X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=blobdiff_plain;f=htsworkflow%2Fpipelines%2Ftest%2Ftest_sequences.py;h=accd43ecf8786b4d25a96683bf861940006cf44f;hp=e621875231d60a0da1207b1e2fb53d0e5c121fbe;hb=28242245c13a034387a0e0a000c45e814ee12945;hpb=1e0aedcf453376920153a795db4c9a9198a808c6 diff --git a/htsworkflow/pipelines/test/test_sequences.py b/htsworkflow/pipelines/test/test_sequences.py index e621875..accd43e 100644 --- a/htsworkflow/pipelines/test/test_sequences.py +++ b/htsworkflow/pipelines/test/test_sequences.py @@ -74,7 +74,7 @@ class SequenceFileTests(unittest.TestCase): self.assertEqual(unicode(f0), unicode(pathname)) self.assertEqual(repr(f0), "" % (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) @@ -99,7 +99,7 @@ class SequenceFileTests(unittest.TestCase): self.assertEqual(unicode(f0), unicode(pathname)) self.assertEqual(repr(f0), "" %(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) @@ -121,7 +121,7 @@ class SequenceFileTests(unittest.TestCase): self.assertEqual(f0.path, pathname) self.assertEqual(unicode(f0), unicode(pathname)) self.assertEqual(repr(f0), "" %(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) @@ -145,7 +145,7 @@ class SequenceFileTests(unittest.TestCase): self.assertEqual(unicode(f0), unicode(pathname)) self.assertEqual(repr(f0), "" % (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) @@ -167,7 +167,7 @@ class SequenceFileTests(unittest.TestCase): self.assertEqual(unicode(f0), unicode(pathname)) self.assertEqual(repr(f0), "" %(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) @@ -191,7 +191,7 @@ class SequenceFileTests(unittest.TestCase): self.assertEqual(unicode(f0), unicode(pathname)) self.assertEqual(repr(f0), "" %(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') @@ -215,7 +215,7 @@ class SequenceFileTests(unittest.TestCase): self.assertEqual(unicode(f0), unicode(pathname)) self.assertEqual(repr(f0), "" % (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') @@ -275,7 +275,7 @@ class SequenceFileTests(unittest.TestCase): 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) @@ -290,7 +290,7 @@ class SequenceFileTests(unittest.TestCase): 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) @@ -346,7 +346,7 @@ class SequenceFileTests(unittest.TestCase): 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, @@ -411,13 +411,13 @@ class SequenceFileTests(unittest.TestCase): 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) @@ -472,7 +472,7 @@ class SequenceFileTests(unittest.TestCase): 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) @@ -491,7 +491,7 @@ class SequenceFileTests(unittest.TestCase): 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: @@ -512,7 +512,7 @@ class SequenceFileTests(unittest.TestCase): 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: