import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import bustard
from htsworkflow.pipelines import eland
obj.gerald_dir = gerald_dir
-class RunfolderTests(unittest.TestCase):
+class RunfolderTests(TestCase):
"""
Test components of the runfolder processing code
which includes firecrest, bustard, and gerald
g_eland = g.eland_results
g2_eland = g2.eland_results
- for lane in g_eland.results[0].keys():
- g_results = g_eland.results[0][lane]
- g2_results = g2_eland.results[0][lane]
+ for key in g_eland:
+ g_results = g_eland[key]
+ g2_results = g2_eland[key]
self.failUnlessEqual(g_results.reads,
g2_results.reads)
if isinstance(g_results, eland.ElandLane):
# test fastq
for i in range(1,4):
- lane = eland_container.results[0][i]
+ key = eland.SampleKey(lane=i, read=1, sample='s')
+ lane = eland_container[key]
self.failUnlessEqual(lane.reads, 3)
self.failUnlessEqual(lane.sample_name, 's')
self.failUnlessEqual(lane.lane_id, i)
# I added sequence lanes to the last 2 lanes of this test case
for i in range(4,9):
- lane = eland_container.results[0][i]
+ key = eland.SampleKey(lane=i, read=1, sample='s')
+ lane = eland_container[key]
self.failUnlessEqual(lane.reads, 28)
self.failUnlessEqual(lane.sample_name, "s")
self.failUnlessEqual(lane.lane_id, i)
xml_str = ElementTree.tostring(xml)
e2 = gerald.ELAND(xml=xml)
- for i in range(1,9):
- l1 = eland_container.results[0][i]
- l2 = e2.results[0][i]
+ for key in eland_container:
+ l1 = eland_container[key]
+ l2 = e2[key]
self.failUnlessEqual(l1.reads, l2.reads)
self.failUnlessEqual(l1.sample_name, l2.sample_name)
self.failUnlessEqual(l1.lane_id, l2.lane_id)
def suite():
- return unittest.makeSuite(RunfolderTests,'test')
+ from unittest2 import TestSuite, defaultTestLoader
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
+ return suite
if __name__ == "__main__":
- unittest.main(defaultTest="suite")
-
+ from unittest2 import main
+ main(defaultTest="suite")