import os
import tempfile
import shutil
-import unittest
+from unittest2 import TestCase
from htsworkflow.pipelines import firecrest
from htsworkflow.pipelines import bustard
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
Construct a firecrest object
"""
f = firecrest.firecrest(self.firecrest_dir)
+ self.failUnlessEqual(f.software, 'Firecrest')
self.failUnlessEqual(f.version, '1.8.28')
self.failUnlessEqual(f.start, 1)
self.failUnlessEqual(f.stop, 33)
xml_str = ElementTree.tostring(xml)
f2 = firecrest.Firecrest(xml=xml)
- self.failUnlessEqual(f.version, f2.version)
- self.failUnlessEqual(f.start, f2.start)
- self.failUnlessEqual(f.stop, f2.stop)
- self.failUnlessEqual(f.user, f2.user)
- self.failUnlessEqual(f.date, f2.date)
+ self.failUnlessEqual(f.software, f2.software)
+ self.failUnlessEqual(f.version, f2.version)
+ self.failUnlessEqual(f.start, f2.start)
+ self.failUnlessEqual(f.stop, f2.stop)
+ self.failUnlessEqual(f.user, f2.user)
+ self.failUnlessEqual(f.date, f2.date)
def test_bustard(self):
"""
construct a bustard object
"""
b = bustard.bustard(self.bustard_dir)
+ self.failUnlessEqual(b.software, 'Bustard')
self.failUnlessEqual(b.version, '1.8.28')
self.failUnlessEqual(b.date, date(2008,4,12))
self.failUnlessEqual(b.user, 'diane')
xml = b.get_elements()
b2 = bustard.Bustard(xml=xml)
- self.failUnlessEqual(b.version, b2.version)
- self.failUnlessEqual(b.date, b2.date )
- self.failUnlessEqual(b.user, b2.user)
+ self.failUnlessEqual(b.software, b2.software)
+ self.failUnlessEqual(b.version, b2.version)
+ self.failUnlessEqual(b.date, b2.date )
+ self.failUnlessEqual(b.user, b2.user)
self.failUnlessEqual(len(b.phasing), len(b2.phasing))
for key in b.phasing.keys():
self.failUnlessEqual(b.phasing[key].lane,
# need to update gerald and make tests for it
g = gerald.gerald(self.gerald_dir)
+ self.failUnlessEqual(g.software, 'GERALD')
self.failUnlessEqual(g.version, '1.68.2.2')
self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
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)
self.failUnlessEqual(len(g_results.mapped_reads),
5:dm3_map, 6:dm3_map, 7:dm3_map, 8:dm3_map }
eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
- for i in range(1,9):
- lane = eland.results[0][i]
+ for key in eland:
+ lane = eland[key]
self.failUnlessEqual(lane.reads, 4)
self.failUnlessEqual(lane.sample_name, "s")
- self.failUnlessEqual(lane.lane_id, i)
+ self.failUnlessEqual(lane.lane_id, key.lane)
self.failUnlessEqual(len(lane.mapped_reads), 3)
self.failUnlessEqual(lane.mapped_reads['Lambda.fa'], 1)
self.failUnlessEqual(lane.mapped_reads['dm3/chr2L.fa'], 1)
xml_str = ElementTree.tostring(xml)
e2 = gerald.ELAND(xml=xml)
- for i in range(1,9):
- l1 = eland.results[0][i]
- l2 = e2.results[0][i]
+ for key in eland:
+ l1 = eland[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")