Lines Matching refs:alignment
230 alignment = alignments[0]
231 self.assertAlmostEqual(alignment.score, 3.0)
233 str(alignment),
240 self.assertEqual(alignment.shape, (2, 5))
241 self.assertEqual(alignment.aligned, (((0, 2), (4, 5)), ((0, 2), (2, 3))))
242 alignment = alignments[1]
243 self.assertAlmostEqual(alignment.score, 3.0)
245 str(alignment),
252 self.assertEqual(alignment.shape, (2, 5))
254 alignment.aligned, (((0, 1), (2, 3), (4, 5)), ((0, 1), (1, 2), (2, 3)))
258 alignment = alignments[0]
259 self.assertAlmostEqual(alignment.score, 3.0)
261 str(alignment),
268 self.assertEqual(alignment.shape, (2, 5))
269 self.assertEqual(alignment.aligned, (((0, 2), (4, 5)), ((3, 1), (1, 0))))
270 alignment = alignments[1]
271 self.assertAlmostEqual(alignment.score, 3.0)
273 str(alignment),
280 self.assertEqual(alignment.shape, (2, 5))
282 alignment.aligned, (((0, 1), (2, 3), (4, 5)), ((3, 2), (2, 1), (1, 0)))
355 alignment = alignments[0]
356 self.assertAlmostEqual(alignment.score, 1.9)
358 str(alignment),
365 self.assertEqual(alignment.shape, (2, 3))
366 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((1, 2), (2, 3))))
400 alignment = alignments[0]
401 self.assertAlmostEqual(alignment.score, 1.9)
403 str(alignment),
410 self.assertEqual(alignment.shape, (2, 3))
411 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((1, 2), (2, 3))))
429 alignment = alignments[0]
430 self.assertAlmostEqual(alignment.score, 3.0)
432 str(alignment),
439 self.assertEqual(alignment.shape, (2, 4))
440 self.assertEqual(alignment.aligned, (((0, 4),), ((0, 4),)))
443 alignment = alignments[0]
444 self.assertAlmostEqual(alignment.score, 3.0)
446 str(alignment),
453 self.assertEqual(alignment.shape, (2, 4))
454 self.assertEqual(alignment.aligned, (((0, 4),), ((4, 0),)))
463 alignment = alignments[0]
464 self.assertAlmostEqual(alignment.score, 3.0)
466 str(alignment),
473 self.assertEqual(alignment.shape, (2, 4))
474 self.assertEqual(alignment.aligned, (((0, 4),), ((0, 4),)))
477 alignment = alignments[0]
478 self.assertAlmostEqual(alignment.score, 3.0)
480 str(alignment),
487 self.assertEqual(alignment.shape, (2, 4))
488 self.assertEqual(alignment.aligned, (((0, 4),), ((4, 0),)))
496 alignment = alignments[0]
497 self.assertAlmostEqual(alignment.score, 2.0)
499 str(alignment),
506 self.assertEqual(alignment.shape, (2, 4))
507 self.assertEqual(alignment.aligned, (((0, 4),), ((0, 4),)))
510 alignment = alignments[0]
511 self.assertAlmostEqual(alignment.score, 2.0)
513 str(alignment),
520 self.assertEqual(alignment.shape, (2, 4))
521 self.assertEqual(alignment.aligned, (((0, 4),), ((4, 0),)))
535 alignment = alignments[0]
536 self.assertAlmostEqual(alignment.score, 4.0)
538 str(alignment),
545 self.assertEqual(alignment.shape, (2, 6))
547 alignment.aligned, (((0, 2), (3, 4), (4, 5)), ((0, 2), (2, 3), (4, 5)))
551 alignment = alignments[0]
552 self.assertAlmostEqual(alignment.score, 4.0)
554 str(alignment),
561 self.assertEqual(alignment.shape, (2, 6))
563 alignment.aligned, (((0, 2), (3, 4), (4, 5)), ((5, 3), (3, 2), (1, 0)))
574 alignment = alignments[0]
575 self.assertAlmostEqual(alignment.score, 4.0)
577 str(alignment),
584 self.assertEqual(alignment.shape, (2, 6))
586 alignment.aligned, (((0, 2), (3, 4), (4, 5)), ((0, 2), (2, 3), (4, 5)))
590 alignment = alignments[0]
591 self.assertAlmostEqual(alignment.score, 4.0)
593 str(alignment),
600 self.assertEqual(alignment.shape, (2, 6))
602 alignment.aligned, (((0, 2), (3, 4), (4, 5)), ((5, 3), (3, 2), (1, 0)))
645 alignment = alignments[0]
646 self.assertAlmostEqual(alignment.score, 1.9)
648 str(alignment),
655 self.assertEqual(alignment.shape, (2, 2))
656 self.assertEqual(alignment.aligned, (((1, 2),), ((0, 1),)))
657 alignment = alignments[1]
658 self.assertAlmostEqual(alignment.score, 1.9)
660 str(alignment),
667 self.assertEqual(alignment.shape, (2, 2))
668 self.assertEqual(alignment.aligned, (((0, 1),), ((0, 1),)))
671 alignment = alignments[0]
672 self.assertAlmostEqual(alignment.score, 1.9)
674 str(alignment),
681 self.assertEqual(alignment.shape, (2, 2))
682 self.assertEqual(alignment.aligned, (((1, 2),), ((1, 0),)))
683 alignment = alignments[1]
684 self.assertAlmostEqual(alignment.score, 1.9)
686 str(alignment),
693 self.assertEqual(alignment.shape, (2, 2))
694 self.assertEqual(alignment.aligned, (((0, 1),), ((1, 0),)))
734 alignment = alignments[0]
735 self.assertAlmostEqual(alignment.score, 2.9)
737 str(alignment),
744 self.assertEqual(alignment.shape, (2, 3))
745 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((0, 1), (1, 2))))
746 alignment = alignments[1]
747 self.assertAlmostEqual(alignment.score, 2.9)
749 str(alignment),
756 self.assertEqual(alignment.shape, (2, 3))
757 self.assertEqual(alignment.aligned, (((0, 2),), ((0, 2),)))
760 alignment = alignments[0]
761 self.assertAlmostEqual(alignment.score, 2.9)
763 str(alignment),
770 self.assertEqual(alignment.shape, (2, 3))
771 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((2, 1), (1, 0))))
772 alignment = alignments[1]
773 self.assertAlmostEqual(alignment.score, 2.9)
775 str(alignment),
782 self.assertEqual(alignment.shape, (2, 3))
783 self.assertEqual(alignment.aligned, (((0, 2),), ((2, 0),)))
821 alignment = alignments[0]
822 self.assertAlmostEqual(alignment.score, 2.9)
824 str(alignment),
831 self.assertEqual(alignment.shape, (2, 5))
832 self.assertEqual(alignment.aligned, (((0, 2), (4, 5)), ((0, 2), (2, 3))))
835 alignment = alignments[0]
836 self.assertAlmostEqual(alignment.score, 2.9)
838 str(alignment),
845 self.assertEqual(alignment.shape, (2, 5))
846 self.assertEqual(alignment.aligned, (((0, 2), (4, 5)), ((3, 1), (1, 0))))
885 alignment = alignments[0]
886 self.assertAlmostEqual(alignment.score, 1.7)
888 str(alignment),
895 self.assertEqual(alignment.shape, (2, 5))
896 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((0, 1), (2, 3))))
897 alignment = alignments[1]
898 self.assertAlmostEqual(alignment.score, 1.7)
900 str(alignment),
907 self.assertEqual(alignment.shape, (2, 5))
908 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((0, 1), (2, 3))))
911 alignment = alignments[0]
912 self.assertAlmostEqual(alignment.score, 1.7)
914 str(alignment),
921 self.assertEqual(alignment.shape, (2, 5))
922 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((4, 3), (2, 1))))
923 alignment = alignments[1]
924 self.assertAlmostEqual(alignment.score, 1.7)
926 str(alignment),
933 self.assertEqual(alignment.shape, (2, 5))
934 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((4, 3), (2, 1))))
974 alignment = alignments[0]
975 self.assertAlmostEqual(alignment.score, 1.3)
977 str(alignment),
984 self.assertEqual(alignment.shape, (2, 4))
985 self.assertEqual(alignment.aligned, (((0, 1), (3, 4)), ((0, 1), (1, 2))))
988 alignment = alignments[0]
989 self.assertAlmostEqual(alignment.score, 1.3)
991 str(alignment),
998 self.assertEqual(alignment.shape, (2, 4))
999 self.assertEqual(alignment.aligned, (((0, 1), (3, 4)), ((2, 1), (1, 0))))
1037 alignment = alignments[0]
1038 self.assertAlmostEqual(alignment.score, 0.6)
1040 str(alignment),
1047 self.assertEqual(alignment.shape, (2, 4))
1048 self.assertEqual(alignment.aligned, (((1, 2), (3, 4)), ((0, 1), (1, 2))))
1049 alignment = alignments[1]
1050 self.assertAlmostEqual(alignment.score, 0.6)
1052 str(alignment),
1059 self.assertEqual(alignment.shape, (2, 4))
1060 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((0, 1), (1, 2))))
1063 alignment = alignments[0]
1064 self.assertAlmostEqual(alignment.score, 0.6)
1066 str(alignment),
1073 self.assertEqual(alignment.shape, (2, 4))
1074 self.assertEqual(alignment.aligned, (((1, 2), (3, 4)), ((2, 1), (1, 0))))
1075 alignment = alignments[1]
1076 self.assertAlmostEqual(alignment.score, 0.6)
1078 str(alignment),
1085 self.assertEqual(alignment.shape, (2, 4))
1086 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((2, 1), (1, 0))))
1126 alignment = alignments[0]
1127 self.assertAlmostEqual(alignment.score, -1.2)
1129 str(alignment),
1136 self.assertEqual(alignment.shape, (2, 4))
1137 self.assertEqual(alignment.aligned, (((0, 1), (3, 4)), ((0, 1), (1, 2))))
1140 alignment = alignments[0]
1141 self.assertAlmostEqual(alignment.score, -1.2)
1143 str(alignment),
1150 self.assertEqual(alignment.shape, (2, 4))
1151 self.assertEqual(alignment.aligned, (((0, 1), (3, 4)), ((2, 1), (1, 0))))
1194 alignment = alignments[0]
1195 self.assertAlmostEqual(alignment.score, 1.0)
1197 str(alignment),
1204 self.assertEqual(alignment.shape, (2, 4))
1205 self.assertEqual(alignment.aligned, (((2, 4),), ((0, 2),)))
1206 alignment = alignments[1]
1207 self.assertAlmostEqual(alignment.score, 1.0)
1209 str(alignment),
1216 self.assertEqual(alignment.shape, (2, 4))
1217 self.assertEqual(alignment.aligned, (((0, 1), (3, 4)), ((0, 1), (1, 2))))
1218 alignment = alignments[2]
1219 self.assertAlmostEqual(alignment.score, 1.0)
1221 str(alignment),
1228 self.assertEqual(alignment.shape, (2, 4))
1229 self.assertEqual(alignment.aligned, (((0, 2),), ((0, 2),)))
1232 alignment = alignments[0]
1233 self.assertAlmostEqual(alignment.score, 1.0)
1235 str(alignment),
1242 self.assertEqual(alignment.shape, (2, 4))
1243 self.assertEqual(alignment.aligned, (((2, 4),), ((2, 0),)))
1244 alignment = alignments[1]
1245 self.assertAlmostEqual(alignment.score, 1.0)
1247 str(alignment),
1254 self.assertEqual(alignment.shape, (2, 4))
1255 self.assertEqual(alignment.aligned, (((0, 1), (3, 4)), ((2, 1), (1, 0))))
1256 alignment = alignments[2]
1257 self.assertAlmostEqual(alignment.score, 1.0)
1259 str(alignment),
1266 self.assertEqual(alignment.shape, (2, 4))
1267 self.assertEqual(alignment.aligned, (((0, 2),), ((2, 0),)))
1315 alignment = alignments[0]
1316 self.assertAlmostEqual(alignment.score, 1.7)
1318 str(alignment),
1325 self.assertEqual(alignment.shape, (2, 4))
1326 self.assertEqual(alignment.aligned, (((0, 1), (1, 3)), ((0, 1), (2, 4))))
1327 alignment = alignments[1]
1328 self.assertAlmostEqual(alignment.score, 1.7)
1330 str(alignment),
1337 self.assertEqual(alignment.shape, (2, 4))
1338 self.assertEqual(alignment.aligned, (((0, 2), (2, 3)), ((0, 2), (3, 4))))
1341 alignment = alignments[0]
1342 self.assertAlmostEqual(alignment.score, 1.7)
1344 str(alignment),
1351 self.assertEqual(alignment.shape, (2, 4))
1352 self.assertEqual(alignment.aligned, (((0, 1), (1, 3)), ((4, 3), (2, 0))))
1353 alignment = alignments[1]
1354 self.assertAlmostEqual(alignment.score, 1.7)
1356 str(alignment),
1363 self.assertEqual(alignment.shape, (2, 4))
1364 self.assertEqual(alignment.aligned, (((0, 2), (2, 3)), ((4, 2), (1, 0))))
1404 alignment = alignments[0]
1405 self.assertAlmostEqual(alignment.score, 1.8)
1407 str(alignment),
1414 self.assertEqual(alignment.shape, (2, 3))
1415 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((0, 1), (1, 2))))
1418 alignment = alignments[0]
1419 self.assertAlmostEqual(alignment.score, 1.8)
1421 str(alignment),
1428 self.assertEqual(alignment.shape, (2, 3))
1429 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((4, 3), (3, 2))))
1475 alignment = alignments[0]
1476 self.assertAlmostEqual(alignment.score, 1.9)
1478 str(alignment),
1485 self.assertEqual(alignment.shape, (2, 5))
1486 self.assertEqual(alignment.aligned, (((0, 1), (1, 4)), ((0, 1), (2, 5))))
1487 alignment = alignments[1]
1488 self.assertAlmostEqual(alignment.score, 1.9)
1490 str(alignment),
1497 self.assertEqual(alignment.shape, (2, 5))
1498 self.assertEqual(alignment.aligned, (((0, 2), (2, 4)), ((0, 2), (3, 5))))
1499 alignment = alignments[2]
1500 self.assertAlmostEqual(alignment.score, 1.9)
1502 str(alignment),
1509 self.assertEqual(alignment.shape, (2, 5))
1510 self.assertEqual(alignment.aligned, (((0, 3), (3, 4)), ((0, 3), (4, 5))))
1513 alignment = alignments[0]
1514 self.assertAlmostEqual(alignment.score, 1.9)
1516 str(alignment),
1523 self.assertEqual(alignment.shape, (2, 5))
1524 self.assertEqual(alignment.aligned, (((0, 1), (1, 4)), ((5, 4), (3, 0))))
1525 alignment = alignments[1]
1526 self.assertAlmostEqual(alignment.score, 1.9)
1528 str(alignment),
1535 self.assertEqual(alignment.shape, (2, 5))
1536 self.assertEqual(alignment.aligned, (((0, 2), (2, 4)), ((5, 3), (2, 0))))
1537 alignment = alignments[2]
1538 self.assertAlmostEqual(alignment.score, 1.9)
1540 str(alignment),
1547 self.assertEqual(alignment.shape, (2, 5))
1548 self.assertEqual(alignment.aligned, (((0, 3), (3, 4)), ((5, 2), (1, 0))))
1597 alignment = alignments[0]
1598 self.assertAlmostEqual(alignment.score, 3.0)
1600 str(alignment),
1607 self.assertEqual(alignment.shape, (2, 3))
1608 self.assertEqual(alignment.aligned, (((0, 3),), ((0, 3),)))
1609 alignment = alignments[1]
1610 self.assertAlmostEqual(alignment.score, 3.0)
1612 str(alignment),
1619 self.assertEqual(alignment.shape, (2, 4))
1620 self.assertEqual(alignment.aligned, (((0, 2), (3, 4)), ((0, 2), (2, 3))))
1623 alignment = alignments[0]
1624 self.assertAlmostEqual(alignment.score, 3.0)
1626 str(alignment),
1633 self.assertEqual(alignment.shape, (2, 3))
1634 self.assertEqual(alignment.aligned, (((0, 3),), ((3, 0),)))
1635 alignment = alignments[1]
1636 self.assertAlmostEqual(alignment.score, 3.0)
1638 str(alignment),
1645 self.assertEqual(alignment.shape, (2, 4))
1646 self.assertEqual(alignment.aligned, (((0, 2), (3, 4)), ((3, 1), (1, 0))))
1689 alignment = alignments[0]
1690 self.assertAlmostEqual(alignment.score, 3.0)
1692 str(alignment),
1699 self.assertEqual(alignment.shape, (2, 3))
1700 self.assertEqual(alignment.aligned, (((0, 3),), ((0, 3),)))
1703 alignment = alignments[0]
1704 self.assertAlmostEqual(alignment.score, 3.0)
1706 str(alignment),
1713 self.assertEqual(alignment.shape, (2, 3))
1714 self.assertEqual(alignment.aligned, (((0, 3),), ((3, 0),)))
1757 alignment = alignments[0]
1758 self.assertAlmostEqual(alignment.score, 3.0)
1760 str(alignment),
1767 self.assertEqual(alignment.shape, (2, 3))
1768 self.assertEqual(alignment.aligned, (((0, 3),), ((0, 3),)))
1771 alignment = alignments[0]
1772 self.assertAlmostEqual(alignment.score, 3.0)
1774 str(alignment),
1781 self.assertEqual(alignment.shape, (2, 3))
1782 self.assertEqual(alignment.aligned, (((0, 3),), ((4, 1),)))
1828 alignment = alignments[0]
1829 self.assertAlmostEqual(alignment.score, 3.0)
1831 str(alignment),
1838 self.assertEqual(alignment.shape, (2, 3))
1839 self.assertEqual(alignment.aligned, (((0, 3),), ((0, 3),)))
1840 alignment = alignments[1]
1841 self.assertAlmostEqual(alignment.score, 3.0)
1843 str(alignment),
1850 self.assertEqual(alignment.shape, (2, 4))
1851 self.assertEqual(alignment.aligned, (((0, 2), (3, 4)), ((0, 2), (2, 3))))
1854 alignment = alignments[0]
1855 self.assertAlmostEqual(alignment.score, 3.0)
1857 str(alignment),
1864 self.assertEqual(alignment.shape, (2, 3))
1865 self.assertEqual(alignment.aligned, (((0, 3),), ((3, 0),)))
1866 alignment = alignments[1]
1867 self.assertAlmostEqual(alignment.score, 3.0)
1869 str(alignment),
1876 self.assertEqual(alignment.shape, (2, 4))
1877 self.assertEqual(alignment.aligned, (((0, 2), (3, 4)), ((3, 1), (1, 0))))
1922 alignment = alignments[0]
1923 self.assertAlmostEqual(alignment.score, 3.0)
1925 str(alignment),
1932 self.assertEqual(alignment.shape, (2, 3))
1933 self.assertEqual(alignment.aligned, (((0, 3),), ((0, 3),)))
1936 alignment = alignments[0]
1937 self.assertAlmostEqual(alignment.score, 3.0)
1939 str(alignment),
1946 self.assertEqual(alignment.shape, (2, 3))
1947 self.assertEqual(alignment.aligned, (((0, 3),), ((3, 0),)))
1992 alignment = alignments[0]
1993 self.assertAlmostEqual(alignment.score, 3.0)
1995 str(alignment),
2002 self.assertEqual(alignment.shape, (2, 3))
2003 self.assertEqual(alignment.aligned, (((0, 3),), ((0, 3),)))
2006 alignment = alignments[0]
2007 self.assertAlmostEqual(alignment.score, 3.0)
2009 str(alignment),
2016 self.assertEqual(alignment.shape, (2, 3))
2017 self.assertEqual(alignment.aligned, (((0, 3),), ((4, 1),)))
2053 alignment = alignments[0]
2054 self.assertAlmostEqual(alignment.score, 1)
2056 str(alignment),
2063 self.assertEqual(alignment.shape, (2, 1))
2064 self.assertEqual(alignment.aligned, (((2, 3),), ((0, 1),)))
2098 alignment = alignments[0]
2099 self.assertAlmostEqual(alignment.score, 1)
2101 str(alignment),
2108 self.assertEqual(alignment.shape, (2, 1))
2109 self.assertEqual(alignment.aligned, (((2, 3),), ((0, 1),)))
2110 alignment = alignments[1]
2111 self.assertAlmostEqual(alignment.score, 1)
2113 str(alignment),
2120 self.assertEqual(alignment.shape, (2, 1))
2121 self.assertEqual(alignment.aligned, (((3, 4),), ((0, 1),)))
2157 alignment = alignments[0]
2158 self.assertAlmostEqual(alignment.score, 0.2)
2160 str(alignment),
2167 self.assertEqual(alignment.shape, (2, 5))
2168 self.assertEqual(alignment.aligned, (((2, 3),), ((0, 1),)))
2253 alignment = alignments[0]
2254 self.assertAlmostEqual(alignment.score, 2)
2256 str(alignment),
2263 self.assertEqual(alignment.shape, (2, 36))
2264 self.assertEqual(alignment.aligned, (((2, 13), (23, 34)), ((0, 11), (11, 22))))
2267 alignment = alignments[0]
2268 self.assertAlmostEqual(alignment.score, 2)
2270 str(alignment),
2277 self.assertEqual(alignment.shape, (2, 36))
2278 self.assertEqual(alignment.aligned, (((2, 13), (23, 34)), ((22, 11), (11, 0))))
2329 alignment = alignments[0]
2330 self.assertAlmostEqual(alignment.score, -10)
2332 str(alignment),
2339 self.assertEqual(alignment.shape, (2, 36))
2340 self.assertEqual(alignment.aligned, (((2, 5), (15, 34)), ((0, 3), (3, 22))))
2341 alignment = alignments[1]
2342 self.assertAlmostEqual(alignment.score, -10)
2344 str(alignment),
2351 self.assertEqual(alignment.shape, (2, 36))
2352 self.assertEqual(alignment.aligned, (((0, 3), (15, 34)), ((0, 3), (3, 22))))
2355 alignment = alignments[0]
2356 self.assertAlmostEqual(alignment.score, -10)
2358 str(alignment),
2365 self.assertEqual(alignment.shape, (2, 36))
2366 self.assertEqual(alignment.aligned, (((2, 21), (33, 36)), ((22, 3), (3, 0))))
2367 alignment = alignments[1]
2368 self.assertAlmostEqual(alignment.score, -10)
2370 str(alignment),
2377 self.assertEqual(alignment.shape, (2, 36))
2378 self.assertEqual(alignment.aligned, (((2, 21), (31, 34)), ((22, 3), (3, 0))))
2424 alignment = alignments[0]
2425 self.assertAlmostEqual(alignment.score, 2.0)
2427 str(alignment),
2434 self.assertEqual(alignment.shape, (2, 8))
2435 self.assertEqual(alignment.aligned, (((0, 2), (4, 6)), ((0, 2), (4, 6))))
2438 alignment = alignments[0]
2439 self.assertAlmostEqual(alignment.score, 2.0)
2441 str(alignment),
2448 self.assertEqual(alignment.shape, (2, 8))
2449 self.assertEqual(alignment.aligned, (((0, 2), (4, 6)), ((6, 4), (2, 0))))
2470 alignment = alignments[0]
2471 self.assertAlmostEqual(alignment.score, -8.0)
2473 str(alignment),
2480 self.assertEqual(alignment.shape, (2, 7))
2482 alignment.aligned, (((0, 2), (2, 3), (4, 6)), ((0, 2), (3, 4), (4, 6)))
2484 alignment = alignments[1]
2485 self.assertAlmostEqual(alignment.score, -8.0)
2487 str(alignment),
2494 self.assertEqual(alignment.shape, (2, 8))
2495 self.assertEqual(alignment.aligned, (((0, 2), (4, 6)), ((0, 2), (4, 6))))
2496 alignment = alignments[2]
2497 self.assertAlmostEqual(alignment.score, -8.0)
2499 str(alignment),
2506 self.assertEqual(alignment.shape, (2, 7))
2508 alignment.aligned, (((0, 2), (3, 4), (4, 6)), ((0, 2), (2, 3), (4, 6)))
2510 alignment = alignments[3]
2511 self.assertAlmostEqual(alignment.score, -8.0)
2513 str(alignment),
2520 self.assertEqual(alignment.shape, (2, 8))
2521 self.assertEqual(alignment.aligned, (((0, 2), (4, 6)), ((0, 2), (4, 6))))
2524 alignment = alignments[0]
2525 self.assertAlmostEqual(alignment.score, -8.0)
2527 str(alignment),
2534 self.assertEqual(alignment.shape, (2, 7))
2536 alignment.aligned, (((0, 2), (2, 3), (4, 6)), ((6, 4), (3, 2), (2, 0)))
2538 alignment = alignments[1]
2539 self.assertAlmostEqual(alignment.score, -8.0)
2541 str(alignment),
2548 self.assertEqual(alignment.shape, (2, 8))
2549 self.assertEqual(alignment.aligned, (((0, 2), (4, 6)), ((6, 4), (2, 0))))
2550 alignment = alignments[2]
2551 self.assertAlmostEqual(alignment.score, -8.0)
2553 str(alignment),
2560 self.assertEqual(alignment.shape, (2, 7))
2562 alignment.aligned, (((0, 2), (3, 4), (4, 6)), ((6, 4), (4, 3), (2, 0)))
2564 alignment = alignments[3]
2565 self.assertAlmostEqual(alignment.score, -8.0)
2567 str(alignment),
2574 self.assertEqual(alignment.shape, (2, 8))
2575 self.assertEqual(alignment.aligned, (((0, 2), (4, 6)), ((6, 4), (2, 0))))
2621 alignment = alignments[0]
2622 self.assertAlmostEqual(alignment.score, 13)
2624 str(alignment),
2631 self.assertEqual(alignment.shape, (2, 13))
2632 self.assertEqual(alignment.aligned, (((2, 15),), ((0, 13),)))
2633 alignment = alignments[1]
2634 self.assertAlmostEqual(alignment.score, 13)
2636 str(alignment),
2643 self.assertEqual(alignment.shape, (2, 13))
2644 self.assertEqual(alignment.aligned, (((21, 34),), ((9, 22),)))
2647 alignment = alignments[0]
2648 self.assertAlmostEqual(alignment.score, 13)
2650 str(alignment),
2657 self.assertEqual(alignment.shape, (2, 13))
2658 self.assertEqual(alignment.aligned, (((2, 15),), ((22, 9),)))
2659 alignment = alignments[1]
2660 self.assertAlmostEqual(alignment.score, 13)
2662 str(alignment),
2669 self.assertEqual(alignment.shape, (2, 13))
2670 self.assertEqual(alignment.aligned, (((21, 34),), ((13, 0),)))
2721 alignment = alignments[0]
2722 self.assertAlmostEqual(alignment.score, 13)
2724 str(alignment),
2731 self.assertEqual(alignment.shape, (2, 13))
2732 self.assertEqual(alignment.aligned, (((2, 15),), ((0, 13),)))
2733 alignment = alignments[1]
2734 self.assertAlmostEqual(alignment.score, 13)
2736 str(alignment),
2743 self.assertEqual(alignment.shape, (2, 13))
2744 self.assertEqual(alignment.aligned, (((21, 34),), ((9, 22),)))
2747 alignment = alignments[0]
2748 self.assertAlmostEqual(alignment.score, 13)
2750 str(alignment),
2757 self.assertEqual(alignment.shape, (2, 13))
2758 self.assertEqual(alignment.aligned, (((2, 15),), ((22, 9),)))
2759 alignment = alignments[1]
2760 self.assertAlmostEqual(alignment.score, 13)
2762 str(alignment),
2769 self.assertEqual(alignment.shape, (2, 13))
2770 self.assertEqual(alignment.aligned, (((21, 34),), ((13, 0),)))
2816 alignment = alignments[0]
2817 self.assertAlmostEqual(alignment.score, 2.0)
2819 str(alignment),
2826 self.assertEqual(alignment.shape, (2, 2))
2827 self.assertEqual(alignment.aligned, (((0, 2),), ((0, 2),)))
2828 alignment = alignments[1]
2829 self.assertAlmostEqual(alignment.score, 2.0)
2831 str(alignment),
2838 self.assertEqual(alignment.shape, (2, 2))
2839 self.assertEqual(alignment.aligned, (((4, 6),), ((4, 6),)))
2842 alignment = alignments[0]
2843 self.assertAlmostEqual(alignment.score, 2.0)
2845 str(alignment),
2852 self.assertEqual(alignment.shape, (2, 2))
2853 self.assertEqual(alignment.aligned, (((0, 2),), ((6, 4),)))
2854 alignment = alignments[1]
2855 self.assertAlmostEqual(alignment.score, 2.0)
2857 str(alignment),
2864 self.assertEqual(alignment.shape, (2, 2))
2865 self.assertEqual(alignment.aligned, (((4, 6),), ((2, 0),)))
2886 alignment = alignments[0]
2887 self.assertAlmostEqual(alignment.score, 2.0)
2889 str(alignment),
2896 self.assertEqual(alignment.shape, (2, 2))
2897 self.assertEqual(alignment.aligned, (((0, 2),), ((0, 2),)))
2898 alignment = alignments[1]
2899 self.assertAlmostEqual(alignment.score, 2.0)
2901 str(alignment),
2908 self.assertEqual(alignment.shape, (2, 2))
2909 self.assertEqual(alignment.aligned, (((4, 6),), ((4, 6),)))
2912 alignment = alignments[0]
2913 self.assertAlmostEqual(alignment.score, 2.0)
2915 str(alignment),
2922 self.assertEqual(alignment.shape, (2, 2))
2923 self.assertEqual(alignment.aligned, (((0, 2),), ((6, 4),)))
2924 alignment = alignments[1]
2925 self.assertAlmostEqual(alignment.score, 2.0)
2927 str(alignment),
2934 self.assertEqual(alignment.shape, (2, 2))
2935 self.assertEqual(alignment.aligned, (((4, 6),), ((2, 0),)))
3212 alignment = alignments[0]
3214 str(alignment),
3221 self.assertEqual(alignment.shape, (2, 1811))
3222 self.assertAlmostEqual(alignment.score, 1286.0)
3232 alignment = alignments[0]
3234 str(alignment),
3241 self.assertAlmostEqual(alignment.score, 1286.0)
3242 self.assertEqual(alignment.shape, (2, 1811))
3289 alignment = alignments[0]
3290 self.assertAlmostEqual(alignment.score, 3.0)
3292 str(alignment),
3299 self.assertEqual(alignment.shape, (2, 5))
3300 self.assertEqual(alignment.aligned, (((0, 2), (4, 5)), ((0, 2), (2, 3))))
3301 alignment = alignments[1]
3302 self.assertAlmostEqual(alignment.score, 3.0)
3304 str(alignment),
3311 self.assertEqual(alignment.shape, (2, 5))
3313 alignment.aligned, (((0, 1), (2, 3), (4, 5)), ((0, 1), (1, 2), (2, 3)))
3338 alignment = alignments[0]
3339 self.assertAlmostEqual(alignment.score, 1.9)
3341 str(alignment),
3348 self.assertEqual(alignment.shape, (2, 3))
3349 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((1, 2), (2, 3))))
3362 alignment = alignments[0]
3363 self.assertAlmostEqual(alignment.score, 1.9)
3365 str(alignment),
3372 self.assertEqual(alignment.shape, (2, 3))
3373 self.assertEqual(alignment.aligned, (((0, 1), (2, 3)), ((1, 2), (2, 3))))
3551 alignment = alignments[0]
3552 self.assertAlmostEqual(alignment.score, 19.0)
3554 str(alignment),
3561 self.assertEqual(alignment.shape, (2, 80))
3563 alignment.format("psl"),
3569 alignment.format("bed"),
3575 alignment.format("sam"),
3584 alignment = alignments[0]
3585 self.assertAlmostEqual(alignment.score, 19.0)
3587 str(alignment),
3594 self.assertEqual(alignment.shape, (2, 80))
3596 alignment.format("psl"),
3602 alignment.format("bed"),
3608 alignment.format("sam"),
3622 alignment = alignments[0]
3624 str(alignment),
3631 self.assertEqual(alignment.shape, (2, 17))
3633 alignment.format("psl"),
3639 alignment.format("bed"),
3645 alignment.format("sam"),
3655 alignment = alignments[0]
3657 str(alignment),
3664 self.assertEqual(alignment.shape, (2, 17))
3666 alignment.format("psl"),
3672 alignment.format("bed"),
3678 alignment.format("sam"),
3685 alignment = alignments[0]
3686 self.assertAlmostEqual(alignment.score, 13.0)
3688 str(alignment),
3695 self.assertEqual(alignment.shape, (2, 17))
3697 alignment.format("psl"),
3703 alignment.format("bed"),
3709 alignment.format("sam"),
3718 alignment = alignments[0]
3719 self.assertAlmostEqual(alignment.score, 13.0)
3721 str(alignment),
3728 self.assertEqual(alignment.shape, (2, 17))
3730 alignment.format("psl"),
3736 alignment.format("bed"),
3742 alignment.format("sam"),
3749 alignment = alignments[0]
3751 str(alignment),
3758 self.assertEqual(alignment.shape, (2, 17))
3760 alignment.format("psl"),
3766 alignment.format("bed"),
3772 alignment.format("sam"),
3781 alignment = alignments[0]
3783 str(alignment),
3790 self.assertEqual(alignment.shape, (2, 17))
3792 alignment.format("psl"),
3798 alignment.format("bed"),
3804 alignment.format("sam"),
3811 alignment = alignments[0]
3812 self.assertAlmostEqual(alignment.score, 13.0)
3814 str(alignment),
3821 self.assertEqual(alignment.shape, (2, 17))
3823 alignment.format("psl"),
3829 alignment.format("bed"),
3835 alignment.format("sam"),
3844 alignment = alignments[0]
3845 self.assertAlmostEqual(alignment.score, 13.0)
3847 str(alignment),
3854 self.assertEqual(alignment.shape, (2, 17))
3856 alignment.format("psl"),
3862 alignment.format("bed"),
3868 alignment.format("sam"),
3885 alignment = alignments[0]
3887 str(alignment),
3894 self.assertEqual(alignment.shape, (2, 28))
3896 alignment.format("psl"),
3902 alignment.format("bed"),
3908 alignment.format("sam"),
3915 alignment = alignments[0]
3917 str(alignment),
3924 self.assertEqual(alignment.shape, (2, 28))
3926 alignment.format("psl"),
3932 alignment.format("bed"),
3938 alignment.format("sam"),
3946 alignment = alignments[0]
3948 str(alignment),
3955 self.assertEqual(alignment.shape, (2, 28))
3957 alignment.format("psl"),
3963 alignment.format("bed"),
3969 alignment.format("sam"),
3978 alignment = alignments[0]
3980 str(alignment),
3987 self.assertEqual(alignment.shape, (2, 28))
3989 alignment.format("psl"),
3995 alignment.format("bed"),
4001 alignment.format("sam"),
4013 alignment = alignments[0]
4015 str(alignment),
4022 self.assertAlmostEqual(alignment.score, 6.0)
4023 self.assertAlmostEqual(alignment[:, :].score, 6.0)
4025 str(alignment[:, :]),
4032 self.assertAlmostEqual(alignment[:, 0:].score, 6.0)
4034 str(alignment[:, 0:]),
4041 self.assertAlmostEqual(alignment[:, :12].score, 6.0)
4043 str(alignment[:, :12]),
4050 self.assertAlmostEqual(alignment[:, 0:12].score, 6.0)
4052 str(alignment[:, 0:12]),
4059 self.assertIsNone(alignment[:, 1:].score)
4061 str(alignment[:, 1:]),
4068 self.assertIsNone(alignment[:, 2:].score)
4070 str(alignment[:, 2:]),
4077 self.assertIsNone(alignment[:, 3:].score)
4079 str(alignment[:, 3:]),
4086 self.assertIsNone(alignment[:, 4:].score)
4088 str(alignment[:, 4:]),
4095 self.assertIsNone(alignment[:, :-1].score)
4097 str(alignment[:, :-1]),
4104 self.assertIsNone(alignment[:, :-2].score)
4106 str(alignment[:, :-2]),
4113 self.assertIsNone(alignment[:, :-3].score)
4115 str(alignment[:, :-3]),
4122 self.assertIsNone(alignment[:, 1:-1].score)
4124 str(alignment[:, 1:-1]),
4131 self.assertIsNone(alignment[:, 1:-2].score)
4133 str(alignment[:, 1:-2]),
4140 self.assertIsNone(alignment[:, 2:-1].score)
4142 str(alignment[:, 2:-1]),
4149 self.assertIsNone(alignment[:, 2:-2].score)
4151 str(alignment[:, 2:-2]),
4159 alignment[:1]
4161 alignment[0]
4163 alignment[0, :]
4165 alignment[:1, :]
4167 alignment[:, 0]
4169 alignment[:, ::3]
4178 alignment = alignments[0]
4180 str(alignment),
4187 alignment.sort()
4189 str(alignment),
4196 alignment.sort(reverse=True)
4198 str(alignment),
4207 alignment.sort()
4209 str(alignment),
4216 alignment.sort(reverse=True)
4218 str(alignment),
4225 alignment.sort(key=GC)
4227 str(alignment),
4234 alignment.sort(key=GC, reverse=True)
4236 str(alignment),
4260 alignment = alignments[0]
4261 m = alignment.substitutions