Lines Matching refs:sgc
21 self.sgc = GeneticCode.from_ncbi(1)
43 self.assertEqual(self.sgc.reading_frames, exp)
48 self.assertEqual(self.sgc.reading_frames, exp)
51 self.sgc.reading_frames = [1, 2, 42]
54 self.assertEqual(self.sgc.name, 'Standard')
59 self.sgc.name = 'foo'
112 self.assertEqual(str(self.sgc), exp)
136 self.assertEqual(repr(self.sgc), exp)
197 obs = self.sgc.translate(
208 obs = self.sgc.translate(seq)
212 obs = self.sgc.translate(RNA('CCU'))
217 obs = self.sgc.translate(RNA('CAUUUGCUGAAA'))
221 obs = self.sgc.translate(RNA('UUUUUUUAAAGUUAAGGGAU'))
228 obs = self.sgc.translate(seq, reading_frame=reading_frame)
233 obs = self.sgc.translate(RNA('AUG'), reading_frame=reading_frame)
241 obs = self.sgc.translate(seq, reading_frame=reading_frame)
248 obs = self.sgc.translate(seq, start=start)
253 self.sgc.translate(seq, start='require')
262 obs = self.sgc.translate(seq, start=start)
267 obs = self.sgc.translate(seq, start='ignore')
274 obs = self.sgc.translate(seq, start=start)
281 obs = self.sgc.translate(seq, start=start)
285 obs = self.sgc.translate(seq, start='ignore')
292 obs = self.sgc.translate(seq, start=start)
297 self.sgc.translate(seq, start='require')
305 obs = self.sgc.translate(seq, start=start)
310 self.sgc.translate(seq, start='require')
318 offset_table = self.sgc._offset_table.copy()
321 obs = self.sgc.translate(seq, start='require')
324 npt.assert_array_equal(self.sgc._offset_table, offset_table)
330 obs = self.sgc.translate(seq, stop=stop)
335 self.sgc.translate(seq, stop='require')
342 obs = self.sgc.translate(seq, stop=stop)
347 obs = self.sgc.translate(seq, stop='ignore')
354 obs = self.sgc.translate(seq, stop=stop)
358 obs = self.sgc.translate(seq, stop='ignore')
365 obs = self.sgc.translate(seq, stop=stop)
369 obs = self.sgc.translate(seq, stop='ignore')
376 obs = self.sgc.translate(seq, stop=stop)
381 self.sgc.translate(seq, stop='require')
391 obs = self.sgc.translate(seq, start=param, stop=param)
395 obs = self.sgc.translate(seq, start='ignore', stop='ignore')
403 self.sgc.translate(seq, reading_frame=2, start='require')
406 self.sgc.translate(seq, reading_frame=2, stop='require')
410 obs = self.sgc.translate(seq, reading_frame=2, start=param,
417 self.sgc.translate(DNA('ACG'))
419 self.sgc.translate('ACG')
423 self.sgc.translate(RNA('AUG'), reading_frame=0)
427 self.sgc.translate(RNA('AUG'), start='foo')
431 self.sgc.translate(RNA('AUG'), stop='foo')
435 self.sgc.translate(RNA('UU-G'))
439 self.sgc.translate(RNA('RUG'))
481 obs = list(self.sgc.translate_six_frames(seq))
487 obs = list(self.sgc.translate_six_frames(seq, start='optional',
494 obs = list(self.sgc.translate_six_frames(seq))[:2]