obj.image_analysis_dir = intensities_dir
obj.bustard_dir = unaligned_dir
obj.gerald_dir = aligned_dir
+ obj.reads = 2
class RunfolderTests(unittest.TestCase):
(1854131, 429053.2), (4777517, 592904.0),
]
- self.failUnlessEqual(len(g.summary), 2)
+ self.failUnlessEqual(len(g.summary), self.reads)
for i in range(1,9):
summary_lane = g.summary[0][i]
self.failUnlessEqual(summary_lane.cluster, clusters[i])
xml = g.get_elements()
# just make sure that element tree can serialize the tree
xml_str = ElementTree.tostring(xml)
- g2 = gerald.Gerald(xml=xml)
- return
+ g2 = gerald.CASAVA(xml=xml)
# do it all again after extracting from the xml file
self.failUnlessEqual(g.software, g2.software)
self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
# test lane specific parameters from gerald config file
- for i in range(1,9):
+ for i in g.lanes.keys():
g_lane = g.lanes[i]
g2_lane = g2.lanes[i]
self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
# test (some) summary elements
- self.failUnlessEqual(len(g.summary), 1)
+ self.failUnlessEqual(len(g.summary), self.reads)
for i in range(1,9):
g_summary = g.summary[0][i]
g2_summary = g2.summary[0][i]
def test_eland(self):
- return
hg_map = {'Lambda.fa': 'Lambda.fa'}
for i in range(1,22):
short_name = 'chr%d.fa' % (i,)