- f = sequences.parse_fastq(path, name)
-
- self.failUnlessEqual(f.filetype, 'split_fastq')
- self.failUnlessEqual(f.path, pathname)
- self.failUnlessEqual(f.flowcell, '42BW9AAXX')
- self.failUnlessEqual(f.lane, 1)
- self.failUnlessEqual(f.read, 2)
- self.failUnlessEqual(f.pf, True)
- self.failUnlessEqual(f.project, '11112')
- self.failUnlessEqual(f.index, 'AAATTT')
- self.failUnlessEqual(f.cycle, 38)
+ f0 = sequences.parse_fastq(path, name)
+ f1 = sequences.parse_fastq(path, name)
+ fother = sequences.parse_fastq(path, other)
+
+ self.assertEqual(f0.filetype, 'split_fastq')
+ self.assertEqual(f0.path, pathname)
+ 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.read, 2)
+ self.assertEqual(f0.pf, True)
+ self.assertEqual(f0.project, '11112')
+ self.assertEqual(f0.index, 'AAATTT')
+ self.assertEqual(f0.cycle, 38)
+ self.assertEqual(f0.make_target_name('/tmp'),
+ os.path.join('/tmp', name))
+
+ self.assertEqual(f0, f1)
+ self.assertNotEqual(f0, fother)
+
+ def test_parse_fastq_pf_flag(self):
+ other = 'woldlab_090622_HWI-EAS229_0120_42BW9AAXX_l1_r2_nopass.fastq.bz2'
+ data = ['woldlab', '090622', 'HWI-EAS229', '0120', '42BW9AAXX',
+ 'l1', 'r2', 'nopass']
+ self.assertEqual(sequences.parse_fastq_pf_flag(data), False)
+
+ data = ['woldlab', '090622', 'HWI-EAS229', '0120', '42BW9AAXX',
+ 'l1', 'r2', 'pass']
+ self.assertEqual(sequences.parse_fastq_pf_flag(data), True)
+
+ data = ['woldlab', '090622', 'HWI-EAS229', '0120', '42BW9AAXX',
+ 'l1', 'r2', 'all']
+ self.assertEqual(sequences.parse_fastq_pf_flag(data), None)
+
+ data = ['woldlab', '090622', 'HWI-EAS229', '0120', '42BW9AAXX',
+ 'l1', 'r2']
+ self.assertEqual(sequences.parse_fastq_pf_flag(data), None)
+
+ data = ['woldlab', '090622', 'HWI-EAS229', '0120', '42BW9AAXX',
+ 'l1', 'r2', 'all', 'newthing']
+ self.assertRaises(ValueError, sequences.parse_fastq_pf_flag, data)
+