X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=blobdiff_plain;f=htsworkflow%2Fsubmission%2Ftest%2Ftest_condorfastq.py;h=dbeb71cd6baac0e2c23f80873b38dc16482a60db;hp=09d68083c1ec50052c450a71e9d9e24356573cf7;hb=refs%2Fheads%2Fpython3-django1.5;hpb=4262586d10cc0cc227390873b301b55244204c11 diff --git a/htsworkflow/submission/test/test_condorfastq.py b/htsworkflow/submission/test/test_condorfastq.py index 09d6808..dbeb71c 100644 --- a/htsworkflow/submission/test/test_condorfastq.py +++ b/htsworkflow/submission/test/test_condorfastq.py @@ -436,7 +436,7 @@ class TestCondorFastq(TestCase): stream.write('testfile') self.result_map = ResultMap() - for lib_id in [u'11154', u'12345']: + for lib_id in ['11154', '12345']: subname = 'sub-%s' % (lib_id,) sub_dir = os.path.join(self.tempdir, subname) os.mkdir(sub_dir) @@ -469,21 +469,21 @@ class TestCondorFastq(TestCase): seqs = self.extract.find_archive_sequence_files(self.result_map) expected = set([ - (u'11154', u'42JUYAAXX', '5', 1, 76, True, 'qseq'), - (u'11154', u'42JUYAAXX', '5', 2, 76, True, 'qseq'), - (u'11154', u'61MJTAAXX', '6', 1, 76, False, 'qseq'), - (u'11154', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'), - (u'11154', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'), - (u'11154', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'), - (u'11154', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'), - (u'12345', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'), - (u'12345', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'), - (u'12345', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'), - (u'12345', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'), - (u'12345', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'), - (u'12345', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'), - (u'11154', u'30221AAXX', '4', 1, 33, False, 'srf'), - (u'11154', u'30DY0AAXX', '8', 1, 151, True, 'srf') + ('11154', '42JUYAAXX', '5', 1, 76, True, 'qseq'), + ('11154', '42JUYAAXX', '5', 2, 76, True, 'qseq'), + ('11154', '61MJTAAXX', '6', 1, 76, False, 'qseq'), + ('11154', 'C02F9ACXX', '3', 2, 202, True, 'split_fastq'), + ('11154', 'C02F9ACXX', '3', 1, 202, True, 'split_fastq'), + ('11154', 'C02F9ACXX', '3', 1, 202, True, 'split_fastq'), + ('11154', 'C02F9ACXX', '3', 2, 202, True, 'split_fastq'), + ('12345', 'C02F9ACXX', '3', 1, 202, True, 'split_fastq'), + ('12345', 'C02F9ACXX', '3', 2, 202, True, 'split_fastq'), + ('12345', 'C02F9ACXX', '3', 2, 202, True, 'split_fastq'), + ('12345', 'C02F9ACXX', '3', 1, 202, True, 'split_fastq'), + ('12345', 'C02F9ACXX', '3', 1, 202, True, 'split_fastq'), + ('12345', 'C02F9ACXX', '3', 2, 202, True, 'split_fastq'), + ('11154', '30221AAXX', '4', 1, 33, False, 'srf'), + ('11154', '30DY0AAXX', '8', 1, 151, True, 'srf') ]) found = set([(l.library_id, l.flowcell_id, l.lane_number, l.read, l.cycle, l.ispaired, l.filetype) for l in seqs]) self.assertEqual(expected, found) @@ -495,17 +495,17 @@ class TestCondorFastq(TestCase): lib_db) self.assertEqual(len(needed_targets), 9) srf_30221 = needed_targets[ - self.result_map['11154'] + u'/11154_30221AAXX_c33_l4.fastq'] + self.result_map['11154'] + '/11154_30221AAXX_c33_l4.fastq'] qseq_42JUY_r1 = needed_targets[ - self.result_map['11154'] + u'/11154_42JUYAAXX_c76_l5_r1.fastq'] + self.result_map['11154'] + '/11154_42JUYAAXX_c76_l5_r1.fastq'] qseq_42JUY_r2 = needed_targets[ - self.result_map['11154'] + u'/11154_42JUYAAXX_c76_l5_r2.fastq'] + self.result_map['11154'] + '/11154_42JUYAAXX_c76_l5_r2.fastq'] qseq_61MJT = needed_targets[ - self.result_map['11154'] + u'/11154_61MJTAAXX_c76_l6.fastq'] + self.result_map['11154'] + '/11154_61MJTAAXX_c76_l6.fastq'] split_C02F9_r1 = needed_targets[ - self.result_map['11154'] + u'/11154_C02F9ACXX_c202_l3_r1.fastq'] + self.result_map['11154'] + '/11154_C02F9ACXX_c202_l3_r1.fastq'] split_C02F9_r2 = needed_targets[ - self.result_map['11154'] + u'/11154_C02F9ACXX_c202_l3_r2.fastq'] + self.result_map['11154'] + '/11154_C02F9ACXX_c202_l3_r2.fastq'] self.assertEqual(len(srf_30221['srf']), 1) self.assertEqual(len(qseq_42JUY_r1['qseq']), 1) @@ -530,24 +530,24 @@ class TestCondorFastq(TestCase): '11154_30221AAXX_c33_l4.fastq'): { 'mid': None, 'ispaired': False, - 'sources': [u'woldlab_090425_HWI-EAS229_0110_30221AAXX_4.srf'], - 'flowcell': u'30221AAXX', + 'sources': ['woldlab_090425_HWI-EAS229_0110_30221AAXX_4.srf'], + 'flowcell': '30221AAXX', 'target': os.path.join(self.result_map['11154'], - u'11154_30221AAXX_c33_l4.fastq'), + '11154_30221AAXX_c33_l4.fastq'), }, os.path.join(self.result_map['11154'], '11154_30DY0AAXX_c151_l8_r1.fastq'): { 'mid': None, 'ispaired': True, - 'flowcell': u'30DY0AAXX', - 'sources': [u'woldlab_090725_HWI-EAS229_0110_30DY0AAXX_8.srf'], + 'flowcell': '30DY0AAXX', + 'sources': ['woldlab_090725_HWI-EAS229_0110_30DY0AAXX_8.srf'], 'mid': 76, 'target': os.path.join(self.result_map['11154'], - u'11154_30DY0AAXX_c151_l8_r1.fastq'), + '11154_30DY0AAXX_c151_l8_r1.fastq'), 'target_right': os.path.join(self.result_map['11154'], - u'11154_30DY0AAXX_c151_l8_r2.fastq'), + '11154_30DY0AAXX_c151_l8_r2.fastq'), } } for args in srf: @@ -569,21 +569,21 @@ class TestCondorFastq(TestCase): 'istar': True, 'ispaired': True, 'sources': [ - u'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r1.tar.bz2'] + 'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r1.tar.bz2'] }, os.path.join(self.result_map['11154'], '11154_42JUYAAXX_c76_l5_r2.fastq'): { 'istar': True, 'ispaired': True, 'sources': [ - u'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r2.tar.bz2'] + 'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r2.tar.bz2'] }, os.path.join(self.result_map['11154'], '11154_61MJTAAXX_c76_l6.fastq'): { 'istar': True, 'ispaired': False, 'sources': [ - u'woldlab_100826_HSI-123_0001_61MJTAAXX_l6_r1.tar.bz2'], + 'woldlab_100826_HSI-123_0001_61MJTAAXX_l6_r1.tar.bz2'], }, } for args in qseq: @@ -596,26 +596,26 @@ class TestCondorFastq(TestCase): split_test = dict((( x['target'], x) for x in - [{'sources': [u'11154_NoIndex_L003_R1_001.fastq.gz', - u'11154_NoIndex_L003_R1_002.fastq.gz'], + [{'sources': ['11154_NoIndex_L003_R1_001.fastq.gz', + '11154_NoIndex_L003_R1_002.fastq.gz'], 'pyscript': 'desplit_fastq.pyc', - 'target': u'11154_C02F9ACXX_c202_l3_r1.fastq'}, - {'sources': [u'11154_NoIndex_L003_R2_001.fastq.gz', - u'11154_NoIndex_L003_R2_002.fastq.gz'], + 'target': '11154_C02F9ACXX_c202_l3_r1.fastq'}, + {'sources': ['11154_NoIndex_L003_R2_001.fastq.gz', + '11154_NoIndex_L003_R2_002.fastq.gz'], 'pyscript': 'desplit_fastq.pyc', - 'target': u'11154_C02F9ACXX_c202_l3_r2.fastq'}, - {'sources': [u'12345_CGATGT_L003_R1_001.fastq.gz', - u'12345_CGATGT_L003_R1_002.fastq.gz', - u'12345_CGATGT_L003_R1_003.fastq.gz', + 'target': '11154_C02F9ACXX_c202_l3_r2.fastq'}, + {'sources': ['12345_CGATGT_L003_R1_001.fastq.gz', + '12345_CGATGT_L003_R1_002.fastq.gz', + '12345_CGATGT_L003_R1_003.fastq.gz', ], 'pyscript': 'desplit_fastq.pyc', - 'target': u'12345_C02F9ACXX_c202_l3_r1.fastq'}, - {'sources': [u'12345_CGATGT_L003_R2_001.fastq.gz', - u'12345_CGATGT_L003_R2_002.fastq.gz', - u'12345_CGATGT_L003_R2_003.fastq.gz', + 'target': '12345_C02F9ACXX_c202_l3_r1.fastq'}, + {'sources': ['12345_CGATGT_L003_R2_001.fastq.gz', + '12345_CGATGT_L003_R2_002.fastq.gz', + '12345_CGATGT_L003_R2_003.fastq.gz', ], 'pyscript': 'desplit_fastq.pyc', - 'target': u'12345_C02F9ACXX_c202_l3_r2.fastq'} + 'target': '12345_C02F9ACXX_c202_l3_r2.fastq'} ] )) for arg in split: @@ -691,11 +691,11 @@ def tearDownModule(): def suite(): - from unittest2 import TestSuite, defaultTestLoader + from unittest import TestSuite, defaultTestLoader suite = TestSuite() suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestCondorFastq)) return suite if __name__ == "__main__": - from unittest2 import main + from unittest import main main(defaultTest='suite')