3 from datetime import datetime, date
7 from unittest import TestCase
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 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 '081017_HWI-EAS229_0062_30J55AAXX')
27 os.mkdir(runfolder_dir)
29 data_dir = os.path.join(runfolder_dir, 'Data')
32 firecrest_dir = os.path.join(data_dir,
33 'C1-37_Firecrest1.9.6_20-10-2008_diane')
34 os.mkdir(firecrest_dir)
36 bustard_dir = os.path.join(firecrest_dir,
37 'Bustard1.9.6_20-10-2008_diane')
39 make_phasing_params(bustard_dir)
41 matrix_name = os.path.join(bustard_dir, 'matrix1.txt')
42 make_matrix(matrix_name)
45 gerald_dir = os.path.join(bustard_dir,
46 'GERALD_20-10-2008_diane')
48 make_gerald_config_100(gerald_dir)
49 make_summary_htm_110(gerald_dir)
50 make_eland_multi(gerald_dir)
53 obj.temp_dir = temp_dir
54 obj.runfolder_dir = runfolder_dir
55 obj.data_dir = data_dir
56 obj.image_analysis_dir = firecrest_dir
57 obj.bustard_dir = bustard_dir
58 obj.gerald_dir = gerald_dir
61 class RunfolderTests(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, 37)
82 self.failUnlessEqual(f.user, 'diane')
83 self.failUnlessEqual(f.date, date(2008,10,20))
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.software, f2.software)
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.software, 'Bustard')
102 self.failUnlessEqual(b.version, '1.9.6')
103 self.failUnlessEqual(b.date, date(2008,10,20))
104 self.failUnlessEqual(b.user, 'diane')
105 self.failUnlessEqual(len(b.phasing), 8)
106 self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
108 xml = b.get_elements()
109 b2 = bustard.Bustard(xml=xml)
110 self.failUnlessEqual(b.software, b2.software)
111 self.failUnlessEqual(b.version, b2.version)
112 self.failUnlessEqual(b.date, b2.date )
113 self.failUnlessEqual(b.user, b2.user)
114 self.failUnlessEqual(len(b.phasing), len(b2.phasing))
115 for key in b.phasing.keys():
116 self.failUnlessEqual(b.phasing[key].lane,
117 b2.phasing[key].lane)
118 self.failUnlessEqual(b.phasing[key].phasing,
119 b2.phasing[key].phasing)
120 self.failUnlessEqual(b.phasing[key].prephasing,
121 b2.phasing[key].prephasing)
123 def test_gerald(self):
124 # need to update gerald and make tests for it
125 g = gerald.gerald(self.gerald_dir)
127 self.failUnlessEqual(g.software, 'GERALD')
128 self.failUnlessEqual(g.version, '1.171')
129 self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
130 self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
131 self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
134 # list of genomes, matches what was defined up in
135 # make_gerald_config.
136 # the first None is to offset the genomes list to be 1..9
137 # instead of pythons default 0..8
142 '/g/arabidopsis01222004',
148 # test lane specific parameters from gerald config file
150 cur_lane = g.lanes[i]
151 self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
152 self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
153 self.failUnlessEqual(cur_lane.read_length, '37')
154 self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
156 # I want to be able to use a simple iterator
157 for l in g.lanes.values():
158 self.failUnlessEqual(l.analysis, 'eland_extended')
159 self.failUnlessEqual(l.read_length, '37')
160 self.failUnlessEqual(l.use_bases, 'Y'*37)
162 # raw cluster numbers extracted from summary file
163 # its the first +/- value in the lane results summary
166 (190220, 15118), (190560, 14399),
167 (187597, 12369), (204142, 16877),
168 (247308, 11600), (204298, 15640),
169 (202707, 15404), (198075, 14702),]
171 self.failUnlessEqual(len(g.summary), 1)
173 summary_lane = g.summary[0][i]
174 self.failUnlessEqual(summary_lane.cluster, clusters[i])
175 self.failUnlessEqual(summary_lane.lane, i)
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.software, g2.software)
184 self.failUnlessEqual(g.version, g2.version)
185 self.failUnlessEqual(g.date, g2.date)
186 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
187 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
189 # test lane specific parameters from gerald config file
192 g2_lane = g2.lanes[i]
193 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
194 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
195 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
196 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
198 self.failUnlessEqual(len(g.summary), 1)
199 # test (some) summary elements
201 g_summary = g.summary[0][i]
202 g2_summary = g2.summary[0][i]
203 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
204 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
206 g_eland = g.eland_results
207 g2_eland = g2.eland_results
209 g_results = g_eland[key]
210 g2_results = g2_eland[key]
211 self.failUnlessEqual(g_results.reads,
213 self.failUnlessEqual(len(g_results.mapped_reads),
214 len(g2_results.mapped_reads))
215 for k in g_results.mapped_reads.keys():
216 self.failUnlessEqual(g_results.mapped_reads[k],
217 g2_results.mapped_reads[k])
219 self.failUnlessEqual(len(g_results.match_codes),
220 len(g2_results.match_codes))
221 for k in g_results.match_codes.keys():
222 self.failUnlessEqual(g_results.match_codes[k],
223 g2_results.match_codes[k])
226 def test_eland(self):
227 hg_map = {'Lambda.fa': 'Lambda.fa'}
228 for i in range(1,22):
229 short_name = 'chr%d.fa' % (i,)
230 long_name = 'hg18/chr%d.fa' % (i,)
231 hg_map[short_name] = long_name
233 genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
234 5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
235 eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
239 self.failUnlessEqual(lane.reads, 6)
240 self.failUnlessEqual(lane.sample_name, "s")
241 self.failUnlessEqual(lane.lane_id, key.lane)
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)
253 xml = eland.get_elements()
254 # just make sure that element tree can serialize the tree
255 xml_str = ElementTree.tostring(xml)
256 e2 = gerald.ELAND(xml=xml)
261 self.failUnlessEqual(l1.reads, l2.reads)
262 self.failUnlessEqual(l1.sample_name, l2.sample_name)
263 self.failUnlessEqual(l1.lane_id, l2.lane_id)
264 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
265 self.failUnlessEqual(len(l1.mapped_reads), 17)
266 for k in l1.mapped_reads.keys():
267 self.failUnlessEqual(l1.mapped_reads[k],
270 self.failUnlessEqual(len(l1.match_codes), 9)
271 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
272 for k in l1.match_codes.keys():
273 self.failUnlessEqual(l1.match_codes[k],
276 def test_runfolder(self):
277 runs = runfolder.get_runs(self.runfolder_dir)
279 # do we get the flowcell id from the filename?
280 self.failUnlessEqual(len(runs), 1)
281 name = 'run_30J55AAXX_2009-02-22.xml'
282 self.failUnlessEqual(runs[0].serialization_filename, name)
284 # do we get the flowcell id from the FlowcellId.xml file
285 make_flowcell_id(self.runfolder_dir, '30J55AAXX')
286 runs = runfolder.get_runs(self.runfolder_dir)
287 self.failUnlessEqual(len(runs), 1)
288 name = 'run_30J55AAXX_2009-02-22.xml'
289 self.failUnlessEqual(runs[0].serialization_filename, name)
292 xml = r1.get_elements()
293 xml_str = ElementTree.tostring(xml)
295 r2 = runfolder.PipelineRun(xml=xml)
296 self.failUnlessEqual(r1.serialization_filename, r2.serialization_filename)
297 self.failIfEqual(r2.image_analysis, None)
298 self.failIfEqual(r2.bustard, None)
299 self.failIfEqual(r2.gerald, None)
303 from unittest import TestSuite, defaultTestLoader
305 suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
309 if __name__ == "__main__":
310 from unittest import main
311 main(defaultTest="suite")