import os
import shutil
import tempfile
-import unittest
+from unittest import TestCase
import RDF
from htsworkflow.util.rdfhelp import get_model, load_string_into_model, \
rdfNS, libraryOntology, dump_model, fromTypedNode
-class SequenceFileTests(unittest.TestCase):
+class SequenceFileTests(TestCase):
"""
Make sure the sequence archive class works
"""
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<srf 42BW9AAXX 4 %s>" % (pathname,))
self.assertEqual(f0.flowcell, '42BW9AAXX')
- self.assertEqual(f0.lane, 4)
+ self.assertEqual(f0.lane, '4')
self.assertEqual(f0.read, None)
self.assertEqual(f0.pf, None)
self.assertEqual(f0.cycle, 38)
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<qseq 42BW9AAXX 4 %s>" %(pathname,))
self.assertEqual(f0.flowcell, '42BW9AAXX')
- self.assertEqual(f0.lane, 4)
+ self.assertEqual(f0.lane, '4')
self.assertEqual(f0.read, 1)
self.assertEqual(f0.pf, None)
self.assertEqual(f0.cycle, 36)
self.assertEqual(f0.path, pathname)
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<qseq ilmn200901 1 %s>" %(pathname,))
- self.assertEqual(f0.lane, 1)
+ self.assertEqual(f0.lane, '1')
self.assertEqual(f0.read, 1)
self.assertEqual(f0.pf, None)
self.assertEqual(f0.cycle, 202)
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<fastq 42BW9AAXX 4 %s>" % (pathname,))
self.assertEqual(f0.flowcell, '42BW9AAXX')
- self.assertEqual(f0.lane, 4)
+ self.assertEqual(f0.lane, '4')
self.assertEqual(f0.read, 1)
self.assertEqual(f0.pf, True)
self.assertEqual(f0.cycle, 38)
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<fastq 42BW9AAXX 4 %s>" %(pathname,))
self.assertEqual(f0.flowcell, '42BW9AAXX')
- self.assertEqual(f0.lane, 4)
+ self.assertEqual(f0.lane, '4')
self.assertEqual(f0.read, 2)
self.assertEqual(f0.pf, False)
self.assertEqual(f0.cycle, 38)
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<split_fastq 42BW9AAXX 1 %s>" %(pathname,))
self.assertEqual(f0.flowcell, '42BW9AAXX')
- self.assertEqual(f0.lane, 1)
+ self.assertEqual(f0.lane, '1')
self.assertEqual(f0.read, 1)
self.assertEqual(f0.pf, True)
self.assertEqual(f0.project, '11111')
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<split_fastq 42BW9AAXX 1 %s>" % (pathname,))
self.assertEqual(f0.flowcell, '42BW9AAXX')
- self.assertEqual(f0.lane, 1)
+ self.assertEqual(f0.lane, '1')
self.assertEqual(f0.read, 2)
self.assertEqual(f0.pf, True)
self.assertEqual(f0.project, '11112')
self.assertEqual(f.filetype, 'eland')
self.assertEqual(f.path, pathname)
self.assertEqual(f.flowcell, '42BW9AAXX')
- self.assertEqual(f.lane, 4)
+ self.assertEqual(f.lane, '4')
self.assertEqual(f.read, None)
self.assertEqual(f.pf, None)
self.assertEqual(f.cycle, 38)
self.assertEqual(f.filetype, 'eland')
self.assertEqual(f.path, pathname)
self.assertEqual(f.flowcell, '42BW9AAXX')
- self.assertEqual(f.lane, 4)
+ self.assertEqual(f.lane, '4')
self.assertEqual(f.read, 1)
self.assertEqual(f.pf, None)
self.assertEqual(f.cycle, 152)
files = list(model.find_statements(
RDF.Statement(None,
rdfNS['type'],
- libraryOntology['illumina_result'])))
+ libraryOntology['IlluminaResult'])))
self.assertEqual(len(files), 5)
files = list(model.find_statements(
RDF.Statement(None,
a libns:IlluminaFlowcell .
<{base}/lane/1169>
- libns:lane_number 1 ; libns:library <{base}/library/10923/> .
+ libns:lane_number "1" ; libns:library <{base}/library/10923/> .
<{base}/lane/1170>
- libns:lane_number 2 ; libns:library <{base}/library/10924/> .
+ libns:lane_number "2" ; libns:library <{base}/library/10924/> .
<{base}/lane/1171>
- libns:lane_number 3 ; libns:library <{base}/library/12345/> .
+ libns:lane_number "3" ; libns:library <{base}/library/12345/> .
<{base}/lane/1172>
- libns:lane_number 3 ; libns:library <{base}/library/10930/> .
+ libns:lane_number "3" ; libns:library <{base}/library/10930/> .
""".format(base=base_url)
model = get_model()
load_string_into_model(model, 'turtle', flowcellInfo)
self.assertEqual(seq.filetype, seq2.filetype)
self.assertEqual(seq2.filetype, 'split_fastq')
self.assertEqual(seq.lane, seq2.lane)
- self.assertEqual(seq2.lane, 3)
+ self.assertEqual(seq2.lane, '3')
self.assertEqual(seq.read, seq2.read)
self.assertEqual(seq2.read, 1)
self.assertEqual(seq.project, seq2.project)
file_types_seen = set()
file_types_to_see = set(['fastq', 'srf', 'eland', 'qseq'])
lanes = set()
- lanes_to_see = set((1,2,3))
+ lanes_to_see = set(('1','2','3'))
with SimulateSimpleTree() as tree:
seqs = sequences.scan_for_sequences([tree.root, '/a/b/c/98345'])
for s in seqs:
file_types_seen = set()
file_types_to_see = set(['split_fastq'])
lanes = set()
- lanes_to_see = set((1,2))
+ lanes_to_see = set(('1','2'))
projects_seen = set()
projects_to_see = set(('11111', '21111', '31111'))
with SimulateHiSeqTree() as tree:
def suite():
- return unittest.makeSuite(SequenceFileTests,'test')
+ from unittest import TestSuite, defaultTestLoader
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(SequenceFileTests))
+ return suite
+
if __name__ == "__main__":
- unittest.main(defaultTest="suite")
+ from unittest import main
+ main(defaultTest="suite")