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_multi(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 # I want to be able to use a simple iterator
144 for l in g.lanes.values():
145 self.failUnlessEqual(l.analysis, 'eland')
146 self.failUnlessEqual(l.read_length, '32')
147 self.failUnlessEqual(l.use_bases, 'Y'*32)
149 # test data extracted from summary file
151 (96483, 9074), (133738, 7938),
152 (152142, 10002), (15784, 2162),
153 (119735, 8465), (152177, 8146),
154 (84649, 7325), (54622, 4812),]
157 summary_lane = g.summary[str(i)]
158 self.failUnlessEqual(summary_lane.cluster, clusters[i])
159 self.failUnlessEqual(summary_lane.lane, str(i))
161 xml = g.get_elements()
162 # just make sure that element tree can serialize the tree
163 xml_str = ElementTree.tostring(xml)
164 g2 = gerald.Gerald(xml=xml)
166 # do it all again after extracting from the xml file
167 self.failUnlessEqual(g.version, g2.version)
168 self.failUnlessEqual(g.date, g2.date)
169 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
170 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
172 # test lane specific parameters from gerald config file
174 g_lane = g.lanes[str(i)]
175 g2_lane = g2.lanes[str(i)]
176 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
177 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
178 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
179 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
181 # test (some) summary elements
183 g_summary = g.summary[str(i)]
184 g2_summary = g2.summary[str(i)]
185 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
186 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
188 g_eland = g.eland_results
189 g2_eland = g2.eland_results
190 for lane in g_eland.keys():
191 self.failUnlessEqual(g_eland[lane].reads,
192 g2_eland[lane].reads)
193 self.failUnlessEqual(len(g_eland[lane].mapped_reads),
194 len(g2_eland[lane].mapped_reads))
195 for k in g_eland[lane].mapped_reads.keys():
196 self.failUnlessEqual(g_eland[lane].mapped_reads[k],
197 g2_eland[lane].mapped_reads[k])
199 self.failUnlessEqual(len(g_eland[lane].match_codes),
200 len(g2_eland[lane].match_codes))
201 for k in g_eland[lane].match_codes.keys():
202 self.failUnlessEqual(g_eland[lane].match_codes[k],
203 g2_eland[lane].match_codes[k])
206 def test_eland(self):
207 hg_map = {'Lambda.fa': 'Lambda.fa'}
208 for i in range(1,22):
209 short_name = 'chr%d.fa' % (i,)
210 long_name = 'hg18/chr%d.fa' % (i,)
211 hg_map[short_name] = long_name
213 genome_maps = { '1':hg_map, '2':hg_map, '3':hg_map, '4':hg_map,
214 '5':hg_map, '6':hg_map, '7':hg_map, '8':hg_map }
215 eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
219 self.failUnlessEqual(lane.reads, 4)
220 self.failUnlessEqual(lane.sample_name, "s")
221 self.failUnlessEqual(lane.lane_id, unicode(i))
222 self.failUnlessEqual(len(lane.mapped_reads), 15)
223 self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
224 self.failUnlessEqual(lane.match_codes['U1'], 10)
225 self.failUnlessEqual(lane.match_codes['NM'], 1)
226 self.failUnlessEqual(lane.match_codes['QC'], 0)
228 xml = eland.get_elements()
229 # just make sure that element tree can serialize the tree
230 xml_str = ElementTree.tostring(xml)
231 e2 = gerald.ELAND(xml=xml)
236 self.failUnlessEqual(l1.reads, l2.reads)
237 self.failUnlessEqual(l1.sample_name, l2.sample_name)
238 self.failUnlessEqual(l1.lane_id, l2.lane_id)
239 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
240 self.failUnlessEqual(len(l1.mapped_reads), 15)
241 for k in l1.mapped_reads.keys():
242 self.failUnlessEqual(l1.mapped_reads[k],
245 self.failUnlessEqual(len(l1.match_codes), 9)
246 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
247 for k in l1.match_codes.keys():
248 self.failUnlessEqual(l1.match_codes[k],
251 def test_runfolder(self):
252 runs = runfolder.get_runs(self.runfolder_dir)
254 # do we get the flowcell id from the filename?
255 self.failUnlessEqual(len(runs), 1)
256 name = 'run_207BTAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
257 self.failUnlessEqual(runs[0].name, name)
259 # do we get the flowcell id from the FlowcellId.xml file
260 make_flowcell_id(self.runfolder_dir, '207BTAAXY')
261 runs = runfolder.get_runs(self.runfolder_dir)
262 self.failUnlessEqual(len(runs), 1)
263 name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
264 self.failUnlessEqual(runs[0].name, name)
267 xml = r1.get_elements()
268 xml_str = ElementTree.tostring(xml)
270 r2 = runfolder.PipelineRun(xml=xml)
271 self.failUnlessEqual(r1.name, r2.name)
272 self.failIfEqual(r2.image_analysis, None)
273 self.failIfEqual(r2.bustard, None)
274 self.failIfEqual(r2.gerald, None)
278 return unittest.makeSuite(RunfolderTests,'test')
280 if __name__ == "__main__":
281 unittest.main(defaultTest="suite")