3 from datetime import datetime, date
9 from htsworkflow.pipelines import eland
10 from htsworkflow.pipelines import ipar
11 from htsworkflow.pipelines import bustard
12 from htsworkflow.pipelines import gerald
13 from htsworkflow.pipelines import runfolder
14 from htsworkflow.pipelines.runfolder import ElementTree
16 from htsworkflow.pipelines.test.simulate_runfolder import *
19 def make_runfolder(obj=None):
21 Make a fake runfolder, attach all the directories to obj if defined
23 # make a fake runfolder directory
24 temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
26 runfolder_dir = os.path.join(temp_dir,
27 '090608_HWI-EAS229_0117_4286GAAXX')
28 os.mkdir(runfolder_dir)
30 data_dir = os.path.join(runfolder_dir, 'Data')
33 intensities_dir = make_rta_intensities_1460(data_dir)
35 basecalls_dir = make_rta_basecalls_1460(intensities_dir)
37 #make_phasing_params(bustard_dir)
38 #make_bustard_config132(bustard_dir)
40 gerald_dir = os.path.join(basecalls_dir,
41 'GERALD_16-06-2009_diane')
43 make_gerald_config_100(gerald_dir)
44 make_summary_ipar130_htm(gerald_dir)
45 make_eland_multi(gerald_dir, lane_list=[1,2,3,4,5,6,])
46 make_scarf(gerald_dir, lane_list=[7,])
47 make_fastq(gerald_dir, lane_list=[8,])
50 obj.temp_dir = temp_dir
51 obj.runfolder_dir = runfolder_dir
52 obj.data_dir = data_dir
53 obj.image_analysis_dir = intensities_dir
54 obj.bustard_dir = basecalls_dir
55 obj.gerald_dir = gerald_dir
58 class RunfolderTests(unittest.TestCase):
60 Test components of the runfolder processing code
61 which includes firecrest, bustard, and gerald
64 # attaches all the directories to the object passed in
68 shutil.rmtree(self.temp_dir)
72 Construct a firecrest object
74 i = ipar.ipar(self.image_analysis_dir)
75 self.failUnlessEqual(i.version, '1.4.6.0')
76 self.failUnlessEqual(i.start, 1)
77 self.failUnlessEqual(i.stop, 38)
79 xml = i.get_elements()
80 # just make sure that element tree can serialize the tree
81 xml_str = ElementTree.tostring(xml)
83 i2 = ipar.IPAR(xml=xml)
84 self.failUnlessEqual(i.version, i2.version)
85 self.failUnlessEqual(i.start, i2.start)
86 self.failUnlessEqual(i.stop, i2.stop)
87 self.failUnlessEqual(i.date, i2.date)
89 def test_bustard(self):
91 construct a bustard object
93 b = bustard.bustard(self.bustard_dir)
94 self.failUnlessEqual(b.version, '1.4.6.0')
95 self.failUnlessEqual(b.date, None)
96 self.failUnlessEqual(b.user, None)
97 self.failUnlessEqual(len(b.phasing), 0)
99 xml = b.get_elements()
100 b2 = bustard.Bustard(xml=xml)
101 self.failUnlessEqual(b.version, b2.version)
102 self.failUnlessEqual(b.date, b2.date )
103 self.failUnlessEqual(b.user, b2.user)
105 def test_gerald(self):
106 # need to update gerald and make tests for it
107 g = gerald.gerald(self.gerald_dir)
109 self.failUnlessEqual(g.version, '1.171')
110 self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
111 self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
112 self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
115 # list of genomes, matches what was defined up in
116 # make_gerald_config.
117 # the first None is to offset the genomes list to be 1..9
118 # instead of pythons default 0..8
123 '/g/arabidopsis01222004',
129 # test lane specific parameters from gerald config file
131 cur_lane = g.lanes[i]
132 self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
133 self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
134 self.failUnlessEqual(cur_lane.read_length, '37')
135 self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
137 # I want to be able to use a simple iterator
138 for l in g.lanes.values():
139 self.failUnlessEqual(l.analysis, 'eland_extended')
140 self.failUnlessEqual(l.read_length, '37')
141 self.failUnlessEqual(l.use_bases, 'Y'*37)
143 # test data extracted from summary file
145 (126910, 4300), (165739, 6792),
146 (196565, 8216), (153897, 8501),
147 (135536, 3908), (154083, 9315),
148 (159991, 9292), (198479, 17671),]
150 self.failUnlessEqual(len(g.summary), 1)
152 summary_lane = g.summary[0][i]
153 self.failUnlessEqual(summary_lane.cluster, clusters[i])
154 self.failUnlessEqual(summary_lane.lane, i)
156 xml = g.get_elements()
157 # just make sure that element tree can serialize the tree
158 xml_str = ElementTree.tostring(xml)
159 g2 = gerald.Gerald(xml=xml)
162 # do it all again after extracting from the xml file
163 self.failUnlessEqual(g.version, g2.version)
164 self.failUnlessEqual(g.date, g2.date)
165 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
166 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
168 # test lane specific parameters from gerald config file
171 g2_lane = g2.lanes[i]
172 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
173 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
174 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
175 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
177 # test (some) summary elements
178 self.failUnlessEqual(len(g.summary), 1)
180 g_summary = g.summary[0][i]
181 g2_summary = g2.summary[0][i]
182 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
183 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
185 g_eland = g.eland_results
186 g2_eland = g2.eland_results
187 for lane in g_eland.results[0].keys():
188 g_results = g_eland.results[0][lane]
189 g2_results = g2_eland.results[0][lane]
190 self.failUnlessEqual(g_results.reads,
192 if isinstance(g_results, eland.ElandLane):
193 self.failUnlessEqual(len(g_results.mapped_reads),
194 len(g2_results.mapped_reads))
195 for k in g_results.mapped_reads.keys():
196 self.failUnlessEqual(g_results.mapped_reads[k],
197 g2_results.mapped_reads[k])
199 self.failUnlessEqual(len(g_results.match_codes),
200 len(g2_results.match_codes))
201 for k in g_results.match_codes.keys():
202 self.failUnlessEqual(g_results.match_codes[k],
203 g2_results.match_codes[k])
206 def test_eland(self):
208 hg_map = {'Lambda.fa': 'Lambda.fa'}
209 for i in range(1,22):
210 short_name = 'chr%d.fa' % (i,)
211 long_name = 'hg18/chr%d.fa' % (i,)
212 hg_map[short_name] = long_name
214 genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
215 5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
216 eland_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
218 # I added sequence lanes to the last 2 lanes of this test case
220 lane = eland_container.results[0][i]
221 self.failUnlessEqual(lane.reads, 6)
222 self.failUnlessEqual(lane.sample_name, "s")
223 self.failUnlessEqual(lane.lane_id, i)
224 self.failUnlessEqual(len(lane.mapped_reads), 17)
225 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
226 self.failUnlessEqual(lane.match_codes['U0'], 3)
227 self.failUnlessEqual(lane.match_codes['R0'], 2)
228 self.failUnlessEqual(lane.match_codes['U1'], 1)
229 self.failUnlessEqual(lane.match_codes['R1'], 9)
230 self.failUnlessEqual(lane.match_codes['U2'], 0)
231 self.failUnlessEqual(lane.match_codes['R2'], 12)
232 self.failUnlessEqual(lane.match_codes['NM'], 1)
233 self.failUnlessEqual(lane.match_codes['QC'], 0)
236 lane = eland_container.results[0][7]
237 self.failUnlessEqual(lane.reads, 5)
238 self.failUnlessEqual(lane.sample_name, 's')
239 self.failUnlessEqual(lane.lane_id, 7)
240 self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.SCARF_TYPE)
243 lane = eland_container.results[0][8]
244 self.failUnlessEqual(lane.reads, 3)
245 self.failUnlessEqual(lane.sample_name, 's')
246 self.failUnlessEqual(lane.lane_id, 8)
247 self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.FASTQ_TYPE)
249 xml = eland_container.get_elements()
250 # just make sure that element tree can serialize the tree
251 xml_str = ElementTree.tostring(xml)
252 e2 = gerald.ELAND(xml=xml)
255 l1 = eland_container.results[0][i]
256 l2 = e2.results[0][i]
257 self.failUnlessEqual(l1.reads, l2.reads)
258 self.failUnlessEqual(l1.sample_name, l2.sample_name)
259 self.failUnlessEqual(l1.lane_id, l2.lane_id)
260 if isinstance(l1, eland.ElandLane):
261 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
262 self.failUnlessEqual(len(l1.mapped_reads), 17)
263 for k in l1.mapped_reads.keys():
264 self.failUnlessEqual(l1.mapped_reads[k],
267 self.failUnlessEqual(len(l1.match_codes), 9)
268 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
269 for k in l1.match_codes.keys():
270 self.failUnlessEqual(l1.match_codes[k],
272 elif isinstance(l1, eland.SequenceLane):
273 self.failUnlessEqual(l1.sequence_type, l2.sequence_type)
275 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_4286GAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
282 self.failUnlessEqual(runs[0].name, name)
284 # do we get the flowcell id from the FlowcellId.xml file
285 make_flowcell_id(self.runfolder_dir, '207BTAAXY')
286 runs = runfolder.get_runs(self.runfolder_dir)
287 self.failUnlessEqual(len(runs), 1)
288 name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
289 self.failUnlessEqual(runs[0].name, name)
292 xml = r1.get_elements()
293 xml_str = ElementTree.tostring(xml)
295 r2 = runfolder.PipelineRun(xml=xml)
296 self.failUnlessEqual(r1.name, r2.name)
297 self.failIfEqual(r2.image_analysis, None)
298 self.failIfEqual(r2.bustard, None)
299 self.failIfEqual(r2.gerald, None)
303 return unittest.makeSuite(RunfolderTests,'test')
305 if __name__ == "__main__":
306 unittest.main(defaultTest="suite")