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.software, 'Firecrest')
79 self.failUnlessEqual(f.version, '1.9.6')
80 self.failUnlessEqual(f.start, 1)
81 self.failUnlessEqual(f.stop, 152)
82 self.failUnlessEqual(f.user, 'diane')
83 # As of 2008-12-8, the date was being set in
84 # simulate_runfolder.make_firecrest_dir
85 self.failUnlessEqual(f.date, date(2008,4,12))
87 xml = f.get_elements()
88 # just make sure that element tree can serialize the tree
89 xml_str = ElementTree.tostring(xml)
91 f2 = firecrest.Firecrest(xml=xml)
92 self.failUnlessEqual(f.software, f2.software)
93 self.failUnlessEqual(f.version, f2.version)
94 self.failUnlessEqual(f.start, f2.start)
95 self.failUnlessEqual(f.stop, f2.stop)
96 self.failUnlessEqual(f.user, f2.user)
98 def test_bustard(self):
100 construct a bustard object
102 b = bustard.bustard(self.bustard_dir)
103 self.failUnlessEqual(b.software, 'Bustard')
104 self.failUnlessEqual(b.version, '1.8.28')
105 self.failUnlessEqual(b.date, date(2008,4,12))
106 self.failUnlessEqual(b.user, 'diane')
107 self.failUnlessEqual(len(b.phasing), 8)
108 self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
110 xml = b.get_elements()
111 b2 = bustard.Bustard(xml=xml)
112 self.failUnlessEqual(b.software, b2.software)
113 self.failUnlessEqual(b.version, b2.version)
114 self.failUnlessEqual(b.date, b2.date )
115 self.failUnlessEqual(b.user, b2.user)
116 self.failUnlessEqual(len(b.phasing), len(b2.phasing))
117 for key in b.phasing.keys():
118 self.failUnlessEqual(b.phasing[key].lane,
119 b2.phasing[key].lane)
120 self.failUnlessEqual(b.phasing[key].phasing,
121 b2.phasing[key].phasing)
122 self.failUnlessEqual(b.phasing[key].prephasing,
123 b2.phasing[key].prephasing)
125 def test_gerald(self):
126 # need to update gerald and make tests for it
127 g = gerald.gerald(self.gerald_dir)
129 self.failUnlessEqual(g.software, 'GERALD')
130 self.failUnlessEqual(g.version, '1.171')
131 self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
132 self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
133 self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
136 # list of genomes, matches what was defined up in
137 # make_gerald_config.
138 # the first None is to offset the genomes list to be 1..9
139 # instead of pythons default 0..8
144 '/g/arabidopsis01222004',
150 # test lane specific parameters from gerald config file
152 cur_lane = g.lanes[i]
153 self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
154 self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
155 self.failUnlessEqual(cur_lane.read_length, '37')
156 self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
158 # I want to be able to use a simple iterator
159 for l in g.lanes.values():
160 self.failUnlessEqual(l.analysis, 'eland_extended')
161 self.failUnlessEqual(l.read_length, '37')
162 self.failUnlessEqual(l.use_bases, 'Y'*37)
164 # test data extracted from summary file
166 (103646, 4515), (106678, 4652),
167 (84583, 5963), (68813, 4782),
168 (104854, 4664), (43555, 1632),
169 (54265, 1588), (64363, 2697),],
171 (103647, 4516), (106679, 4653),
172 (84584, 5964), (68814, 4783),
173 (104855, 4665), (43556, 1633),
174 (54266, 1589), (64364, 2698),],]
177 for lane in range(1,9):
178 summary_lane = g.summary[end][lane]
179 self.failUnlessEqual(summary_lane.cluster, clusters[end][lane])
180 self.failUnlessEqual(summary_lane.lane, lane)
182 xml = g.get_elements()
183 # just make sure that element tree can serialize the tree
184 xml_str = ElementTree.tostring(xml)
185 g2 = gerald.Gerald(xml=xml)
187 # do it all again after extracting from the xml file
188 self.failUnlessEqual(g.software, g2.software)
189 self.failUnlessEqual(g.version, g2.version)
190 self.failUnlessEqual(g.date, g2.date)
191 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
192 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
194 # test lane specific parameters from gerald config file
197 g2_lane = g2.lanes[i]
198 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
199 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
200 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
201 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
203 # test (some) summary elements
206 g_summary = g.summary[end][i]
207 g2_summary = g2.summary[end][i]
208 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
209 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
211 g_eland = g.eland_results
212 g2_eland = g2.eland_results
213 for lane in g_eland.results[end].keys():
214 g_results = g_eland.results[end][lane]
215 g2_results = g_eland.results[end][lane]
216 self.failUnlessEqual(g_results.reads,
218 self.failUnlessEqual(len(g_results.mapped_reads),
219 len(g2_results.mapped_reads))
220 for k in g_results.mapped_reads.keys():
221 self.failUnlessEqual(g_results.mapped_reads[k],
222 g2_results.mapped_reads[k])
224 self.failUnlessEqual(len(g_results.match_codes),
225 len(g2_results.match_codes))
226 for k in g_results.match_codes.keys():
227 self.failUnlessEqual(g_results.match_codes[k],
228 g2_results.match_codes[k])
231 def test_eland(self):
232 hg_map = {'Lambda.fa': 'Lambda.fa'}
233 for i in range(1,22):
234 short_name = 'chr%d.fa' % (i,)
235 long_name = 'hg18/chr%d.fa' % (i,)
236 hg_map[short_name] = long_name
238 genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
239 5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
240 eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
244 lane = eland.results[0][i]
245 self.failUnlessEqual(lane.reads, 6)
246 self.failUnlessEqual(lane.sample_name, "s")
247 self.failUnlessEqual(lane.lane_id, i)
248 self.failUnlessEqual(len(lane.mapped_reads), 17)
249 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
250 self.failUnlessEqual(lane.match_codes['U0'], 3)
251 self.failUnlessEqual(lane.match_codes['R0'], 2)
252 self.failUnlessEqual(lane.match_codes['U1'], 1)
253 self.failUnlessEqual(lane.match_codes['R1'], 9)
254 self.failUnlessEqual(lane.match_codes['U2'], 0)
255 self.failUnlessEqual(lane.match_codes['R2'], 12)
256 self.failUnlessEqual(lane.match_codes['NM'], 1)
257 self.failUnlessEqual(lane.match_codes['QC'], 0)
261 lane = eland.results[1][i]
262 self.failUnlessEqual(lane.reads, 7)
263 self.failUnlessEqual(lane.sample_name, "s")
264 self.failUnlessEqual(lane.lane_id, i)
265 self.failUnlessEqual(len(lane.mapped_reads), 17)
266 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
267 self.failUnlessEqual(lane.match_codes['U0'], 3)
268 self.failUnlessEqual(lane.match_codes['R0'], 2)
269 self.failUnlessEqual(lane.match_codes['U1'], 1)
270 self.failUnlessEqual(lane.match_codes['R1'], 9)
271 self.failUnlessEqual(lane.match_codes['U2'], 0)
272 self.failUnlessEqual(lane.match_codes['R2'], 12)
273 self.failUnlessEqual(lane.match_codes['NM'], 1)
274 self.failUnlessEqual(lane.match_codes['QC'], 1)
276 xml = eland.get_elements()
277 # just make sure that element tree can serialize the tree
278 xml_str = ElementTree.tostring(xml)
279 e2 = gerald.ELAND(xml=xml)
283 l1 = eland.results[end][i]
284 l2 = e2.results[end][i]
285 self.failUnlessEqual(l1.reads, l2.reads)
286 self.failUnlessEqual(l1.sample_name, l2.sample_name)
287 self.failUnlessEqual(l1.lane_id, l2.lane_id)
288 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
289 self.failUnlessEqual(len(l1.mapped_reads), 17)
290 for k in l1.mapped_reads.keys():
291 self.failUnlessEqual(l1.mapped_reads[k],
294 self.failUnlessEqual(len(l1.match_codes), 9)
295 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
296 for k in l1.match_codes.keys():
297 self.failUnlessEqual(l1.match_codes[k],
300 def test_runfolder(self):
301 runs = runfolder.get_runs(self.runfolder_dir)
303 # do we get the flowcell id from the filename?
304 self.failUnlessEqual(len(runs), 1)
305 # firecrest's date depends on filename not the create time.
306 name = 'run_207BTAAXX_2009-02-22.xml'
307 self.failUnlessEqual(runs[0].name, name)
309 # do we get the flowcell id from the FlowcellId.xml file
310 make_flowcell_id(self.runfolder_dir, '207BTAAXY')
311 runs = runfolder.get_runs(self.runfolder_dir)
312 self.failUnlessEqual(len(runs), 1)
313 name = 'run_207BTAAXY_2009-02-22.xml'
314 self.failUnlessEqual(runs[0].name, name)
317 xml = r1.get_elements()
318 xml_str = ElementTree.tostring(xml)
320 r2 = runfolder.PipelineRun(xml=xml)
321 self.failUnlessEqual(r1.name, r2.name)
322 self.failIfEqual(r2.image_analysis, None)
323 self.failIfEqual(r2.bustard, None)
324 self.failIfEqual(r2.gerald, None)
328 return unittest.makeSuite(RunfolderTests,'test')
330 if __name__ == "__main__":
331 unittest.main(defaultTest="suite")