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 matrix_dir = os.path.join(firecrest_dir, 'Matrix')
38 make_matrix(matrix_dir)
40 bustard_dir = os.path.join(firecrest_dir,
41 'Bustard1.9.6_20-10-2008_diane')
43 make_phasing_params(bustard_dir)
45 gerald_dir = os.path.join(bustard_dir,
46 'GERALD_20-10-2008_diane')
48 make_gerald_config(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.matrix_dir = matrix_dir
58 obj.bustard_dir = bustard_dir
59 obj.gerald_dir = gerald_dir
62 class RunfolderTests(unittest.TestCase):
64 Test components of the runfolder processing code
65 which includes firecrest, bustard, and gerald
68 # attaches all the directories to the object passed in
72 shutil.rmtree(self.temp_dir)
74 def test_firecrest(self):
76 Construct a firecrest object
78 f = firecrest.firecrest(self.image_analysis_dir)
79 self.failUnlessEqual(f.version, '1.9.6')
80 self.failUnlessEqual(f.start, 1)
81 self.failUnlessEqual(f.stop, 37)
82 self.failUnlessEqual(f.user, 'diane')
83 self.failUnlessEqual(f.date, date(2008,10,20))
85 xml = f.get_elements()
86 # just make sure that element tree can serialize the tree
87 xml_str = ElementTree.tostring(xml)
89 f2 = firecrest.Firecrest(xml=xml)
90 self.failUnlessEqual(f.version, f2.version)
91 self.failUnlessEqual(f.start, f2.start)
92 self.failUnlessEqual(f.stop, f2.stop)
93 self.failUnlessEqual(f.user, f2.user)
95 def test_bustard(self):
97 construct a bustard object
99 b = bustard.bustard(self.bustard_dir)
100 self.failUnlessEqual(b.version, '1.9.6')
101 self.failUnlessEqual(b.date, date(2008,10,20))
102 self.failUnlessEqual(b.user, 'diane')
103 self.failUnlessEqual(len(b.phasing), 8)
104 self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
106 xml = b.get_elements()
107 b2 = bustard.Bustard(xml=xml)
108 self.failUnlessEqual(b.version, b2.version)
109 self.failUnlessEqual(b.date, b2.date )
110 self.failUnlessEqual(b.user, b2.user)
111 self.failUnlessEqual(len(b.phasing), len(b2.phasing))
112 for key in b.phasing.keys():
113 self.failUnlessEqual(b.phasing[key].lane,
114 b2.phasing[key].lane)
115 self.failUnlessEqual(b.phasing[key].phasing,
116 b2.phasing[key].phasing)
117 self.failUnlessEqual(b.phasing[key].prephasing,
118 b2.phasing[key].prephasing)
120 def test_gerald(self):
121 # need to update gerald and make tests for it
122 g = gerald.gerald(self.gerald_dir)
124 self.failUnlessEqual(g.version,
125 '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp')
126 self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
127 self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
128 self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
131 # list of genomes, matches what was defined up in
132 # make_gerald_config.
133 # the first None is to offset the genomes list to be 1..9
134 # instead of pythons default 0..8
135 genomes = [None, '/g/dm3', '/g/equcab1', '/g/equcab1', '/g/canfam2',
136 '/g/hg18', '/g/hg18', '/g/hg18', '/g/hg18', ]
138 # test lane specific parameters from gerald config file
140 cur_lane = g.lanes[str(i)]
141 self.failUnlessEqual(cur_lane.analysis, 'eland')
142 self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
143 self.failUnlessEqual(cur_lane.read_length, '32')
144 self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
146 # I want to be able to use a simple iterator
147 for l in g.lanes.values():
148 self.failUnlessEqual(l.analysis, 'eland')
149 self.failUnlessEqual(l.read_length, '32')
150 self.failUnlessEqual(l.use_bases, 'Y'*32)
152 # raw cluster numbers extracted from summary file
153 # its the first +/- value in the lane results summary
156 (190220, 15118), (190560, 14399),
157 (187597, 12369), (204142, 16877),
158 (247308, 11600), (204298, 15640),
159 (202707, 15404), (198075, 14702),]
162 summary_lane = g.summary[str(i)]
163 self.failUnlessEqual(summary_lane.cluster, clusters[i])
164 self.failUnlessEqual(summary_lane.lane, str(i))
166 xml = g.get_elements()
167 # just make sure that element tree can serialize the tree
168 xml_str = ElementTree.tostring(xml)
169 g2 = gerald.Gerald(xml=xml)
171 # do it all again after extracting from the xml file
172 self.failUnlessEqual(g.version, g2.version)
173 self.failUnlessEqual(g.date, g2.date)
174 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
175 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
177 # test lane specific parameters from gerald config file
179 g_lane = g.lanes[str(i)]
180 g2_lane = g2.lanes[str(i)]
181 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
182 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
183 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
184 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
186 # test (some) summary elements
188 g_summary = g.summary[str(i)]
189 g2_summary = g2.summary[str(i)]
190 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
191 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
193 g_eland = g.eland_results
194 g2_eland = g2.eland_results
195 for lane in g_eland.keys():
196 self.failUnlessEqual(g_eland[lane].reads,
197 g2_eland[lane].reads)
198 self.failUnlessEqual(len(g_eland[lane].mapped_reads),
199 len(g2_eland[lane].mapped_reads))
200 for k in g_eland[lane].mapped_reads.keys():
201 self.failUnlessEqual(g_eland[lane].mapped_reads[k],
202 g2_eland[lane].mapped_reads[k])
204 self.failUnlessEqual(len(g_eland[lane].match_codes),
205 len(g2_eland[lane].match_codes))
206 for k in g_eland[lane].match_codes.keys():
207 self.failUnlessEqual(g_eland[lane].match_codes[k],
208 g2_eland[lane].match_codes[k])
211 def test_eland(self):
212 hg_map = {'Lambda.fa': 'Lambda.fa'}
213 for i in range(1,22):
214 short_name = 'chr%d.fa' % (i,)
215 long_name = 'hg18/chr%d.fa' % (i,)
216 hg_map[short_name] = long_name
218 genome_maps = { '1':hg_map, '2':hg_map, '3':hg_map, '4':hg_map,
219 '5':hg_map, '6':hg_map, '7':hg_map, '8':hg_map }
220 eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
224 self.failUnlessEqual(lane.reads, 4)
225 self.failUnlessEqual(lane.sample_name, "s")
226 self.failUnlessEqual(lane.lane_id, unicode(i))
227 self.failUnlessEqual(len(lane.mapped_reads), 15)
228 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
229 self.failUnlessEqual(lane.match_codes['U0'], 1)
230 self.failUnlessEqual(lane.match_codes['R0'], 2)
231 self.failUnlessEqual(lane.match_codes['U1'], 1)
232 self.failUnlessEqual(lane.match_codes['R1'], 9)
233 self.failUnlessEqual(lane.match_codes['U2'], 0)
234 self.failUnlessEqual(lane.match_codes['R2'], 12)
235 self.failUnlessEqual(lane.match_codes['NM'], 1)
236 self.failUnlessEqual(lane.match_codes['QC'], 0)
238 xml = eland.get_elements()
239 # just make sure that element tree can serialize the tree
240 xml_str = ElementTree.tostring(xml)
241 e2 = gerald.ELAND(xml=xml)
246 self.failUnlessEqual(l1.reads, l2.reads)
247 self.failUnlessEqual(l1.sample_name, l2.sample_name)
248 self.failUnlessEqual(l1.lane_id, l2.lane_id)
249 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
250 self.failUnlessEqual(len(l1.mapped_reads), 15)
251 for k in l1.mapped_reads.keys():
252 self.failUnlessEqual(l1.mapped_reads[k],
255 self.failUnlessEqual(len(l1.match_codes), 9)
256 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
257 for k in l1.match_codes.keys():
258 self.failUnlessEqual(l1.match_codes[k],
261 def test_runfolder(self):
262 runs = runfolder.get_runs(self.runfolder_dir)
264 # do we get the flowcell id from the filename?
265 self.failUnlessEqual(len(runs), 1)
266 name = 'run_30J55AAXX_2008-10-20.xml'
267 self.failUnlessEqual(runs[0].name, name)
269 # do we get the flowcell id from the FlowcellId.xml file
270 make_flowcell_id(self.runfolder_dir, '30J55AAXX')
271 runs = runfolder.get_runs(self.runfolder_dir)
272 self.failUnlessEqual(len(runs), 1)
273 name = 'run_30J55AAXX_2008-10-20.xml'
274 self.failUnlessEqual(runs[0].name, name)
277 xml = r1.get_elements()
278 xml_str = ElementTree.tostring(xml)
280 r2 = runfolder.PipelineRun(xml=xml)
281 self.failUnlessEqual(r1.name, r2.name)
282 self.failIfEqual(r2.image_analysis, None)
283 self.failIfEqual(r2.bustard, None)
284 self.failIfEqual(r2.gerald, None)
288 return unittest.makeSuite(RunfolderTests,'test')
290 if __name__ == "__main__":
291 unittest.main(defaultTest="suite")