3 from datetime import datetime, date
7 from unittest2 import TestCase
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 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(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.software, 'IPAR')
79 self.failUnlessEqual(i.version, '2.01.192.0')
80 self.failUnlessEqual(i.start, 1)
81 self.failUnlessEqual(i.stop, 37)
83 xml = i.get_elements()
84 # just make sure that element tree can serialize the tree
85 xml_str = ElementTree.tostring(xml)
87 i2 = ipar.IPAR(xml=xml)
88 self.failUnlessEqual(i.software, i2.software)
89 self.failUnlessEqual(i.version, i2.version)
90 self.failUnlessEqual(i.start, i2.start)
91 self.failUnlessEqual(i.stop, i2.stop)
92 self.failUnlessEqual(i.date, i2.date)
93 self.failUnlessEqual(i.file_list(), i2.file_list())
95 def test_bustard(self):
97 construct a bustard object
99 b = bustard.bustard(self.bustard_dir)
100 self.failUnlessEqual(b.software, 'Bustard')
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.software, b2.software)
110 self.failUnlessEqual(b.version, b2.version)
111 self.failUnlessEqual(b.date, b2.date )
112 self.failUnlessEqual(b.user, b2.user)
113 self.failUnlessEqual(len(b.phasing), len(b2.phasing))
114 for key in b.phasing.keys():
115 self.failUnlessEqual(b.phasing[key].lane,
116 b2.phasing[key].lane)
117 self.failUnlessEqual(b.phasing[key].phasing,
118 b2.phasing[key].phasing)
119 self.failUnlessEqual(b.phasing[key].prephasing,
120 b2.phasing[key].prephasing)
122 def test_gerald(self):
123 # need to update gerald and make tests for it
124 g = gerald.gerald(self.gerald_dir)
126 self.failUnlessEqual(g.software, 'GERALD')
127 self.failUnlessEqual(g.version, '1.171')
128 self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
129 self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
130 self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
133 # list of genomes, matches what was defined up in
134 # make_gerald_config.
135 # the first None is to offset the genomes list to be 1..9
136 # instead of pythons default 0..8
141 '/g/arabidopsis01222004',
147 # test lane specific parameters from gerald config file
149 cur_lane = g.lanes[i]
150 self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
151 self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
152 self.failUnlessEqual(cur_lane.read_length, '37')
153 self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
155 # I want to be able to use a simple iterator
156 for l in g.lanes.values():
157 self.failUnlessEqual(l.analysis, 'eland_extended')
158 self.failUnlessEqual(l.read_length, '37')
159 self.failUnlessEqual(l.use_bases, 'Y'*37)
161 # test data extracted from summary file
163 (96483, 9074), (133738, 7938),
164 (152142, 10002), (15784, 2162),
165 (119735, 8465), (152177, 8146),
166 (84649, 7325), (54622, 4812),]
168 self.failUnlessEqual(len(g.summary), 1)
170 summary_lane = g.summary[0][i]
171 self.failUnlessEqual(summary_lane.cluster, clusters[i])
172 self.failUnlessEqual(summary_lane.lane, i)
174 xml = g.get_elements()
175 # just make sure that element tree can serialize the tree
176 xml_str = ElementTree.tostring(xml)
177 g2 = gerald.Gerald(xml=xml)
179 # do it all again after extracting from the xml file
180 self.failUnlessEqual(g.software, g2.software)
181 self.failUnlessEqual(g.version, g2.version)
182 self.failUnlessEqual(g.date, g2.date)
183 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
184 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
186 # test lane specific parameters from gerald config file
189 g2_lane = g2.lanes[i]
190 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
191 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
192 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
193 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
195 # test (some) summary elements
196 self.failUnlessEqual(len(g.summary), 1)
198 g_summary = g.summary[0][i]
199 g2_summary = g2.summary[0][i]
200 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
201 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
203 g_eland = g.eland_results
204 g2_eland = g2.eland_results
206 g_results = g_eland[key]
207 g2_results = g2_eland[key]
208 self.failUnlessEqual(g_results.reads,
210 self.failUnlessEqual(len(g_results.mapped_reads),
211 len(g2_results.mapped_reads))
212 for k in g_results.mapped_reads.keys():
213 self.failUnlessEqual(g_results.mapped_reads[k],
214 g2_results.mapped_reads[k])
216 self.failUnlessEqual(len(g_results.match_codes),
217 len(g2_results.match_codes))
218 for k in g_results.match_codes.keys():
219 self.failUnlessEqual(g_results.match_codes[k],
220 g2_results.match_codes[k])
223 def test_eland(self):
224 hg_map = {'Lambda.fa': 'Lambda.fa'}
225 for i in range(1,22):
226 short_name = 'chr%d.fa' % (i,)
227 long_name = 'hg18/chr%d.fa' % (i,)
228 hg_map[short_name] = long_name
230 genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
231 5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
232 eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
236 self.failUnlessEqual(lane.reads, 6)
237 self.failUnlessEqual(lane.sample_name, "s")
238 self.failUnlessEqual(lane.lane_id, key.lane)
239 self.failUnlessEqual(len(lane.mapped_reads), 17)
240 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
241 self.failUnlessEqual(lane.mapped_reads['spike.fa/sample1'], 1)
242 self.failUnlessEqual(lane.mapped_reads['spike.fa/sample2'], 1)
243 self.failUnlessEqual(lane.match_codes['U0'], 3)
244 self.failUnlessEqual(lane.match_codes['R0'], 2)
245 self.failUnlessEqual(lane.match_codes['U1'], 1)
246 self.failUnlessEqual(lane.match_codes['R1'], 9)
247 self.failUnlessEqual(lane.match_codes['U2'], 0)
248 self.failUnlessEqual(lane.match_codes['R2'], 12)
249 self.failUnlessEqual(lane.match_codes['NM'], 1)
250 self.failUnlessEqual(lane.match_codes['QC'], 0)
252 xml = eland.get_elements()
253 # just make sure that element tree can serialize the tree
254 xml_str = ElementTree.tostring(xml)
255 e2 = gerald.ELAND(xml=xml)
260 self.failUnlessEqual(l1.reads, l2.reads)
261 self.failUnlessEqual(l1.sample_name, l2.sample_name)
262 self.failUnlessEqual(l1.lane_id, l2.lane_id)
263 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
264 self.failUnlessEqual(len(l1.mapped_reads), 17)
265 for k in l1.mapped_reads.keys():
266 self.failUnlessEqual(l1.mapped_reads[k],
269 self.failUnlessEqual(len(l1.match_codes), 9)
270 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
271 for k in l1.match_codes.keys():
272 self.failUnlessEqual(l1.match_codes[k],
275 def test_runfolder(self):
276 runs = runfolder.get_runs(self.runfolder_dir)
278 # do we get the flowcell id from the filename?
279 self.failUnlessEqual(len(runs), 1)
280 name = 'run_207BTAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
281 self.failUnlessEqual(runs[0].name, name)
283 # do we get the flowcell id from the FlowcellId.xml file
284 make_flowcell_id(self.runfolder_dir, '207BTAAXY')
285 runs = runfolder.get_runs(self.runfolder_dir)
286 self.failUnlessEqual(len(runs), 1)
287 name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
288 self.failUnlessEqual(runs[0].name, name)
291 xml = r1.get_elements()
292 xml_str = ElementTree.tostring(xml)
294 r2 = runfolder.PipelineRun(xml=xml)
295 self.failUnlessEqual(r1.name, r2.name)
296 self.failIfEqual(r2.image_analysis, None)
297 self.failIfEqual(r2.bustard, None)
298 self.failIfEqual(r2.gerald, None)
302 from unittest2 import TestSuite, defaultTestLoader
304 suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
308 if __name__ == "__main__":
309 from unittest2 import main
310 main(defaultTest="suite")