_results.mapped_reads[k])
 219
 220                 self.failUnlessEqual(len(g_results.match_codes),
 221                                      len(g2_results.match_codes))
 222                 for k in g_results.match_codes.keys():
 223                     self.failUnlessEqual(g_results.match_codes[k],
 224                                          g2_results.match_codes[k])
 225
 226
 227     def test_eland(self):
 228         hg_map = {'Lambda.fa': 'Lambda.fa'}
 229         for i in range(1,22):
 230           short_name = 'chr%d.fa' % (i,)
 231           long_name = 'hg18/chr%d.fa' % (i,)
 232           hg_map[short_name] = long_name
 233
 234         genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
 235                         5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
 236         eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
 237
 238         for key in eland:
 239             lane = eland[key]
 240             self.failUnlessEqual(lane.reads, 6)
 241             self.failUnlessEqual(lane.sample_name, "s")
 242             self.failUnlessEqual(lane.lane_id, key.lane)
 243             self.failUnlessEqual(len(lane.mapped_reads), 17)
 244             self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
 245             self.failUnlessEqual(lane.match_codes['U0'], 3)
 246             self.failUnlessEqual(lane.match_codes['R0'], 2)
 247             self.failUnlessEqual(lane.match_codes['U1'], 1)
 248             self.failUnlessEqual(lane.match_codes['R1'], 9)
 249             self.failUnlessEqual(lane.match_codes['U2'], 0)
 250             self.failUnlessEqual(lane.match_codes['R2'], 12)
 251             self.failUnlessEqual(lane.match_codes['NM'], 1)
 252             self.failUnlessEqual(lane.match_codes['QC'], 0)
 253
 254         xml = eland.get_elements()
 255         # just make sure that element tree can serialize the tree
 256         xml_str = ElementTree.tostring(xml)
 257         e2 = gerald.ELAND(xml=xml)
 258
 259         for key in eland:
 260             l1 = eland[key]
 261             l2 = e2[key]
 262             self.failUnlessEqual(l1.reads, l2.reads)
 263             self.failUnlessEqual(l1.sample_name, l2.sample_name)
 264             self.failUnlessEqual(l1.lane_id, l2.lane_id)
 265             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
 266             self.failUnlessEqual(len(l1.mapped_reads), 17)
 267             for k in l1.mapped_reads.keys():
 268                 self.failUnlessEqual(l1.mapped_reads[k],
 269                                      l2.mapped_reads[k])
 270
 271             self.failUnlessEqual(len(l1.match_codes), 9)
 272             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
 273             for k in l1.match_codes.keys():
 274                 self.failUnlessEqual(l1.match_codes[k],
 275                                      l2.match_codes[k])
 276
 277     def test_runfolder(self):
 278         runs = runfolder.get_runs(self.runfolder_dir)
 279
 280         # do we get the flowcell id from the filename?
 281         self.failUnlessEqual(len(runs), 1)
 282         name = 'run_30J55AAXX_2009-02-22.xml'
 283         self.failUnlessEqual(runs[0].serialization_filename, name)
 284
 285         # do we get the flowcell id from the FlowcellId.xml file
 286         make_flowcell_id(self.runfolder_dir, '30J55AAXX')
 287         runs = runfolder.get_runs(self.runfolder_dir)
 288         self.failUnlessEqual(len(runs), 1)
 289         name = 'run_30J55AAXX_2009-02-22.xml'
 290         self.failUnlessEqual(runs[0].serialization_filename, name)
 291
 292         r1 = runs[0]
 293         xml = r1.get_elements()
 294         xml_str = ElementTree.tostring(xml)
 295
 296         r2 = runfolder.PipelineRun(xml=xml)
 297         self.failUnlessEqual(r1.serialization_filename, r2.serialization_filename)
 298         self.failIfEqual(r2.image_analysis, None)
 299         self.failIfEqual(r2.bustard, None)
 300         self.failIfEqual(r2.gerald, None)
 301
 302
 303 def suite():
 304     from unittest import TestSuite, defaultTestLoader
 305     suite = TestSuite()
 306     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
 307     return suite
 308
 309
 310 if __name__ == "__main__":
 311     from unittest import main
 312     main(defaultTest="suite")