3 from datetime import datetime, date
9 from htsworkflow.pipelines import firecrest
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_firecrest_dir(data_dir, "1.9.6", 1, 152)
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_paired_htm(gerald_dir)
49 make_eland_multi(gerald_dir, paired=True)
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)
73 def test_firecrest(self):
75 Construct a firecrest object
77 f = firecrest.firecrest(self.image_analysis_dir)
78 self.failUnlessEqual(f.version, '1.9.6')
79 self.failUnlessEqual(f.start, 1)
80 self.failUnlessEqual(f.stop, 152)
81 self.failUnlessEqual(f.user, 'diane')
82 # As of 2008-12-8, the date was being set in
83 # simulate_runfolder.make_firecrest_dir
84 self.failUnlessEqual(f.date, date(2008,4,12))
86 xml = f.get_elements()
87 # just make sure that element tree can serialize the tree
88 xml_str = ElementTree.tostring(xml)
90 f2 = firecrest.Firecrest(xml=xml)
91 self.failUnlessEqual(f.version, f2.version)
92 self.failUnlessEqual(f.start, f2.start)
93 self.failUnlessEqual(f.stop, f2.stop)
94 self.failUnlessEqual(f.user, f2.user)
96 def test_bustard(self):
98 construct a bustard object
100 b = bustard.bustard(self.bustard_dir)
101 self.failUnlessEqual(b.version, '1.8.28')
102 self.failUnlessEqual(b.date, date(2008,4,12))
103 self.failUnlessEqual(b.user, 'diane')
104 self.failUnlessEqual(len(b.phasing), 8)
105 self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
107 xml = b.get_elements()
108 b2 = bustard.Bustard(xml=xml)
109 self.failUnlessEqual(b.version, b2.version)
110 self.failUnlessEqual(b.date, b2.date )
111 self.failUnlessEqual(b.user, b2.user)
112 self.failUnlessEqual(len(b.phasing), len(b2.phasing))
113 for key in b.phasing.keys():
114 self.failUnlessEqual(b.phasing[key].lane,
115 b2.phasing[key].lane)
116 self.failUnlessEqual(b.phasing[key].phasing,
117 b2.phasing[key].phasing)
118 self.failUnlessEqual(b.phasing[key].prephasing,
119 b2.phasing[key].prephasing)
121 def test_gerald(self):
122 # need to update gerald and make tests for it
123 g = gerald.gerald(self.gerald_dir)
125 self.failUnlessEqual(g.version, '1.171')
126 self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
127 self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
128 self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
131 # list of genomes, matches what was defined up in
132 # make_gerald_config.
133 # the first None is to offset the genomes list to be 1..9
134 # instead of pythons default 0..8
139 '/g/arabidopsis01222004',
145 # test lane specific parameters from gerald config file
147 cur_lane = g.lanes[i]
148 self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
149 self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
150 self.failUnlessEqual(cur_lane.read_length, '37')
151 self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
153 # I want to be able to use a simple iterator
154 for l in g.lanes.values():
155 self.failUnlessEqual(l.analysis, 'eland_extended')
156 self.failUnlessEqual(l.read_length, '37')
157 self.failUnlessEqual(l.use_bases, 'Y'*37)
159 # test data extracted from summary file
161 (103646, 4515), (106678, 4652),
162 (84583, 5963), (68813, 4782),
163 (104854, 4664), (43555, 1632),
164 (54265, 1588), (64363, 2697),],
166 (103647, 4516), (106679, 4653),
167 (84584, 5964), (68814, 4783),
168 (104855, 4665), (43556, 1633),
169 (54266, 1589), (64364, 2698),],]
172 for lane in range(1,9):
173 summary_lane = g.summary[end][lane]
174 self.failUnlessEqual(summary_lane.cluster, clusters[end][lane])
175 self.failUnlessEqual(summary_lane.lane, lane)
177 xml = g.get_elements()
178 # just make sure that element tree can serialize the tree
179 xml_str = ElementTree.tostring(xml)
180 g2 = gerald.Gerald(xml=xml)
182 # do it all again after extracting from the xml file
183 self.failUnlessEqual(g.version, g2.version)
184 self.failUnlessEqual(g.date, g2.date)
185 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
186 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
188 # test lane specific parameters from gerald config file
191 g2_lane = g2.lanes[i]
192 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
193 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
194 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
195 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
197 # test (some) summary elements
200 g_summary = g.summary[end][i]
201 g2_summary = g2.summary[end][i]
202 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
203 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
205 g_eland = g.eland_results
206 g2_eland = g2.eland_results
207 for lane in g_eland.results[end].keys():
208 g_results = g_eland.results[end][lane]
209 g2_results = g_eland.results[end][lane]
210 self.failUnlessEqual(g_results.reads,
212 self.failUnlessEqual(len(g_results.mapped_reads),
213 len(g2_results.mapped_reads))
214 for k in g_results.mapped_reads.keys():
215 self.failUnlessEqual(g_results.mapped_reads[k],
216 g2_results.mapped_reads[k])
218 self.failUnlessEqual(len(g_results.match_codes),
219 len(g2_results.match_codes))
220 for k in g_results.match_codes.keys():
221 self.failUnlessEqual(g_results.match_codes[k],
222 g2_results.match_codes[k])
225 def test_eland(self):
226 hg_map = {'Lambda.fa': 'Lambda.fa'}
227 for i in range(1,22):
228 short_name = 'chr%d.fa' % (i,)
229 long_name = 'hg18/chr%d.fa' % (i,)
230 hg_map[short_name] = long_name
232 genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
233 5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
234 eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
238 lane = eland.results[0][i]
239 self.failUnlessEqual(lane.reads, 6)
240 self.failUnlessEqual(lane.sample_name, "s")
241 self.failUnlessEqual(lane.lane_id, i)
242 self.failUnlessEqual(len(lane.mapped_reads), 17)
243 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
244 self.failUnlessEqual(lane.match_codes['U0'], 3)
245 self.failUnlessEqual(lane.match_codes['R0'], 2)
246 self.failUnlessEqual(lane.match_codes['U1'], 1)
247 self.failUnlessEqual(lane.match_codes['R1'], 9)
248 self.failUnlessEqual(lane.match_codes['U2'], 0)
249 self.failUnlessEqual(lane.match_codes['R2'], 12)
250 self.failUnlessEqual(lane.match_codes['NM'], 1)
251 self.failUnlessEqual(lane.match_codes['QC'], 0)
255 lane = eland.results[1][i]
256 self.failUnlessEqual(lane.reads, 7)
257 self.failUnlessEqual(lane.sample_name, "s")
258 self.failUnlessEqual(lane.lane_id, i)
259 self.failUnlessEqual(len(lane.mapped_reads), 17)
260 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
261 self.failUnlessEqual(lane.match_codes['U0'], 3)
262 self.failUnlessEqual(lane.match_codes['R0'], 2)
263 self.failUnlessEqual(lane.match_codes['U1'], 1)
264 self.failUnlessEqual(lane.match_codes['R1'], 9)
265 self.failUnlessEqual(lane.match_codes['U2'], 0)
266 self.failUnlessEqual(lane.match_codes['R2'], 12)
267 self.failUnlessEqual(lane.match_codes['NM'], 1)
268 self.failUnlessEqual(lane.match_codes['QC'], 1)
270 xml = eland.get_elements()
271 # just make sure that element tree can serialize the tree
272 xml_str = ElementTree.tostring(xml)
273 e2 = gerald.ELAND(xml=xml)
277 l1 = eland.results[end][i]
278 l2 = e2.results[end][i]
279 self.failUnlessEqual(l1.reads, l2.reads)
280 self.failUnlessEqual(l1.sample_name, l2.sample_name)
281 self.failUnlessEqual(l1.lane_id, l2.lane_id)
282 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
283 self.failUnlessEqual(len(l1.mapped_reads), 17)
284 for k in l1.mapped_reads.keys():
285 self.failUnlessEqual(l1.mapped_reads[k],
288 self.failUnlessEqual(len(l1.match_codes), 9)
289 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
290 for k in l1.match_codes.keys():
291 self.failUnlessEqual(l1.match_codes[k],
294 def test_runfolder(self):
295 runs = runfolder.get_runs(self.runfolder_dir)
297 # do we get the flowcell id from the filename?
298 self.failUnlessEqual(len(runs), 1)
299 # firecrest's date depends on filename not the create time.
300 name = 'run_207BTAAXX_2009-02-22.xml'
301 self.failUnlessEqual(runs[0].name, name)
303 # do we get the flowcell id from the FlowcellId.xml file
304 make_flowcell_id(self.runfolder_dir, '207BTAAXY')
305 runs = runfolder.get_runs(self.runfolder_dir)
306 self.failUnlessEqual(len(runs), 1)
307 name = 'run_207BTAAXY_2009-02-22.xml'
308 self.failUnlessEqual(runs[0].name, name)
311 xml = r1.get_elements()
312 xml_str = ElementTree.tostring(xml)
314 r2 = runfolder.PipelineRun(xml=xml)
315 self.failUnlessEqual(r1.name, r2.name)
316 self.failIfEqual(r2.image_analysis, None)
317 self.failIfEqual(r2.bustard, None)
318 self.failIfEqual(r2.gerald, None)
322 return unittest.makeSuite(RunfolderTests,'test')
324 if __name__ == "__main__":
325 unittest.main(defaultTest="suite")