def test_init(self):
"""CutgParser should read records one at a time from lines"""
recs = list(CutgParser(sample_gene))
self.assertEqual(len(recs), 3)
a, b, c = recs
self.assertEqual(a.Species, 'Xenopus laevis')
self.assertEqual(a['CGC'], 7)
self.assertEqual(a.GI, ['1783183'])
self.assertRaises(RecordError, list, CutgParser(sample_gene[1:]))
self.assertEqual(len(list(CutgParser(sample_gene[1:], strict=False))),
2)
def read_cutg(lines):
"""Returns list of CUTG objects from file-like object lines.
Warning: reads whole file into memory as objects.
"""
return list(CutgParser(lines))
def file_to_codon_list(infilename):
"""converts a file from the cutg parser
to a list of codon usages
"""
return list(CutgParser(open(infilename), constructor=CodonUsage))