-from unittest2 import TestCase
+from unittest import TestCase
from htsworkflow.submission.fastqname import FastqName
class TestFastqName(TestCase):
self.assertEqual(fq.lane, "1")
self.assertEqual(fq['lane'], "1")
self.assertEqual(fq.is_paired, False)
+ self.assertEqual(fq.compression_extension, '')
+
+ def test_init_single_filename_gz(self):
+ fq = FastqName(filename="12345_AABBCCDDXX_c100_l1.fastq.gz")
+ self.assertEqual(fq.lib_id, "12345")
+ self.assertEqual(fq['lib_id'], "12345")
+ self.assertEqual(fq.flowcell, "AABBCCDDXX")
+ self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+ self.assertEqual(fq.cycle, "100")
+ self.assertEqual(fq['cycle'], "100")
+ self.assertEqual(fq.lane, "1")
+ self.assertEqual(fq['lane'], "1")
+ self.assertEqual(fq.is_paired, False)
+ self.assertEqual(fq.compression_extension, '.gz')
def test_init_single_filename(self):
fq = FastqName(filename="12345_AABBCCDDXX_c100_l1_r2.fastq")
self.assertEqual(fq.read, "2")
self.assertEqual(fq['read'], "2")
self.assertEqual(fq.is_paired, True)
+ self.assertEqual(fq.compression_extension, None)
def test_init_bad_filename(self):
attribs = {'filename': 'asdf.bam'}
self.assertEqual(fq['lane'], "1")
self.assertEqual(fq.is_paired, False)
self.assertEqual(fq.filename, "12345_AABBCCDDXX_c100_l1.fastq")
+ self.assertEqual(fq.compression_extension, None)
def test_init_single_attributes_set_single(self):
fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
self.assertEqual(fq.is_valid, False)
self.assertEqual(fq.is_paired, True)
+ def test_init_single_attributes_set_paired_bzip2(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1", is_paired=True,
+ compression_extension='.bzip2')
+ self.assertEqual(fq.is_valid, False)
+ self.assertEqual(fq.is_paired, True)
+ self.assertEqual(fq.compression_extension, '.bzip2')
+
def test_init_paired_attributes(self):
fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
cycle = "100", lane="1", read="2")
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestFastqName))
return suite
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest='suite')