3 from datetime import datetime, date
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
15 from htsworkflow.pipelines.test.simulate_runfolder import *
18 def make_runfolder(obj=None):
20 Make a fake runfolder, attach all the directories to obj if defined
22 # make a fake runfolder directory
23 temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
25 runfolder_dir = os.path.join(temp_dir,
26 '080102_HWI-EAS229_0010_207BTAAXX')
27 os.mkdir(runfolder_dir)
29 data_dir = os.path.join(runfolder_dir, 'Data')
32 ipar_dir = make_ipar_dir(data_dir)
34 matrix_dir = os.path.join(ipar_dir, 'Matrix')
36 matrix_name = os.path.join(matrix_dir, 's_matrix.txt')
37 make_matrix(matrix_name)
39 bustard_dir = os.path.join(ipar_dir,
40 'Bustard1.8.28_12-04-2008_diane')
42 make_phasing_params(bustard_dir)
44 gerald_dir = os.path.join(bustard_dir,
45 'GERALD_12-04-2008_diane')
47 make_gerald_config_100(gerald_dir)
48 make_summary_htm_100(gerald_dir)
49 make_eland_multi(gerald_dir)
52 obj.temp_dir = temp_dir
53 obj.runfolder_dir = runfolder_dir
54 obj.data_dir = data_dir
55 obj.image_analysis_dir = ipar_dir
56 obj.matrix_dir = matrix_dir
57 obj.bustard_dir = bustard_dir
58 obj.gerald_dir = gerald_dir
61 class RunfolderTests(unittest.TestCase):
63 Test components of the runfolder processing code
64 which includes firecrest, bustard, and gerald
67 # attaches all the directories to the object passed in
71 shutil.rmtree(self.temp_dir)
75 Construct a firecrest object
77 i = ipar.ipar(self.image_analysis_dir)
78 self.failUnlessEqual(i.version, '2.01.192.0')
79 self.failUnlessEqual(i.start, 1)
80 self.failUnlessEqual(i.stop, 37)
82 xml = i.get_elements()
83 # just make sure that element tree can serialize the tree
84 xml_str = ElementTree.tostring(xml)
86 i2 = ipar.IPAR(xml=xml)
87 self.failUnlessEqual(i.version, i2.version)
88 self.failUnlessEqual(i.start, i2.start)
89 self.failUnlessEqual(i.stop, i2.stop)
90 self.failUnlessEqual(i.date, i2.date)
91 self.failUnlessEqual(i.file_list(), i2.file_list())
93 def test_bustard(self):
95 construct a bustard object
97 b = bustard.bustard(self.bustard_dir)
98 self.failUnlessEqual(b.version, '1.8.28')
99 self.failUnlessEqual(b.date, date(2008,4,12))
100 self.failUnlessEqual(b.user, 'diane')
101 self.failUnlessEqual(len(b.phasing), 8)
102 self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
104 xml = b.get_elements()
105 b2 = bustard.Bustard(xml=xml)
106 self.failUnlessEqual(b.version, b2.version)
107 self.failUnlessEqual(b.date, b2.date )
108 self.failUnlessEqual(b.user, b2.user)
109 self.failUnlessEqual(len(b.phasing), len(b2.phasing))
110 for key in b.phasing.keys():
111 self.failUnlessEqual(b.phasing[key].lane,
112 b2.phasing[key].lane)
113 self.failUnlessEqual(b.phasing[key].phasing,
114 b2.phasing[key].phasing)
115 self.failUnlessEqual(b.phasing[key].prephasing,
116 b2.phasing[key].prephasing)
118 def test_gerald(self):
119 # need to update gerald and make tests for it
120 g = gerald.gerald(self.gerald_dir)
122 self.failUnlessEqual(g.version, '1.171')
123 self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
124 self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
125 self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
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
136 '/g/arabidopsis01222004',
142 # test lane specific parameters from gerald config file
144 cur_lane = g.lanes[i]
145 self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
146 self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
147 self.failUnlessEqual(cur_lane.read_length, '37')
148 self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
150 # I want to be able to use a simple iterator
151 for l in g.lanes.values():
152 self.failUnlessEqual(l.analysis, 'eland_extended')
153 self.failUnlessEqual(l.read_length, '37')
154 self.failUnlessEqual(l.use_bases, 'Y'*37)
156 # test data extracted from summary file
158 (96483, 9074), (133738, 7938),
159 (152142, 10002), (15784, 2162),
160 (119735, 8465), (152177, 8146),
161 (84649, 7325), (54622, 4812),]
163 self.failUnlessEqual(len(g.summary), 1)
165 summary_lane = g.summary[0][i]
166 self.failUnlessEqual(summary_lane.cluster, clusters[i])
167 self.failUnlessEqual(summary_lane.lane, i)
169 xml = g.get_elements()
170 # just make sure that element tree can serialize the tree
171 xml_str = ElementTree.tostring(xml)
172 g2 = gerald.Gerald(xml=xml)
174 # do it all again after extracting from the xml file
175 self.failUnlessEqual(g.version, g2.version)
176 self.failUnlessEqual(g.date, g2.date)
177 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
178 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
180 # test lane specific parameters from gerald config file
183 g2_lane = g2.lanes[i]
184 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
185 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
186 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
187 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
189 # test (some) summary elements
190 self.failUnlessEqual(len(g.summary), 1)
192 g_summary = g.summary[0][i]
193 g2_summary = g2.summary[0][i]
194 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
195 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
197 g_eland = g.eland_results
198 g2_eland = g2.eland_results
199 for lane in g_eland.results[0].keys():
200 g_results = g_eland.results[0][lane]
201 g2_results = g2_eland.results[0][lane]
202 self.failUnlessEqual(g_results.reads,
204 self.failUnlessEqual(len(g_results.mapped_reads),
205 len(g2_results.mapped_reads))
206 for k in g_results.mapped_reads.keys():
207 self.failUnlessEqual(g_results.mapped_reads[k],
208 g2_results.mapped_reads[k])
210 self.failUnlessEqual(len(g_results.match_codes),
211 len(g2_results.match_codes))
212 for k in g_results.match_codes.keys():
213 self.failUnlessEqual(g_results.match_codes[k],
214 g2_results.match_codes[k])
217 def test_eland(self):
218 hg_map = {'Lambda.fa': 'Lambda.fa'}
219 for i in range(1,22):
220 short_name = 'chr%d.fa' % (i,)
221 long_name = 'hg18/chr%d.fa' % (i,)
222 hg_map[short_name] = long_name
224 genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
225 5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
226 eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
229 lane = eland.results[0][i]
230 self.failUnlessEqual(lane.reads, 6)
231 self.failUnlessEqual(lane.sample_name, "s")
232 self.failUnlessEqual(lane.lane_id, i)
233 self.failUnlessEqual(len(lane.mapped_reads), 17)
234 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
235 self.failUnlessEqual(lane.mapped_reads['spike.fa/sample1'], 1)
236 self.failUnlessEqual(lane.mapped_reads['spike.fa/sample2'], 1)
237 self.failUnlessEqual(lane.match_codes['U0'], 3)
238 self.failUnlessEqual(lane.match_codes['R0'], 2)
239 self.failUnlessEqual(lane.match_codes['U1'], 1)
240 self.failUnlessEqual(lane.match_codes['R1'], 9)
241 self.failUnlessEqual(lane.match_codes['U2'], 0)
242 self.failUnlessEqual(lane.match_codes['R2'], 12)
243 self.failUnlessEqual(lane.match_codes['NM'], 1)
244 self.failUnlessEqual(lane.match_codes['QC'], 0)
246 xml = eland.get_elements()
247 # just make sure that element tree can serialize the tree
248 xml_str = ElementTree.tostring(xml)
249 e2 = gerald.ELAND(xml=xml)
252 l1 = eland.results[0][i]
253 l2 = e2.results[0][i]
254 self.failUnlessEqual(l1.reads, l2.reads)
255 self.failUnlessEqual(l1.sample_name, l2.sample_name)
256 self.failUnlessEqual(l1.lane_id, l2.lane_id)
257 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
258 self.failUnlessEqual(len(l1.mapped_reads), 17)
259 for k in l1.mapped_reads.keys():
260 self.failUnlessEqual(l1.mapped_reads[k],
263 self.failUnlessEqual(len(l1.match_codes), 9)
264 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
265 for k in l1.match_codes.keys():
266 self.failUnlessEqual(l1.match_codes[k],
269 def test_runfolder(self):
270 runs = runfolder.get_runs(self.runfolder_dir)
272 # do we get the flowcell id from the filename?
273 self.failUnlessEqual(len(runs), 1)
274 name = 'run_207BTAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
275 self.failUnlessEqual(runs[0].name, name)
277 # do we get the flowcell id from the FlowcellId.xml file
278 make_flowcell_id(self.runfolder_dir, '207BTAAXY')
279 runs = runfolder.get_runs(self.runfolder_dir)
280 self.failUnlessEqual(len(runs), 1)
281 name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
282 self.failUnlessEqual(runs[0].name, name)
285 xml = r1.get_elements()
286 xml_str = ElementTree.tostring(xml)
288 r2 = runfolder.PipelineRun(xml=xml)
289 self.failUnlessEqual(r1.name, r2.name)
290 self.failIfEqual(r2.image_analysis, None)
291 self.failIfEqual(r2.bustard, None)
292 self.failIfEqual(r2.gerald, None)
296 return unittest.makeSuite(RunfolderTests,'test')
298 if __name__ == "__main__":
299 unittest.main(defaultTest="suite")