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 make_matrix(matrix_dir)
38 bustard_dir = os.path.join(ipar_dir,
39 'Bustard1.8.28_12-04-2008_diane')
41 make_phasing_params(bustard_dir)
43 gerald_dir = os.path.join(bustard_dir,
44 'GERALD_12-04-2008_diane')
46 make_gerald_config(gerald_dir)
47 make_summary100_htm(gerald_dir)
48 make_eland_results(gerald_dir)
51 obj.temp_dir = temp_dir
52 obj.runfolder_dir = runfolder_dir
53 obj.data_dir = data_dir
54 obj.image_analysis_dir = ipar_dir
55 obj.matrix_dir = matrix_dir
56 obj.bustard_dir = bustard_dir
57 obj.gerald_dir = gerald_dir
60 class RunfolderTests(unittest.TestCase):
62 Test components of the runfolder processing code
63 which includes firecrest, bustard, and gerald
66 # attaches all the directories to the object passed in
70 shutil.rmtree(self.temp_dir)
74 Construct a firecrest object
76 i = ipar.ipar(self.image_analysis_dir)
77 self.failUnlessEqual(i.version, '2.01.192.0')
78 self.failUnlessEqual(i.start, 1)
79 self.failUnlessEqual(i.stop, 37)
81 xml = i.get_elements()
82 # just make sure that element tree can serialize the tree
83 xml_str = ElementTree.tostring(xml)
85 i2 = ipar.IPAR(xml=xml)
86 self.failUnlessEqual(i.version, i2.version)
87 self.failUnlessEqual(i.start, i2.start)
88 self.failUnlessEqual(i.stop, i2.stop)
89 self.failUnlessEqual(i.date, i2.date)
90 self.failUnlessEqual(i.file_list(), i2.file_list())
92 def test_bustard(self):
94 construct a bustard object
96 b = bustard.bustard(self.bustard_dir)
97 self.failUnlessEqual(b.version, '1.8.28')
98 self.failUnlessEqual(b.date, date(2008,4,12))
99 self.failUnlessEqual(b.user, 'diane')
100 self.failUnlessEqual(len(b.phasing), 8)
101 self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
103 xml = b.get_elements()
104 b2 = bustard.Bustard(xml=xml)
105 self.failUnlessEqual(b.version, b2.version)
106 self.failUnlessEqual(b.date, b2.date )
107 self.failUnlessEqual(b.user, b2.user)
108 self.failUnlessEqual(len(b.phasing), len(b2.phasing))
109 for key in b.phasing.keys():
110 self.failUnlessEqual(b.phasing[key].lane,
111 b2.phasing[key].lane)
112 self.failUnlessEqual(b.phasing[key].phasing,
113 b2.phasing[key].phasing)
114 self.failUnlessEqual(b.phasing[key].prephasing,
115 b2.phasing[key].prephasing)
117 def test_gerald(self):
118 # need to update gerald and make tests for it
119 g = gerald.gerald(self.gerald_dir)
121 self.failUnlessEqual(g.version,
122 '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp')
123 self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
124 self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
125 self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
128 # list of genomes, matches what was defined up in
129 # make_gerald_config.
130 # the first None is to offset the genomes list to be 1..9
131 # instead of pythons default 0..8
132 genomes = [None, '/g/dm3', '/g/equcab1', '/g/equcab1', '/g/canfam2',
133 '/g/hg18', '/g/hg18', '/g/hg18', '/g/hg18', ]
135 # test lane specific parameters from gerald config file
137 cur_lane = g.lanes[str(i)]
138 self.failUnlessEqual(cur_lane.analysis, 'eland')
139 self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
140 self.failUnlessEqual(cur_lane.read_length, '32')
141 self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
143 # test data extracted from summary file
145 (96483, 9074), (133738, 7938),
146 (152142, 10002), (15784, 2162),
147 (119735, 8465), (152177, 8146),
148 (84649, 7325), (54622, 4812),]
151 summary_lane = g.summary[str(i)]
152 self.failUnlessEqual(summary_lane.cluster, clusters[i])
153 self.failUnlessEqual(summary_lane.lane, str(i))
155 xml = g.get_elements()
156 # just make sure that element tree can serialize the tree
157 xml_str = ElementTree.tostring(xml)
158 g2 = gerald.Gerald(xml=xml)
160 # do it all again after extracting from the xml file
161 self.failUnlessEqual(g.version, g2.version)
162 self.failUnlessEqual(g.date, g2.date)
163 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
164 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
166 # test lane specific parameters from gerald config file
168 g_lane = g.lanes[str(i)]
169 g2_lane = g2.lanes[str(i)]
170 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
171 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
172 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
173 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
175 # test (some) summary elements
177 g_summary = g.summary[str(i)]
178 g2_summary = g2.summary[str(i)]
179 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
180 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
182 g_eland = g.eland_results
183 g2_eland = g2.eland_results
184 for lane in g_eland.keys():
185 self.failUnlessEqual(g_eland[lane].reads,
186 g2_eland[lane].reads)
187 self.failUnlessEqual(len(g_eland[lane].mapped_reads),
188 len(g2_eland[lane].mapped_reads))
189 for k in g_eland[lane].mapped_reads.keys():
190 self.failUnlessEqual(g_eland[lane].mapped_reads[k],
191 g2_eland[lane].mapped_reads[k])
193 self.failUnlessEqual(len(g_eland[lane].match_codes),
194 len(g2_eland[lane].match_codes))
195 for k in g_eland[lane].match_codes.keys():
196 self.failUnlessEqual(g_eland[lane].match_codes[k],
197 g2_eland[lane].match_codes[k])
200 def test_eland(self):
201 dm3_map = { 'chrUextra.fa' : 'dm3/chrUextra.fa',
202 'chr2L.fa': 'dm3/chr2L.fa',
203 'Lambda.fa': 'Lambda.fa'}
204 genome_maps = { '1':dm3_map, '2':dm3_map, '3':dm3_map, '4':dm3_map,
205 '5':dm3_map, '6':dm3_map, '7':dm3_map, '8':dm3_map }
206 eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
210 self.failUnlessEqual(lane.reads, 4)
211 self.failUnlessEqual(lane.sample_name, "s")
212 self.failUnlessEqual(lane.lane_id, unicode(i))
213 self.failUnlessEqual(len(lane.mapped_reads), 3)
214 self.failUnlessEqual(lane.mapped_reads['Lambda.fa'], 1)
215 self.failUnlessEqual(lane.mapped_reads['dm3/chr2L.fa'], 1)
216 self.failUnlessEqual(lane.match_codes['U1'], 2)
217 self.failUnlessEqual(lane.match_codes['NM'], 1)
219 xml = eland.get_elements()
220 # just make sure that element tree can serialize the tree
221 xml_str = ElementTree.tostring(xml)
222 e2 = gerald.ELAND(xml=xml)
227 self.failUnlessEqual(l1.reads, l2.reads)
228 self.failUnlessEqual(l1.sample_name, l2.sample_name)
229 self.failUnlessEqual(l1.lane_id, l2.lane_id)
230 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
231 self.failUnlessEqual(len(l1.mapped_reads), 3)
232 for k in l1.mapped_reads.keys():
233 self.failUnlessEqual(l1.mapped_reads[k],
236 self.failUnlessEqual(len(l1.match_codes), 9)
237 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
238 for k in l1.match_codes.keys():
239 self.failUnlessEqual(l1.match_codes[k],
242 def test_runfolder(self):
243 runs = runfolder.get_runs(self.runfolder_dir)
245 # do we get the flowcell id from the filename?
246 self.failUnlessEqual(len(runs), 1)
247 self.failUnlessEqual(runs[0].name, 'run_207BTAAXX_2008-10-30.xml')
249 # do we get the flowcell id from the FlowcellId.xml file
250 make_flowcell_id(self.runfolder_dir, '207BTAAXY')
251 runs = runfolder.get_runs(self.runfolder_dir)
252 self.failUnlessEqual(len(runs), 1)
253 self.failUnlessEqual(runs[0].name, 'run_207BTAAXY_2008-10-30.xml')
256 xml = r1.get_elements()
257 xml_str = ElementTree.tostring(xml)
259 r2 = runfolder.PipelineRun(xml=xml)
260 self.failUnlessEqual(r1.name, r2.name)
261 self.failIfEqual(r2.image_analysis, None)
262 self.failIfEqual(r2.bustard, None)
263 self.failIfEqual(r2.gerald, None)
267 return unittest.makeSuite(RunfolderTests,'test')
269 if __name__ == "__main__":
270 unittest.main(defaultTest="suite")