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,
124 '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
125 self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
126 self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
127 self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
130 # list of genomes, matches what was defined up in
131 # make_gerald_config.
132 # the first None is to offset the genomes list to be 1..9
133 # instead of pythons default 0..8
138 '/g/arabidopsis01222004',
144 # test lane specific parameters from gerald config file
146 cur_lane = g.lanes[i]
147 self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
148 self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
149 self.failUnlessEqual(cur_lane.read_length, '37')
150 self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
152 # I want to be able to use a simple iterator
153 for l in g.lanes.values():
154 self.failUnlessEqual(l.analysis, 'eland_extended')
155 self.failUnlessEqual(l.read_length, '37')
156 self.failUnlessEqual(l.use_bases, 'Y'*37)
158 # raw cluster numbers extracted from summary file
159 # its the first +/- value in the lane results summary
162 (190220, 15118), (190560, 14399),
163 (187597, 12369), (204142, 16877),
164 (247308, 11600), (204298, 15640),
165 (202707, 15404), (198075, 14702),]
167 self.failUnlessEqual(len(g.summary), 1)
169 summary_lane = g.summary[0][i]
170 self.failUnlessEqual(summary_lane.cluster, clusters[i])
171 self.failUnlessEqual(summary_lane.lane, i)
173 xml = g.get_elements()
174 # just make sure that element tree can serialize the tree
175 xml_str = ElementTree.tostring(xml)
176 g2 = gerald.Gerald(xml=xml)
178 # do it all again after extracting from the xml file
179 self.failUnlessEqual(g.version, g2.version)
180 self.failUnlessEqual(g.date, g2.date)
181 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
182 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
184 # test lane specific parameters from gerald config file
187 g2_lane = g2.lanes[i]
188 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
189 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
190 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
191 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
193 self.failUnlessEqual(len(g.summary), 1)
194 # test (some) summary elements
196 g_summary = g.summary[0][i]
197 g2_summary = g2.summary[0][i]
198 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
199 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
201 g_eland = g.eland_results
202 g2_eland = g2.eland_results
203 for lane in g_eland.results[0].keys():
204 g_results = g_eland.results[0][lane]
205 g2_results = g2_eland.results[0][lane]
206 self.failUnlessEqual(g_results.reads,
208 self.failUnlessEqual(len(g_results.mapped_reads),
209 len(g2_results.mapped_reads))
210 for k in g_results.mapped_reads.keys():
211 self.failUnlessEqual(g_results.mapped_reads[k],
212 g2_results.mapped_reads[k])
214 self.failUnlessEqual(len(g_results.match_codes),
215 len(g2_results.match_codes))
216 for k in g_results.match_codes.keys():
217 self.failUnlessEqual(g_results.match_codes[k],
218 g2_results.match_codes[k])
221 def test_eland(self):
222 hg_map = {'Lambda.fa': 'Lambda.fa'}
223 for i in range(1,22):
224 short_name = 'chr%d.fa' % (i,)
225 long_name = 'hg18/chr%d.fa' % (i,)
226 hg_map[short_name] = long_name
228 genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
229 5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
230 eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
233 lane = eland.results[0][i]
234 self.failUnlessEqual(lane.reads, 6)
235 self.failUnlessEqual(lane.sample_name, "s")
236 self.failUnlessEqual(lane.lane_id, i)
237 self.failUnlessEqual(len(lane.mapped_reads), 17)
238 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
239 self.failUnlessEqual(lane.match_codes['U0'], 3)
240 self.failUnlessEqual(lane.match_codes['R0'], 2)
241 self.failUnlessEqual(lane.match_codes['U1'], 1)
242 self.failUnlessEqual(lane.match_codes['R1'], 9)
243 self.failUnlessEqual(lane.match_codes['U2'], 0)
244 self.failUnlessEqual(lane.match_codes['R2'], 12)
245 self.failUnlessEqual(lane.match_codes['NM'], 1)
246 self.failUnlessEqual(lane.match_codes['QC'], 0)
248 xml = eland.get_elements()
249 # just make sure that element tree can serialize the tree
250 xml_str = ElementTree.tostring(xml)
251 e2 = gerald.ELAND(xml=xml)
254 l1 = eland.results[0][i]
255 l2 = e2.results[0][i]
256 self.failUnlessEqual(l1.reads, l2.reads)
257 self.failUnlessEqual(l1.sample_name, l2.sample_name)
258 self.failUnlessEqual(l1.lane_id, l2.lane_id)
259 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
260 self.failUnlessEqual(len(l1.mapped_reads), 17)
261 for k in l1.mapped_reads.keys():
262 self.failUnlessEqual(l1.mapped_reads[k],
265 self.failUnlessEqual(len(l1.match_codes), 9)
266 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
267 for k in l1.match_codes.keys():
268 self.failUnlessEqual(l1.match_codes[k],
271 def test_runfolder(self):
272 runs = runfolder.get_runs(self.runfolder_dir)
274 # do we get the flowcell id from the filename?
275 self.failUnlessEqual(len(runs), 1)
276 name = 'run_30J55AAXX_2009-02-22.xml'
277 self.failUnlessEqual(runs[0].name, name)
279 # do we get the flowcell id from the FlowcellId.xml file
280 make_flowcell_id(self.runfolder_dir, '30J55AAXX')
281 runs = runfolder.get_runs(self.runfolder_dir)
282 self.failUnlessEqual(len(runs), 1)
283 name = 'run_30J55AAXX_2009-02-22.xml'
284 self.failUnlessEqual(runs[0].name, name)
287 xml = r1.get_elements()
288 xml_str = ElementTree.tostring(xml)
290 r2 = runfolder.PipelineRun(xml=xml)
291 self.failUnlessEqual(r1.name, r2.name)
292 self.failIfEqual(r2.image_analysis, None)
293 self.failIfEqual(r2.bustard, None)
294 self.failIfEqual(r2.gerald, None)
298 return unittest.makeSuite(RunfolderTests,'test')
300 if __name__ == "__main__":
301 unittest.main(defaultTest="suite")