3 from datetime import datetime, date
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.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_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(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)
75 Construct a firecrest object
77 i = ipar.ipar(self.image_analysis_dir)
78 self.failUnlessEqual(i.version, '2.01.192.0')
79 self.failUnlessEqual(i.start, 1)
80 self.failUnlessEqual(i.stop, 37)
82 xml = i.get_elements()
83 # just make sure that element tree can serialize the tree
84 xml_str = ElementTree.tostring(xml)
86 i2 = ipar.IPAR(xml=xml)
87 self.failUnlessEqual(i.version, i2.version)
88 self.failUnlessEqual(i.start, i2.start)
89 self.failUnlessEqual(i.stop, i2.stop)
90 self.failUnlessEqual(i.date, i2.date)
91 self.failUnlessEqual(i.file_list(), i2.file_list())
93 def test_bustard(self):
95 construct a bustard object
97 b = bustard.bustard(self.bustard_dir)
98 self.failUnlessEqual(b.version, '1.8.28')
99 self.failUnlessEqual(b.date, date(2008,4,12))
100 self.failUnlessEqual(b.user, 'diane')
101 self.failUnlessEqual(len(b.phasing), 8)
102 self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
104 xml = b.get_elements()
105 b2 = bustard.Bustard(xml=xml)
106 self.failUnlessEqual(b.version, b2.version)
107 self.failUnlessEqual(b.date, b2.date )
108 self.failUnlessEqual(b.user, b2.user)
109 self.failUnlessEqual(len(b.phasing), len(b2.phasing))
110 for key in b.phasing.keys():
111 self.failUnlessEqual(b.phasing[key].lane,
112 b2.phasing[key].lane)
113 self.failUnlessEqual(b.phasing[key].phasing,
114 b2.phasing[key].phasing)
115 self.failUnlessEqual(b.phasing[key].prephasing,
116 b2.phasing[key].prephasing)
118 def test_gerald(self):
119 # need to update gerald and make tests for it
120 g = gerald.gerald(self.gerald_dir)
122 self.failUnlessEqual(g.version,
123 '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
124 self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
125 self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
126 self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
129 # list of genomes, matches what was defined up in
130 # make_gerald_config.
131 # the first None is to offset the genomes list to be 1..9
132 # instead of pythons default 0..8
137 '/g/arabidopsis01222004',
143 # test lane specific parameters from gerald config file
145 cur_lane = g.lanes[i]
146 self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
147 self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
148 self.failUnlessEqual(cur_lane.read_length, '37')
149 self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
151 # I want to be able to use a simple iterator
152 for l in g.lanes.values():
153 self.failUnlessEqual(l.analysis, 'eland_extended')
154 self.failUnlessEqual(l.read_length, '37')
155 self.failUnlessEqual(l.use_bases, 'Y'*37)
157 # test data extracted from summary file
159 (96483, 9074), (133738, 7938),
160 (152142, 10002), (15784, 2162),
161 (119735, 8465), (152177, 8146),
162 (84649, 7325), (54622, 4812),]
164 self.failUnlessEqual(len(g.summary), 1)
166 summary_lane = g.summary[0][i]
167 self.failUnlessEqual(summary_lane.cluster, clusters[i])
168 self.failUnlessEqual(summary_lane.lane, i)
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
191 self.failUnlessEqual(len(g.summary), 1)
193 g_summary = g.summary[0][i]
194 g2_summary = g2.summary[0][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[0].keys():
201 g_results = g_eland.results[0][lane]
202 g2_results = g2_eland.results[0][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)
230 lane = eland.results[0][i]
231 self.failUnlessEqual(lane.reads, 6)
232 self.failUnlessEqual(lane.sample_name, "s")
233 self.failUnlessEqual(lane.lane_id, i)
234 self.failUnlessEqual(len(lane.mapped_reads), 17)
235 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
236 self.failUnlessEqual(lane.mapped_reads['spike.fa/sample1'], 1)
237 self.failUnlessEqual(lane.mapped_reads['spike.fa/sample2'], 1)
238 self.failUnlessEqual(lane.match_codes['U0'], 3)
239 self.failUnlessEqual(lane.match_codes['R0'], 2)
240 self.failUnlessEqual(lane.match_codes['U1'], 1)
241 self.failUnlessEqual(lane.match_codes['R1'], 9)
242 self.failUnlessEqual(lane.match_codes['U2'], 0)
243 self.failUnlessEqual(lane.match_codes['R2'], 12)
244 self.failUnlessEqual(lane.match_codes['NM'], 1)
245 self.failUnlessEqual(lane.match_codes['QC'], 0)
247 xml = eland.get_elements()
248 # just make sure that element tree can serialize the tree
249 xml_str = ElementTree.tostring(xml)
250 e2 = gerald.ELAND(xml=xml)
253 l1 = eland.results[0][i]
254 l2 = e2.results[0][i]
255 self.failUnlessEqual(l1.reads, l2.reads)
256 self.failUnlessEqual(l1.sample_name, l2.sample_name)
257 self.failUnlessEqual(l1.lane_id, l2.lane_id)
258 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
259 self.failUnlessEqual(len(l1.mapped_reads), 17)
260 for k in l1.mapped_reads.keys():
261 self.failUnlessEqual(l1.mapped_reads[k],
264 self.failUnlessEqual(len(l1.match_codes), 9)
265 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
266 for k in l1.match_codes.keys():
267 self.failUnlessEqual(l1.match_codes[k],
270 def test_runfolder(self):
271 runs = runfolder.get_runs(self.runfolder_dir)
273 # do we get the flowcell id from the filename?
274 self.failUnlessEqual(len(runs), 1)
275 name = 'run_207BTAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
276 self.failUnlessEqual(runs[0].name, name)
278 # do we get the flowcell id from the FlowcellId.xml file
279 make_flowcell_id(self.runfolder_dir, '207BTAAXY')
280 runs = runfolder.get_runs(self.runfolder_dir)
281 self.failUnlessEqual(len(runs), 1)
282 name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
283 self.failUnlessEqual(runs[0].name, name)
286 xml = r1.get_elements()
287 xml_str = ElementTree.tostring(xml)
289 r2 = runfolder.PipelineRun(xml=xml)
290 self.failUnlessEqual(r1.name, r2.name)
291 self.failIfEqual(r2.image_analysis, None)
292 self.failIfEqual(r2.bustard, None)
293 self.failIfEqual(r2.gerald, None)
297 return unittest.makeSuite(RunfolderTests,'test')
299 if __name__ == "__main__":
300 unittest.main(defaultTest="suite")