htsworkflow/pipelines/test/test_runfolder_ipar100.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                                  '080102_HWI-EAS229_0010_207BTAAXX')
  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)
  33
  34     matrix_dir = os.path.join(ipar_dir, 'Matrix')
  35     os.mkdir(matrix_dir)
  36     make_matrix(matrix_dir)
  37
  38     bustard_dir = os.path.join(ipar_dir,
  39                                'Bustard1.8.28_12-04-2008_diane')
  40     os.mkdir(bustard_dir)
  41     make_phasing_params(bustard_dir)
  42
  43     gerald_dir = os.path.join(bustard_dir,
  44                               'GERALD_12-04-2008_diane')
  45     os.mkdir(gerald_dir)
  46     make_gerald_config(gerald_dir)
  47     make_summary100_htm(gerald_dir)
  48     make_eland_multi(gerald_dir)
  49
  50     if obj is not None:
  51         obj.temp_dir = temp_dir
  52         obj.runfolder_dir = runfolder_dir
  53         obj.data_dir = data_dir
  54         obj.image_analysis_dir = ipar_dir
  55         obj.matrix_dir = matrix_dir
  56         obj.bustard_dir = bustard_dir
  57         obj.gerald_dir = gerald_dir
  58
  59
  60 class RunfolderTests(unittest.TestCase):
  61     """
  62     Test components of the runfolder processing code
  63     which includes firecrest, bustard, and gerald
  64     """
  65     def setUp(self):
  66         # attaches all the directories to the object passed in
  67         make_runfolder(self)
  68
  69     def tearDown(self):
  70         shutil.rmtree(self.temp_dir)
  71
  72     def test_ipar(self):
  73         """
  74         Construct a firecrest object
  75         """
  76         i = ipar.ipar(self.image_analysis_dir)
  77         self.failUnlessEqual(i.version, '2.01.192.0')
  78         self.failUnlessEqual(i.start, 1)
  79         self.failUnlessEqual(i.stop, 37)
  80
  81         xml = i.get_elements()
  82         # just make sure that element tree can serialize the tree
  83         xml_str = ElementTree.tostring(xml)
  84
  85         i2 = ipar.IPAR(xml=xml)
  86         self.failUnlessEqual(i.version, i2.version)
  87         self.failUnlessEqual(i.start,   i2.start)
  88         self.failUnlessEqual(i.stop,    i2.stop)
  89         self.failUnlessEqual(i.date,    i2.date)
  90         self.failUnlessEqual(i.file_list(), i2.file_list())
  91
  92     def test_bustard(self):
  93         """
  94         construct a bustard object
  95         """
  96         b = bustard.bustard(self.bustard_dir)
  97         self.failUnlessEqual(b.version, '1.8.28')
  98         self.failUnlessEqual(b.date,    date(2008,4,12))
  99         self.failUnlessEqual(b.user,    'diane')
 100         self.failUnlessEqual(len(b.phasing), 8)
 101         self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
 102
 103         xml = b.get_elements()
 104         b2 = bustard.Bustard(xml=xml)
 105         self.failUnlessEqual(b.version, b2.version)
 106         self.failUnlessEqual(b.date,    b2.date )
 107         self.failUnlessEqual(b.user,    b2.user)
 108         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
 109         for key in b.phasing.keys():
 110             self.failUnlessEqual(b.phasing[key].lane,
 111                                  b2.phasing[key].lane)
 112             self.failUnlessEqual(b.phasing[key].phasing,
 113                                  b2.phasing[key].phasing)
 114             self.failUnlessEqual(b.phasing[key].prephasing,
 115                                  b2.phasing[key].prephasing)
 116
 117     def test_gerald(self):
 118         # need to update gerald and make tests for it
 119         g = gerald.gerald(self.gerald_dir)
 120
 121         self.failUnlessEqual(g.version,
 122             '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp')
 123         self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
 124         self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
 125         self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
 126
 127
 128         # list of genomes, matches what was defined up in
 129         # make_gerald_config.
 130         # the first None is to offset the genomes list to be 1..9
 131         # instead of pythons default 0..8
 132         genomes = [None, '/g/dm3', '/g/equcab1', '/g/equcab1', '/g/canfam2',
 133                          '/g/hg18', '/g/hg18', '/g/hg18', '/g/hg18', ]
 134
 135         # test lane specific parameters from gerald config file
 136         for i in range(1,9):
 137             cur_lane = g.lanes[i]
 138             self.failUnlessEqual(cur_lane.analysis, 'eland')
 139             self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
 140             self.failUnlessEqual(cur_lane.read_length, '32')
 141             self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
 142
 143         # I want to be able to use a simple iterator
 144         for l in g.lanes.values():
 145           self.failUnlessEqual(l.analysis, 'eland')
 146           self.failUnlessEqual(l.read_length, '32')
 147           self.failUnlessEqual(l.use_bases, 'Y'*32)
 148
 149         # test data extracted from summary file
 150         clusters = [None,
 151                     (96483, 9074), (133738, 7938),
 152                     (152142, 10002), (15784, 2162),
 153                     (119735, 8465), (152177, 8146),
 154                     (84649, 7325), (54622, 4812),]
 155
 156         self.failUnlessEqual(len(g.summary), 1)
 157         for i in range(1,9):
 158             summary_lane = g.summary[0][i]
 159             self.failUnlessEqual(summary_lane.cluster, clusters[i])
 160             self.failUnlessEqual(summary_lane.lane, i)
 161
 162         xml = g.get_elements()
 163         # just make sure that element tree can serialize the tree
 164         xml_str = ElementTree.tostring(xml)
 165         g2 = gerald.Gerald(xml=xml)
 166
 167         # do it all again after extracting from the xml file
 168         self.failUnlessEqual(g.version, g2.version)
 169         self.failUnlessEqual(g.date, g2.date)
 170         self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
 171         self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
 172
 173         # test lane specific parameters from gerald config file
 174         for i in range(1,9):
 175             g_lane = g.lanes[i]
 176             g2_lane = g2.lanes[i]
 177             self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
 178             self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
 179             self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
 180             self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
 181
 182         # test (some) summary elements
 183         self.failUnlessEqual(len(g.summary), 1)
 184         for i in range(1,9):
 185             g_summary = g.summary[0][i]
 186             g2_summary = g2.summary[0][i]
 187             self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
 188             self.failUnlessEqual(g_summary.lane, g2_summary.lane)
 189
 190             g_eland = g.eland_results
 191             g2_eland = g2.eland_results
 192             for lane in g_eland.keys():
 193                 self.failUnlessEqual(g_eland[lane].reads,
 194                                      g2_eland[lane].reads)
 195                 self.failUnlessEqual(len(g_eland[lane].mapped_reads),
 196                                      len(g2_eland[lane].mapped_reads))
 197                 for k in g_eland[lane].mapped_reads.keys():
 198                     self.failUnlessEqual(g_eland[lane].mapped_reads[k],
 199                                          g2_eland[lane].mapped_reads[k])
 200
 201                 self.failUnlessEqual(len(g_eland[lane].match_codes),
 202                                      len(g2_eland[lane].match_codes))
 203                 for k in g_eland[lane].match_codes.keys():
 204                     self.failUnlessEqual(g_eland[lane].match_codes[k],
 205                                          g2_eland[lane].match_codes[k])
 206
 207
 208     def test_eland(self):
 209         hg_map = {'Lambda.fa': 'Lambda.fa'}
 210         for i in range(1,22):
 211           short_name = 'chr%d.fa' % (i,)
 212           long_name = 'hg18/chr%d.fa' % (i,)
 213           hg_map[short_name] = long_name
 214
 215         genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
 216                         5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
 217         eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
 218
 219         for i in range(1,9):
 220             lane = eland[i]
 221             self.failUnlessEqual(lane.reads, 4)
 222             self.failUnlessEqual(lane.sample_name, "s")
 223             self.failUnlessEqual(lane.lane_id, i)
 224             self.failUnlessEqual(len(lane.mapped_reads), 15)
 225             self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
 226             self.failUnlessEqual(lane.match_codes['U0'], 1)
 227             self.failUnlessEqual(lane.match_codes['R0'], 2)
 228             self.failUnlessEqual(lane.match_codes['U1'], 1)
 229             self.failUnlessEqual(lane.match_codes['R1'], 9)
 230             self.failUnlessEqual(lane.match_codes['U2'], 0)
 231             self.failUnlessEqual(lane.match_codes['R2'], 12)
 232             self.failUnlessEqual(lane.match_codes['NM'], 1)
 233             self.failUnlessEqual(lane.match_codes['QC'], 0)
 234
 235         xml = eland.get_elements()
 236         # just make sure that element tree can serialize the tree
 237         xml_str = ElementTree.tostring(xml)
 238         e2 = gerald.ELAND(xml=xml)
 239
 240         for i in range(1,9):
 241             l1 = eland[i]
 242             l2 = e2[i]
 243             self.failUnlessEqual(l1.reads, l2.reads)
 244             self.failUnlessEqual(l1.sample_name, l2.sample_name)
 245             self.failUnlessEqual(l1.lane_id, l2.lane_id)
 246             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
 247             self.failUnlessEqual(len(l1.mapped_reads), 15)
 248             for k in l1.mapped_reads.keys():
 249                 self.failUnlessEqual(l1.mapped_reads[k],
 250                                      l2.mapped_reads[k])
 251
 252             self.failUnlessEqual(len(l1.match_codes), 9)
 253             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
 254             for k in l1.match_codes.keys():
 255                 self.failUnlessEqual(l1.match_codes[k],
 256                                      l2.match_codes[k])
 257
 258     def test_runfolder(self):
 259         runs = runfolder.get_runs(self.runfolder_dir)
 260
 261         # do we get the flowcell id from the filename?
 262         self.failUnlessEqual(len(runs), 1)
 263         name = 'run_207BTAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
 264         self.failUnlessEqual(runs[0].name, name)
 265
 266         # do we get the flowcell id from the FlowcellId.xml file
 267         make_flowcell_id(self.runfolder_dir, '207BTAAXY')
 268         runs = runfolder.get_runs(self.runfolder_dir)
 269         self.failUnlessEqual(len(runs), 1)
 270         name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
 271         self.failUnlessEqual(runs[0].name, name)
 272
 273         r1 = runs[0]
 274         xml = r1.get_elements()
 275         xml_str = ElementTree.tostring(xml)
 276
 277         r2 = runfolder.PipelineRun(xml=xml)
 278         self.failUnlessEqual(r1.name, r2.name)
 279         self.failIfEqual(r2.image_analysis, None)
 280         self.failIfEqual(r2.bustard, None)
 281         self.failIfEqual(r2.gerald, None)
 282
 283
 284 def suite():
 285     return unittest.makeSuite(RunfolderTests,'test')
 286
 287 if __name__ == "__main__":
 288     unittest.main(defaultTest="suite")
 289