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 make_matrix(matrix_dir)
38 bustard_dir = os.path.join(ipar_dir,
39 'Bustard1.8.28_12-04-2008_diane')
41 make_phasing_params(bustard_dir)
43 gerald_dir = os.path.join(bustard_dir,
44 'GERALD_12-04-2008_diane')
46 make_gerald_config(gerald_dir)
47 make_summary_paired_htm(gerald_dir)
48 make_eland_multi(gerald_dir, paired=True)
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
60 class RunfolderTests(unittest.TestCase):
62 Test components of the runfolder processing code
63 which includes firecrest, bustard, and gerald
66 # attaches all the directories to the object passed in
70 shutil.rmtree(self.temp_dir)
72 def test_firecrest(self):
74 Construct a firecrest object
76 f = firecrest.firecrest(self.image_analysis_dir)
77 self.failUnlessEqual(f.version, '1.9.6')
78 self.failUnlessEqual(f.start, 1)
79 self.failUnlessEqual(f.stop, 152)
80 self.failUnlessEqual(f.user, 'diane')
81 # As of 2008-12-8, the date was being set in
82 # simulate_runfolder.make_firecrest_dir
83 self.failUnlessEqual(f.date, date(2008,4,12))
85 xml = f.get_elements()
86 # just make sure that element tree can serialize the tree
87 xml_str = ElementTree.tostring(xml)
89 f2 = firecrest.Firecrest(xml=xml)
90 self.failUnlessEqual(f.version, f2.version)
91 self.failUnlessEqual(f.start, f2.start)
92 self.failUnlessEqual(f.stop, f2.stop)
93 self.failUnlessEqual(f.user, f2.user)
95 def test_bustard(self):
97 construct a bustard object
99 b = bustard.bustard(self.bustard_dir)
100 self.failUnlessEqual(b.version, '1.8.28')
101 self.failUnlessEqual(b.date, date(2008,4,12))
102 self.failUnlessEqual(b.user, 'diane')
103 self.failUnlessEqual(len(b.phasing), 8)
104 self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
106 xml = b.get_elements()
107 b2 = bustard.Bustard(xml=xml)
108 self.failUnlessEqual(b.version, b2.version)
109 self.failUnlessEqual(b.date, b2.date )
110 self.failUnlessEqual(b.user, b2.user)
111 self.failUnlessEqual(len(b.phasing), len(b2.phasing))
112 for key in b.phasing.keys():
113 self.failUnlessEqual(b.phasing[key].lane,
114 b2.phasing[key].lane)
115 self.failUnlessEqual(b.phasing[key].phasing,
116 b2.phasing[key].phasing)
117 self.failUnlessEqual(b.phasing[key].prephasing,
118 b2.phasing[key].prephasing)
120 def test_gerald(self):
121 # need to update gerald and make tests for it
122 g = gerald.gerald(self.gerald_dir)
124 self.failUnlessEqual(g.version,
125 '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp')
126 self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
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
135 genomes = [None, '/g/dm3', '/g/equcab1', '/g/equcab1', '/g/canfam2',
136 '/g/hg18', '/g/hg18', '/g/hg18', '/g/hg18', ]
138 # test lane specific parameters from gerald config file
140 cur_lane = g.lanes[i]
141 self.failUnlessEqual(cur_lane.analysis, 'eland')
142 self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
143 self.failUnlessEqual(cur_lane.read_length, '32')
144 self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
146 # I want to be able to use a simple iterator
147 for l in g.lanes.values():
148 self.failUnlessEqual(l.analysis, 'eland')
149 self.failUnlessEqual(l.read_length, '32')
150 self.failUnlessEqual(l.use_bases, 'Y'*32)
152 # test data extracted from summary file
154 (103646, 4515), (106678, 4652),
155 (84583, 5963), (68813, 4782),
156 (104854, 4664), (43555, 1632),
157 (54265, 1588), (64363, 2697),],
159 (103647, 4516), (106679, 4653),
160 (84584, 5964), (68814, 4783),
161 (104855, 4665), (43556, 1633),
162 (54266, 1589), (64364, 2698),],]
165 for lane in range(1,9):
166 summary_lane = g.summary[end][lane]
167 self.failUnlessEqual(summary_lane.cluster, clusters[end][lane])
168 self.failUnlessEqual(summary_lane.lane, lane)
170 xml = g.get_elements()
171 # just make sure that element tree can serialize the tree
172 xml_str = ElementTree.tostring(xml)
173 g2 = gerald.Gerald(xml=xml)
175 # do it all again after extracting from the xml file
176 self.failUnlessEqual(g.version, g2.version)
177 self.failUnlessEqual(g.date, g2.date)
178 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
179 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
181 # test lane specific parameters from gerald config file
184 g2_lane = g2.lanes[i]
185 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
186 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
187 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
188 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
190 # test (some) summary elements
193 g_summary = g.summary[end][i]
194 g2_summary = g2.summary[end][i]
195 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
196 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
198 g_eland = g.eland_results
199 g2_eland = g2.eland_results
200 for lane in g_eland.results[end].keys():
201 g_results = g_eland.results[end][lane]
202 g2_results = g_eland.results[end][lane]
203 self.failUnlessEqual(g_results.reads,
205 self.failUnlessEqual(len(g_results.mapped_reads),
206 len(g2_results.mapped_reads))
207 for k in g_results.mapped_reads.keys():
208 self.failUnlessEqual(g_results.mapped_reads[k],
209 g2_results.mapped_reads[k])
211 self.failUnlessEqual(len(g_results.match_codes),
212 len(g2_results.match_codes))
213 for k in g_results.match_codes.keys():
214 self.failUnlessEqual(g_results.match_codes[k],
215 g2_results.match_codes[k])
218 def test_eland(self):
219 hg_map = {'Lambda.fa': 'Lambda.fa'}
220 for i in range(1,22):
221 short_name = 'chr%d.fa' % (i,)
222 long_name = 'hg18/chr%d.fa' % (i,)
223 hg_map[short_name] = long_name
225 genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
226 5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
227 eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
231 lane = eland.results[0][i]
232 self.failUnlessEqual(lane.reads, 4)
233 self.failUnlessEqual(lane.sample_name, "s")
234 self.failUnlessEqual(lane.lane_id, i)
235 self.failUnlessEqual(len(lane.mapped_reads), 15)
236 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
237 self.failUnlessEqual(lane.match_codes['U0'], 1)
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)
248 lane = eland.results[1][i]
249 self.failUnlessEqual(lane.reads, 5)
250 self.failUnlessEqual(lane.sample_name, "s")
251 self.failUnlessEqual(lane.lane_id, i)
252 self.failUnlessEqual(len(lane.mapped_reads), 15)
253 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
254 self.failUnlessEqual(lane.match_codes['U0'], 1)
255 self.failUnlessEqual(lane.match_codes['R0'], 2)
256 self.failUnlessEqual(lane.match_codes['U1'], 1)
257 self.failUnlessEqual(lane.match_codes['R1'], 9)
258 self.failUnlessEqual(lane.match_codes['U2'], 0)
259 self.failUnlessEqual(lane.match_codes['R2'], 12)
260 self.failUnlessEqual(lane.match_codes['NM'], 1)
261 self.failUnlessEqual(lane.match_codes['QC'], 1)
263 xml = eland.get_elements()
264 # just make sure that element tree can serialize the tree
265 xml_str = ElementTree.tostring(xml)
266 e2 = gerald.ELAND(xml=xml)
270 l1 = eland.results[end][i]
271 l2 = e2.results[end][i]
272 self.failUnlessEqual(l1.reads, l2.reads)
273 self.failUnlessEqual(l1.sample_name, l2.sample_name)
274 self.failUnlessEqual(l1.lane_id, l2.lane_id)
275 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
276 self.failUnlessEqual(len(l1.mapped_reads), 15)
277 for k in l1.mapped_reads.keys():
278 self.failUnlessEqual(l1.mapped_reads[k],
281 self.failUnlessEqual(len(l1.match_codes), 9)
282 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
283 for k in l1.match_codes.keys():
284 self.failUnlessEqual(l1.match_codes[k],
287 def test_runfolder(self):
288 runs = runfolder.get_runs(self.runfolder_dir)
290 # do we get the flowcell id from the filename?
291 self.failUnlessEqual(len(runs), 1)
292 # firecrest's date depends on filename not the create time.
293 name = 'run_207BTAAXX_2008-04-19.xml'
294 self.failUnlessEqual(runs[0].name, name)
296 # do we get the flowcell id from the FlowcellId.xml file
297 make_flowcell_id(self.runfolder_dir, '207BTAAXY')
298 runs = runfolder.get_runs(self.runfolder_dir)
299 self.failUnlessEqual(len(runs), 1)
300 name = 'run_207BTAAXY_2008-04-19.xml'
301 self.failUnlessEqual(runs[0].name, name)
304 xml = r1.get_elements()
305 xml_str = ElementTree.tostring(xml)
307 r2 = runfolder.PipelineRun(xml=xml)
308 self.failUnlessEqual(r1.name, r2.name)
309 self.failIfEqual(r2.image_analysis, None)
310 self.failIfEqual(r2.bustard, None)
311 self.failIfEqual(r2.gerald, None)
315 return unittest.makeSuite(RunfolderTests,'test')
317 if __name__ == "__main__":
318 unittest.main(defaultTest="suite")