# test lane specific parameters from gerald config file
for i in range(1,9):
- cur_lane = g.lanes[str(i)]
+ cur_lane = g.lanes[i]
self.failUnlessEqual(cur_lane.analysis, 'eland')
self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
self.failUnlessEqual(cur_lane.read_length, '32')
self.failUnlessEqual(l.use_bases, 'Y'*32)
# test data extracted from summary file
- clusters = [None,
- (96483, 9074), (133738, 7938),
- (152142, 10002), (15784, 2162),
- (119735, 8465), (152177, 8146),
- (84649, 7325), (54622, 4812),]
-
- for i in range(1,9):
- summary_lane = g.summary[str(i)]
- self.failUnlessEqual(summary_lane.cluster, clusters[i])
- self.failUnlessEqual(summary_lane.lane, str(i))
+ clusters = [[None,
+ (103646, 4515), (106678, 4652),
+ (84583, 5963), (68813, 4782),
+ (104854, 4664), (43555, 1632),
+ (54265, 1588), (64363, 2697),],
+ [None,
+ (103647, 4516), (106679, 4653),
+ (84584, 5964), (68814, 4783),
+ (104855, 4665), (43556, 1633),
+ (54266, 1589), (64364, 2698),],]
+
+ for end in [0,1]:
+ for lane in range(1,9):
+ summary_lane = g.summary[end][lane]
+ self.failUnlessEqual(summary_lane.cluster, clusters[end][lane])
+ self.failUnlessEqual(summary_lane.lane, lane)
xml = g.get_elements()
# just make sure that element tree can serialize the tree
# test lane specific parameters from gerald config file
for i in range(1,9):
- g_lane = g.lanes[str(i)]
- g2_lane = g2.lanes[str(i)]
+ g_lane = g.lanes[i]
+ g2_lane = g2.lanes[i]
self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
# test (some) summary elements
- for i in range(1,9):
- g_summary = g.summary[str(i)]
- g2_summary = g2.summary[str(i)]
- self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
- self.failUnlessEqual(g_summary.lane, g2_summary.lane)
-
- g_eland = g.eland_results
- g2_eland = g2.eland_results
- for lane in g_eland.keys():
- self.failUnlessEqual(g_eland[lane].reads,
- g2_eland[lane].reads)
- self.failUnlessEqual(len(g_eland[lane].mapped_reads),
- len(g2_eland[lane].mapped_reads))
- for k in g_eland[lane].mapped_reads.keys():
- self.failUnlessEqual(g_eland[lane].mapped_reads[k],
- g2_eland[lane].mapped_reads[k])
-
- self.failUnlessEqual(len(g_eland[lane].match_codes),
- len(g2_eland[lane].match_codes))
- for k in g_eland[lane].match_codes.keys():
- self.failUnlessEqual(g_eland[lane].match_codes[k],
- g2_eland[lane].match_codes[k])
+ for end in [0,1]:
+ for i in range(1,9):
+ g_summary = g.summary[end][i]
+ g2_summary = g2.summary[end][i]
+ self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
+ self.failUnlessEqual(g_summary.lane, g2_summary.lane)
+
+ g_eland = g.eland_results
+ g2_eland = g2.eland_results
+ for lane in g_eland.keys():
+ self.failUnlessEqual(g_eland[lane].reads,
+ g2_eland[lane].reads)
+ self.failUnlessEqual(len(g_eland[lane].mapped_reads),
+ len(g2_eland[lane].mapped_reads))
+ for k in g_eland[lane].mapped_reads.keys():
+ self.failUnlessEqual(g_eland[lane].mapped_reads[k],
+ g2_eland[lane].mapped_reads[k])
+
+ self.failUnlessEqual(len(g_eland[lane].match_codes),
+ len(g2_eland[lane].match_codes))
+ for k in g_eland[lane].match_codes.keys():
+ self.failUnlessEqual(g_eland[lane].match_codes[k],
+ g2_eland[lane].match_codes[k])
def test_eland(self):
long_name = 'hg18/chr%d.fa' % (i,)
hg_map[short_name] = long_name
- genome_maps = { '1':hg_map, '2':hg_map, '3':hg_map, '4':hg_map,
- '5':hg_map, '6':hg_map, '7':hg_map, '8':hg_map }
+ genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
+ 5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
for i in range(1,9):
- lane = eland[str(i)]
+ lane = eland[i]
self.failUnlessEqual(lane.reads, 4)
self.failUnlessEqual(lane.sample_name, "s")
- self.failUnlessEqual(lane.lane_id, unicode(i))
+ self.failUnlessEqual(lane.lane_id, i)
self.failUnlessEqual(len(lane.mapped_reads), 15)
self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
self.failUnlessEqual(lane.match_codes['U0'], 1)
e2 = gerald.ELAND(xml=xml)
for i in range(1,9):
- l1 = eland[str(i)]
- l2 = e2[str(i)]
+ l1 = eland[i]
+ l2 = e2[i]
self.failUnlessEqual(l1.reads, l2.reads)
self.failUnlessEqual(l1.sample_name, l2.sample_name)
self.failUnlessEqual(l1.lane_id, l2.lane_id)
# do we get the flowcell id from the filename?
self.failUnlessEqual(len(runs), 1)
- name = 'run_207BTAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+ # firecrest's date depends on filename not the create time.
+ name = 'run_207BTAAXX_2008-04-19.xml'
self.failUnlessEqual(runs[0].name, name)
# do we get the flowcell id from the FlowcellId.xml file
make_flowcell_id(self.runfolder_dir, '207BTAAXY')
runs = runfolder.get_runs(self.runfolder_dir)
self.failUnlessEqual(len(runs), 1)
- name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+ name = 'run_207BTAAXY_2008-04-19.xml'
self.failUnlessEqual(runs[0].name, name)
r1 = runs[0]
projects / htsworkflow.git / blobdiff