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 '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(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.version, '1.9.6')
79 self.failUnlessEqual(f.start, 1)
80 self.failUnlessEqual(f.stop, 37)
81 self.failUnlessEqual(f.user, 'diane')
82 self.failUnlessEqual(f.date, date(2008,10,20))
84 xml = f.get_elements()
85 # just make sure that element tree can serialize the tree
86 xml_str = ElementTree.tostring(xml)
88 f2 = firecrest.Firecrest(xml=xml)
89 self.failUnlessEqual(f.version, f2.version)
90 self.failUnlessEqual(f.start, f2.start)
91 self.failUnlessEqual(f.stop, f2.stop)
92 self.failUnlessEqual(f.user, f2.user)
94 def test_bustard(self):
96 construct a bustard object
98 b = bustard.bustard(self.bustard_dir)
99 self.failUnlessEqual(b.version, '1.9.6')
100 self.failUnlessEqual(b.date, date(2008,10,20))
101 self.failUnlessEqual(b.user, 'diane')
102 self.failUnlessEqual(len(b.phasing), 8)
103 self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
105 xml = b.get_elements()
106 b2 = bustard.Bustard(xml=xml)
107 self.failUnlessEqual(b.version, b2.version)
108 self.failUnlessEqual(b.date, b2.date )
109 self.failUnlessEqual(b.user, b2.user)
110 self.failUnlessEqual(len(b.phasing), len(b2.phasing))
111 for key in b.phasing.keys():
112 self.failUnlessEqual(b.phasing[key].lane,
113 b2.phasing[key].lane)
114 self.failUnlessEqual(b.phasing[key].phasing,
115 b2.phasing[key].phasing)
116 self.failUnlessEqual(b.phasing[key].prephasing,
117 b2.phasing[key].prephasing)
119 def test_gerald(self):
120 # need to update gerald and make tests for it
121 g = gerald.gerald(self.gerald_dir)
123 self.failUnlessEqual(g.version, '1.171')
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 # raw cluster numbers extracted from summary file
158 # its the first +/- value in the lane results summary
161 (190220, 15118), (190560, 14399),
162 (187597, 12369), (204142, 16877),
163 (247308, 11600), (204298, 15640),
164 (202707, 15404), (198075, 14702),]
166 self.failUnlessEqual(len(g.summary), 1)
168 summary_lane = g.summary[0][i]
169 self.failUnlessEqual(summary_lane.cluster, clusters[i])
170 self.failUnlessEqual(summary_lane.lane, i)
172 xml = g.get_elements()
173 # just make sure that element tree can serialize the tree
174 xml_str = ElementTree.tostring(xml)
175 g2 = gerald.Gerald(xml=xml)
177 # do it all again after extracting from the xml file
178 self.failUnlessEqual(g.version, g2.version)
179 self.failUnlessEqual(g.date, g2.date)
180 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
181 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
183 # test lane specific parameters from gerald config file
186 g2_lane = g2.lanes[i]
187 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
188 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
189 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
190 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
192 self.failUnlessEqual(len(g.summary), 1)
193 # test (some) summary elements
195 g_summary = g.summary[0][i]
196 g2_summary = g2.summary[0][i]
197 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
198 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
200 g_eland = g.eland_results
201 g2_eland = g2.eland_results
202 for lane in g_eland.results[0].keys():
203 g_results = g_eland.results[0][lane]
204 g2_results = g2_eland.results[0][lane]
205 self.failUnlessEqual(g_results.reads,
207 self.failUnlessEqual(len(g_results.mapped_reads),
208 len(g2_results.mapped_reads))
209 for k in g_results.mapped_reads.keys():
210 self.failUnlessEqual(g_results.mapped_reads[k],
211 g2_results.mapped_reads[k])
213 self.failUnlessEqual(len(g_results.match_codes),
214 len(g2_results.match_codes))
215 for k in g_results.match_codes.keys():
216 self.failUnlessEqual(g_results.match_codes[k],
217 g2_results.match_codes[k])
220 def test_eland(self):
221 hg_map = {'Lambda.fa': 'Lambda.fa'}
222 for i in range(1,22):
223 short_name = 'chr%d.fa' % (i,)
224 long_name = 'hg18/chr%d.fa' % (i,)
225 hg_map[short_name] = long_name
227 genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
228 5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
229 eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
232 lane = eland.results[0][i]
233 self.failUnlessEqual(lane.reads, 6)
234 self.failUnlessEqual(lane.sample_name, "s")
235 self.failUnlessEqual(lane.lane_id, i)
236 self.failUnlessEqual(len(lane.mapped_reads), 17)
237 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
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_30J55AAXX_2009-02-22.xml'
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, '30J55AAXX')
280 runs = runfolder.get_runs(self.runfolder_dir)
281 self.failUnlessEqual(len(runs), 1)
282 name = 'run_30J55AAXX_2009-02-22.xml'
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")