pipeline.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from src.tools import count_all_letters, get_all_frames, fasta_parser, gc, find_stop_codons, get_frame, save_fasta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "gi|142022655|gb|EQ086233.1|43\n",
      "G - 306\n",
      "C - 294\n",
      "A - 192\n",
      "T - 198\n",
      "GC% = 60.61\n",
      "Frame: f1, Stop codons found at: [132, 198, 249, 267, 576, 648, 816, 837, 879, 984]\n",
      "Frame: f2, Stop codons found at: [105, 144, 162, 189, 315, 366, 450, 453, 531, 537, 549, 600, 684, 756]\n",
      "Frame: f3, Stop codons found at: [624]\n",
      "Frame: r1, Stop codons found at: [144, 225, 747, 891]\n",
      "Frame: r2, Stop codons found at: [276, 321]\n",
      "Frame: r3, Stop codons found at: [84, 234, 288, 306, 423, 438, 726, 807, 864]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|160\n",
      "G - 245\n",
      "A - 148\n",
      "T - 137\n",
      "C - 194\n",
      "GC% = 60.64\n",
      "Frame: f1, Stop codons found at: [18, 63, 441, 456, 561]\n",
      "Frame: f2, Stop codons found at: [465, 477, 534, 546, 555, 675, 678]\n",
      "Frame: f3, Stop codons found at: [234, 489, 504, 519, 705]\n",
      "Frame: r1, Stop codons found at: [192, 366, 405, 519, 633]\n",
      "Frame: r2, Stop codons found at: [63, 75, 96, 132, 243, 603]\n",
      "Frame: r3, Stop codons found at: [294, 423, 480]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|41\n",
      "G - 1016\n",
      "A - 583\n",
      "T - 605\n",
      "C - 876\n",
      "GC% = 61.43\n",
      "Frame: f1, Stop codons found at: [861, 1152, 1170, 1194, 1218, 1245, 1362, 1506, 1557, 1596, 1728, 1758, 1776, 1929, 2076, 2301, 2361, 2406, 2463, 2622, 2670, 2706, 2817, 2886]\n",
      "Frame: f2, Stop codons found at: [900, 1038, 1146, 1158, 1266, 1617, 1965, 2766]\n",
      "Frame: f3, Stop codons found at: [12, 114, 156, 183, 207, 324, 498, 597, 624, 885, 975, 1113, 1122, 1182, 2106, 3069]\n",
      "Frame: r1, Stop codons found at: [915, 1149, 1533, 1971, 2010, 2022, 2058, 2115, 2184, 2319, 2583, 2625, 2730, 2862, 2871, 2976, 3039]\n",
      "Frame: r2, Stop codons found at: [174, 195, 462, 525, 621, 702, 732, 855, 1050, 1113, 1134, 1197, 1650, 1740, 1851, 2061, 2691]\n",
      "Frame: r3, Stop codons found at: [15, 72, 327, 429, 456, 549, 687, 798, 996, 1101, 1116, 1140, 1167, 1260, 1269, 1293, 1371, 1509, 1545, 1593, 1836, 1872, 1908, 2175, 2178, 2367, 2673, 2844, 2901, 3003, 3033]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|221\n",
      "G - 753\n",
      "C - 865\n",
      "A - 605\n",
      "T - 640\n",
      "GC% = 56.51\n",
      "Frame: f1, Stop codons found at: [72, 81, 138, 144, 150, 168, 288, 312, 381, 402, 429, 483, 729, 750, 786, 855, 1038, 1053, 1119, 1200, 1506, 1761, 1968, 2145, 2268, 2658, 2694]\n",
      "Frame: f2, Stop codons found at: [42, 177, 264, 393, 408, 450, 486, 516, 576, 633, 648, 798, 873, 924, 1329, 1455, 1521, 1662, 2361]\n",
      "Frame: f3, Stop codons found at: [9, 66, 75, 162, 222, 552, 681, 837, 912, 1104, 1122, 1290, 1317, 1404, 1494, 1572, 1671, 1677, 1914, 2082, 2187, 2235, 2379, 2706, 2754, 2799]\n",
      "Frame: r1, Stop codons found at: [378, 501, 531, 1125, 1176, 1188, 1191, 1287, 1455, 1482, 1902, 1962, 1974, 2022, 2253, 2307, 2322, 2424, 2469, 2535, 2637, 2673, 2793, 2823, 2835]\n",
      "Frame: r2, Stop codons found at: [144, 192, 246, 327, 444, 843, 870, 897, 987, 1101, 1113, 1137, 1197, 1203, 1404, 1509, 1656, 1746, 1827, 1854, 1989, 2061, 2079, 2112, 2163, 2190, 2226, 2298, 2373, 2706, 2730]\n",
      "Frame: r3, Stop codons found at: [792, 903, 1536, 1623, 1647, 1662, 1671, 1722, 1806, 2025, 2028, 2124, 2151, 2202, 2400, 2403, 2457, 2478, 2691, 2751, 2769, 2787]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|294\n",
      "G - 1260\n",
      "A - 678\n",
      "T - 574\n",
      "C - 1320\n",
      "GC% = 67.33\n",
      "Frame: f1, Stop codons found at: [138, 249, 543, 552, 861, 882, 963, 1053, 1095, 1125, 1143, 1146, 1227, 1254, 1260, 1263, 1503, 1518, 1554, 1557, 1719, 1761, 2208, 2391, 2838, 2979, 3273, 3276, 3588, 3780, 3819]\n",
      "Frame: f2, Stop codons found at: [441, 498, 687, 711, 720, 966, 1206, 1233, 1275, 1434, 1578, 1626, 1734, 2784, 3057, 3339, 3705, 3792, 3825]\n",
      "Frame: f3, Stop codons found at: [1743, 2058, 2061, 2385, 2553, 3630]\n",
      "Frame: r1, Stop codons found at: [15, 54, 471, 513, 651, 783, 810, 816, 975, 2097, 2211, 2433, 2469, 2490, 2511, 3087, 3321, 3417, 3597]\n",
      "Frame: r2, Stop codons found at: [1497, 1929, 2499, 2895, 2949, 2976]\n",
      "Frame: r3, Stop codons found at: [996, 1188, 3738, 3825]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|323\n",
      "G - 1580\n",
      "A - 734\n",
      "T - 756\n",
      "C - 1735\n",
      "GC% = 68.99\n",
      "Frame: f1, Stop codons found at: [51, 1566, 2094, 2181, 2187, 2340, 2475, 2508, 2805, 4506, 4587, 4617, 4683, 4689, 4746]\n",
      "Frame: f2, Stop codons found at: [1431, 1494, 2958, 3765, 3981, 4164, 4215, 4227, 4464, 4551]\n",
      "Frame: f3, Stop codons found at: [39, 63, 333, 546, 564, 741, 1266, 3066, 3228, 3390, 3543, 4188]\n",
      "Frame: r1, Stop codons found at: [495, 546, 669, 849, 1044, 1422, 3414, 3450, 3495, 3672, 3801, 3846, 3993, 4134, 4200, 4260, 4269, 4557, 4566]\n",
      "Frame: r2, Stop codons found at: [144, 195, 252, 600, 741, 759, 765, 804, 942, 1272, 1788, 1845, 2058, 2379, 2568, 2787, 2841, 3129, 3333, 3351, 4173]\n",
      "Frame: r3, Stop codons found at: [243, 423, 585, 744, 1215, 1311, 1359, 1380, 1392, 1803, 1824, 2178, 2319, 2331, 2373, 2451, 2865, 3048, 3075, 3087, 3093, 3177, 3183, 3342, 3825, 3960]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|564\n",
      "G - 533\n",
      "C - 543\n",
      "A - 323\n",
      "T - 264\n",
      "GC% = 64.7\n",
      "Frame: f1, Stop codons found at: [27, 186, 195, 492, 636, 1002, 1161, 1218, 1518, 1641]\n",
      "Frame: f2, Stop codons found at: [3, 93, 462, 717, 720, 729, 762, 816, 852]\n",
      "Frame: f3, Stop codons found at: [57, 243, 285, 390, 1326, 1575]\n",
      "Frame: r1, Stop codons found at: [309, 504, 633, 693, 858, 1191]\n",
      "Frame: r2, Stop codons found at: [48, 72, 348, 399, 669, 699, 837, 942, 1077, 1197, 1299, 1353, 1389, 1578]\n",
      "Frame: r3, Stop codons found at: [657, 777, 1104, 1209, 1332, 1368, 1377, 1464, 1551, 1632]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|521\n",
      "G - 161\n",
      "C - 178\n",
      "A - 70\n",
      "T - 103\n",
      "GC% = 66.21\n",
      "Frame: f1, Stop codons found at: [36, 45, 264]\n",
      "Frame: f2, Stop codons found at: []\n",
      "Frame: f3, Stop codons found at: [21, 75, 87, 279, 441, 468]\n",
      "Frame: r1, Stop codons found at: []\n",
      "Frame: r2, Stop codons found at: []\n",
      "Frame: r3, Stop codons found at: [150, 153, 318, 441]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|455\n",
      "G - 216\n",
      "C - 238\n",
      "A - 126\n",
      "T - 111\n",
      "GC% = 65.7\n",
      "Frame: f1, Stop codons found at: [276, 360, 405]\n",
      "Frame: f2, Stop codons found at: [51, 633]\n",
      "Frame: f3, Stop codons found at: [30, 201, 342]\n",
      "Frame: r1, Stop codons found at: [657]\n",
      "Frame: r2, Stop codons found at: [156, 249, 318, 405, 408, 480, 564]\n",
      "Frame: r3, Stop codons found at: [393, 432]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|229\n",
      "G - 1022\n",
      "C - 989\n",
      "A - 531\n",
      "T - 530\n",
      "GC% = 65.46\n",
      "Frame: f1, Stop codons found at: [1503, 1950, 2682, 2832, 3066]\n",
      "Frame: f2, Stop codons found at: [1431, 1497, 1521, 1578, 1803, 1845, 1959, 2010, 2286, 2427, 2550, 2649, 2700, 2715, 2775, 2778, 2937, 2967, 2985]\n",
      "Frame: f3, Stop codons found at: [120, 159, 183, 420, 462, 489, 1104, 1194, 1245, 1263, 1443, 1614, 1770]\n",
      "Frame: r1, Stop codons found at: [189, 192, 228, 330, 999, 1593, 1800, 2067, 2109, 2262, 2319, 2439, 2541, 2745, 2760, 2778, 3000, 3045, 3057]\n",
      "Frame: r2, Stop codons found at: [237, 861, 954, 1278, 1347, 1503, 1542, 1917, 2088, 2139, 2166, 2241, 2301, 2622, 2652, 2754, 2796, 2808, 2820, 2826]\n",
      "Frame: r3, Stop codons found at: [144, 183, 312, 507, 531, 1005, 1134, 1302, 1350, 1362, 1401, 1461]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|422\n",
      "G - 576\n",
      "A - 325\n",
      "T - 306\n",
      "C - 594\n",
      "GC% = 64.96\n",
      "Frame: f1, Stop codons found at: [6, 9, 21, 33, 36, 117, 120, 213, 354, 447, 522, 669, 798, 864, 930, 1029, 1050, 1146]\n",
      "Frame: f2, Stop codons found at: [135, 147, 489, 642, 657, 786, 885, 972, 1044, 1266, 1338, 1455, 1497, 1509, 1512, 1575, 1731]\n",
      "Frame: f3, Stop codons found at: [849, 879, 1014]\n",
      "Frame: r1, Stop codons found at: [24, 63, 183, 423, 501, 549, 954, 987, 1056, 1077, 1452, 1599, 1653, 1698]\n",
      "Frame: r2, Stop codons found at: [624, 717]\n",
      "Frame: r3, Stop codons found at: [33, 507, 597, 657, 747]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|384\n",
      "G - 1131\n",
      "C - 1148\n",
      "A - 694\n",
      "T - 630\n",
      "GC% = 63.25\n",
      "Frame: f1, Stop codons found at: [882, 1347, 1356, 1407, 1440, 1572, 1659, 1806, 1893, 2049, 2070, 2118, 2718, 3051]\n",
      "Frame: f2, Stop codons found at: [198, 456, 603, 690, 696, 834, 990, 1017, 1638, 1860, 2052, 2106, 2178, 2265, 2367, 2478, 2502, 2670, 2682, 2943, 3414]\n",
      "Frame: f3, Stop codons found at: [54, 222, 294, 336, 351, 372, 405, 408, 522, 561, 606, 684, 822, 867, 957, 966, 978, 2061, 2124, 2247, 2487, 2616, 2769, 2772, 2826, 2832, 3180, 3201, 3417]\n",
      "Frame: r1, Stop codons found at: [411, 1488, 1494, 1515, 1557, 2460, 2487, 2514, 2574, 3402, 3450]\n",
      "Frame: r2, Stop codons found at: [36, 51, 135, 201, 354, 366, 504, 549, 561, 579, 630, 939, 945, 1149, 1269, 1314, 1359, 1416, 1467, 1482, 1524, 2493, 2649, 2889, 2940, 3045, 3084, 3147, 3159, 3165, 3249, 3396, 3585]\n",
      "Frame: r3, Stop codons found at: [123, 219, 297, 321, 360, 456, 471, 480, 486, 516, 603, 645, 657, 744, 759, 861, 1170, 1287, 1296, 1323, 1539, 1698, 1848, 1917, 1929, 2217, 2262, 2373, 2790]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|280\n",
      "G - 802\n",
      "C - 762\n",
      "A - 435\n",
      "T - 479\n",
      "GC% = 63.12\n",
      "Frame: f1, Stop codons found at: [24, 69, 225, 252, 363, 474, 528, 753, 891, 918, 951, 1056, 1440, 1632, 1653, 1806, 1950, 2007, 2121, 2151, 2193, 2211, 2268, 2382]\n",
      "Frame: f2, Stop codons found at: [219, 1110, 1713, 1722, 1854, 1998, 2154, 2220]\n",
      "Frame: f3, Stop codons found at: [108, 288, 387, 606, 618, 747, 801, 978, 1215, 1239, 1353, 1503, 1698, 1776, 1779, 1797, 1842, 1860, 2205, 2223, 2298]\n",
      "Frame: r1, Stop codons found at: [90, 441, 561, 645, 663, 753, 798, 831, 837, 918, 1140, 1143, 1302, 1413, 1521, 1545, 1686, 1701, 1842, 1923, 2172, 2217]\n",
      "Frame: r2, Stop codons found at: [105, 228, 288, 324, 507, 567, 756]\n",
      "Frame: r3, Stop codons found at: [249, 267, 303, 450, 483, 549, 675, 696, 1281]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|158\n",
      "G - 519\n",
      "C - 443\n",
      "A - 286\n",
      "T - 360\n",
      "GC% = 59.83\n",
      "Frame: f1, Stop codons found at: [219, 426, 525, 573, 615, 669, 675, 825, 864, 1032, 1209, 1308, 1389, 1404, 1512, 1602]\n",
      "Frame: f2, Stop codons found at: [93, 117, 495, 807, 879, 1521]\n",
      "Frame: f3, Stop codons found at: [36, 144, 1362, 1437]\n",
      "Frame: r1, Stop codons found at: [15, 21, 273, 363, 408, 504, 603, 633, 669, 675, 765, 777, 807, 843, 858, 972, 1020, 1056, 1209, 1302, 1374, 1572, 1596]\n",
      "Frame: r2, Stop codons found at: [27, 48, 1113]\n",
      "Frame: r3, Stop codons found at: [219, 474, 759, 1191, 1314, 1344]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|59\n",
      "G - 1749\n",
      "C - 1616\n",
      "A - 726\n",
      "T - 654\n",
      "GC% = 70.92\n",
      "Frame: f1, Stop codons found at: [738, 741, 897, 993, 1242, 1326, 1527, 1830, 2049, 2313, 2442, 2832, 3324, 3459, 3465, 3489, 3570, 4695]\n",
      "Frame: f2, Stop codons found at: [78, 120, 168, 186, 450, 855, 966, 975, 1113, 2397, 2415, 2445, 2454, 2466, 2478, 2523, 2574, 2820, 2931, 2943, 2997, 3024, 3033, 3042, 3543, 3591, 4551]\n",
      "Frame: f3, Stop codons found at: [0, 105, 249, 258, 354, 396, 420, 1908, 3339, 3564, 3600, 3603, 3675, 3762, 3810, 4122, 4281, 4314, 4440, 4524, 4668]\n",
      "Frame: r1, Stop codons found at: [225, 351, 414, 504, 603, 744, 759, 789, 819, 849, 1020, 1374, 2799, 3261, 4161, 4335, 4356, 4461, 4467, 4602, 4644, 4656, 4707]\n",
      "Frame: r2, Stop codons found at: [75, 1152, 1176, 1548, 1860, 1869, 1938, 2034, 2355, 2367, 2400, 2457, 2475, 2481, 2619, 2712, 2889, 3201, 3504, 3753, 4305]\n",
      "Frame: r3, Stop codons found at: [24, 255, 267, 471, 513, 561, 642, 660, 690, 723, 1116, 1197, 1278, 1365, 1431, 1626, 2844, 3324, 3423, 3720]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|319\n",
      "G - 617\n",
      "C - 619\n",
      "A - 295\n",
      "T - 279\n",
      "GC% = 68.29\n",
      "Frame: f1, Stop codons found at: [633, 654, 1095, 1161, 1203, 1632]\n",
      "Frame: f2, Stop codons found at: [900, 1290, 1560]\n",
      "Frame: f3, Stop codons found at: [72, 750, 957, 990, 1098, 1443, 1674]\n",
      "Frame: r1, Stop codons found at: [9, 120, 123, 132, 138, 411, 507, 612, 708, 774, 849, 1551]\n",
      "Frame: r2, Stop codons found at: [423, 588, 621, 651, 906, 972, 984, 1284, 1422, 1476, 1521, 1569, 1617]\n",
      "Frame: r3, Stop codons found at: [318, 519, 555, 720, 816, 897, 915, 918, 1134, 1383]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|438\n",
      "G - 981\n",
      "C - 1079\n",
      "A - 683\n",
      "T - 681\n",
      "GC% = 60.16\n",
      "Frame: f1, Stop codons found at: [93, 237, 246, 429, 432, 570, 663, 963, 1065, 1158, 1341, 1494, 1581, 1605, 1725, 2127, 2355, 2598, 2622, 2649, 2802, 2943, 2988, 3045, 3342, 3414]\n",
      "Frame: f2, Stop codons found at: [111, 435, 549, 633, 816, 945, 1002, 1134, 1164, 1212, 1389, 1407, 1497, 1566, 1695, 1731, 2034, 2085, 2208, 2211, 2262, 2289, 2310, 2520, 2547, 2574]\n",
      "Frame: f3, Stop codons found at: [6, 96, 141, 300, 384, 390, 411, 606, 642, 819, 1458, 1485, 1662, 1755, 2022, 2106, 2454, 2502, 2577, 2601, 2736, 2955, 2967, 3084, 3150, 3264]\n",
      "Frame: r1, Stop codons found at: [642, 669, 675, 735, 744, 819, 945, 1035, 1113, 1260, 1314, 1776, 1833, 1965, 1968, 1986, 2133, 2205, 2238, 2430, 2484, 2772, 2784, 3243]\n",
      "Frame: r2, Stop codons found at: [147, 255, 321, 396, 522, 606, 657, 828, 1221, 1656, 1701, 1713, 1716, 1854, 1923, 1944, 1980, 2298, 2640, 2874, 2946, 2949, 3237]\n",
      "Frame: r3, Stop codons found at: [33, 453, 810, 978, 1137, 1338, 1425, 1557, 1737, 1803, 1821, 1875, 2451, 2529, 2631, 2634, 2913, 3072]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|210\n",
      "G - 524\n",
      "A - 236\n",
      "T - 227\n",
      "C - 464\n",
      "GC% = 68.09\n",
      "Frame: f1, Stop codons found at: [348, 357, 372, 417, 885, 1260, 1401, 1434, 1440]\n",
      "Frame: f2, Stop codons found at: [138, 240, 246, 306, 375, 969, 1188, 1371]\n",
      "Frame: f3, Stop codons found at: [207, 480, 903, 924, 1029, 1032]\n",
      "Frame: r1, Stop codons found at: [282, 687, 1173, 1296, 1299, 1317]\n",
      "Frame: r2, Stop codons found at: [972, 1131, 1149, 1239, 1263, 1419]\n",
      "Frame: r3, Stop codons found at: [0, 87, 297, 954]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|237\n",
      "G - 961\n",
      "A - 642\n",
      "T - 763\n",
      "C - 910\n",
      "GC% = 57.11\n",
      "Frame: f1, Stop codons found at: [30, 114, 135, 153, 492, 639, 777, 978, 1197, 1215, 1266, 1323, 1365, 1386, 1389, 1398, 1410, 1443, 1518, 1530, 1638, 1701, 1833, 1848, 1938, 1968, 2085, 2133, 2214, 2355, 2649, 2709, 2814, 2817, 2898, 2967, 3114, 3252]\n",
      "Frame: f2, Stop codons found at: [675, 1008, 1182, 1311, 1341, 1653, 1716, 1869, 1872, 1908, 1920, 1977, 2034, 2064, 2274, 2379, 2529, 2607, 2682, 2703, 2772, 2787, 2823, 2868, 2892, 2997, 3018, 3045, 3075, 3090, 3186]\n",
      "Frame: f3, Stop codons found at: [6, 204, 624, 687, 792, 969, 990, 1125, 1413, 1488, 1560, 1590, 1620, 1644, 1707, 1854, 2019, 2025, 2124, 2313, 2370, 2394, 2433, 2490, 2520, 2610, 2715, 2721, 2742, 2802, 2835, 2886, 2979, 3036, 3069, 3123, 3195, 3222]\n",
      "Frame: r1, Stop codons found at: [54, 87, 243, 321, 381, 414, 441, 591, 615, 720, 855, 858, 954, 1062, 1395, 1458, 1461, 1569, 1641, 1836, 2004, 2034, 2274, 2298, 2598, 2604, 2685, 2703, 2895, 2934, 2952]\n",
      "Frame: r2, Stop codons found at: [672, 747, 822, 945, 1020, 1101, 1275, 1281, 1305, 1314, 1323, 1368, 1419, 1539, 1746, 1824, 1830, 1908, 2190, 2253, 2325, 2679, 2706]\n",
      "Frame: r3, Stop codons found at: [0, 48, 108, 147, 216, 270, 384, 423, 468, 579, 678, 780, 789, 906, 1608, 1857, 2037, 2172, 2283, 2364, 2586, 2664]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|507\n",
      "G - 748\n",
      "C - 689\n",
      "A - 363\n",
      "T - 324\n",
      "GC% = 67.66\n",
      "Frame: f1, Stop codons found at: [18, 69, 144, 228, 231, 450, 543, 573, 585, 696, 945, 951, 1014, 1221, 1338, 1365, 1368, 2004, 2031]\n",
      "Frame: f2, Stop codons found at: [246, 336, 1281, 1347, 1623, 1683, 1731, 1764, 1797, 2010, 2043]\n",
      "Frame: f3, Stop codons found at: [21, 54, 249, 528, 615, 810, 873, 906, 1665, 1671, 1689, 2016, 2034]\n",
      "Frame: r1, Stop codons found at: [516, 963, 1104, 1302, 1614, 2094]\n",
      "Frame: r2, Stop codons found at: [96, 165, 168, 201, 306, 375, 426, 480, 543, 720, 879, 951, 1713, 1863, 1983, 1989, 2013, 2082]\n",
      "Frame: r3, Stop codons found at: [447, 594, 846, 1818]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|350\n",
      "G - 504\n",
      "C - 558\n",
      "A - 325\n",
      "T - 325\n",
      "GC% = 62.03\n",
      "Frame: f1, Stop codons found at: [168, 309, 420, 477, 492, 549, 633, 669, 762, 807, 990, 1089, 1410, 1512, 1539, 1557, 1683]\n",
      "Frame: f2, Stop codons found at: [294, 1038]\n",
      "Frame: f3, Stop codons found at: [261, 270, 288, 360, 453, 651, 828, 834, 1275, 1428, 1503, 1668]\n",
      "Frame: r1, Stop codons found at: [87, 141, 264, 384, 423, 435, 504, 552, 612, 720, 1401, 1455, 1659]\n",
      "Frame: r2, Stop codons found at: [1281, 1698]\n",
      "Frame: r3, Stop codons found at: [99, 216, 447, 699, 864, 1011, 1047, 1128, 1152, 1185, 1248, 1272, 1311, 1479, 1500]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|245\n",
      "G - 482\n",
      "C - 419\n",
      "A - 227\n",
      "T - 197\n",
      "GC% = 68.0\n",
      "Frame: f1, Stop codons found at: [564, 600, 738]\n",
      "Frame: f2, Stop codons found at: [252, 780, 783, 1287, 1296]\n",
      "Frame: f3, Stop codons found at: [48, 102, 267, 363, 489, 1236, 1248]\n",
      "Frame: r1, Stop codons found at: [282, 420, 495, 732, 990, 1065, 1116, 1266]\n",
      "Frame: r2, Stop codons found at: [21, 927, 945, 1152]\n",
      "Frame: r3, Stop codons found at: [183, 273, 570, 612, 678, 822, 834]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|279\n",
      "G - 422\n",
      "A - 165\n",
      "T - 172\n",
      "C - 430\n",
      "GC% = 71.66\n",
      "Frame: f1, Stop codons found at: []\n",
      "Frame: f2, Stop codons found at: [285, 561, 639, 759, 762, 966, 969, 1071, 1101]\n",
      "Frame: f3, Stop codons found at: [3, 405, 837, 1008, 1122]\n",
      "Frame: r1, Stop codons found at: []\n",
      "Frame: r2, Stop codons found at: []\n",
      "Frame: r3, Stop codons found at: [66, 312, 369, 381, 489, 552, 702, 747, 975, 1032, 1095]\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|378\n",
      "G - 191\n",
      "C - 188\n",
      "A - 108\n",
      "T - 68\n",
      "GC% = 68.29\n",
      "Frame: f1, Stop codons found at: [219, 393, 420, 510]\n",
      "Frame: f2, Stop codons found at: [531]\n",
      "Frame: f3, Stop codons found at: [99, 141, 288, 444, 495]\n",
      "Frame: r1, Stop codons found at: [324, 381, 492]\n",
      "Frame: r2, Stop codons found at: []\n",
      "Frame: r3, Stop codons found at: []\n",
      "\n",
      "gi|142022655|gb|EQ086233.1|101\n",
      "G - 826\n",
      "C - 815\n",
      "A - 457\n",
      "T - 351\n",
      "GC% = 67.01\n",
      "Frame: f1, Stop codons found at: [279, 309, 438, 522, 957, 1128, 1173, 2268]\n",
      "Frame: f2, Stop codons found at: [33, 66, 120, 186, 195, 255, 300, 366, 417, 582, 624, 918, 921, 948, 1017, 1089, 1098, 1182, 1296, 1578, 1806, 1809, 1812, 1839, 1842, 2430]\n",
      "Frame: f3, Stop codons found at: [1317, 1338, 1359, 1389, 1605, 1677, 1707, 1737, 1740, 1782, 1821, 1977, 2073, 2151, 2199]\n",
      "Frame: r1, Stop codons found at: [1245, 1308, 1380, 1386, 1608, 1647, 1653, 1737, 1776, 1818, 1911, 2073, 2172, 2238, 2400, 2409, 2430]\n",
      "Frame: r2, Stop codons found at: [1206]\n",
      "Frame: r3, Stop codons found at: [108, 264, 303, 390, 573, 729, 966, 984, 1155]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "def fasta_details(file_name):\n",
    "    \"\"\"This function performs some general manipulations\"\"\"\n",
    "    d = fasta_parser(file_name)\n",
    "    for k, v in d.items():\n",
    "        print(k)\n",
    "        letter_counts = count_all_letters(v)\n",
    "        for letter, count in letter_counts.items():\n",
    "            print(f\"{letter} - {count}\")\n",
    "        gc_perc = gc(v)\n",
    "        print(f\"GC% = {round(gc_perc, 2)}\")\n",
    "        frames = get_all_frames(v)\n",
    "        for f, frame in frames.items():\n",
    "            stop_codon_indexes = find_stop_codons(frame)\n",
    "            print(f\"Frame: {f}, Stop codons found at: {stop_codon_indexes}\")\n",
    "        print()\n",
    "\n",
    "\n",
    "fasta_details(\"data/dna_example_1.fasta\")\n",
    "\n",
    "\n",
    "def save_other_frame(file_name, new_file_name, frame):\n",
    "    \"\"\"This function saves all sequences fixed on the desired frame to a new .fasta file.\"\"\"\n",
    "    d = fasta_parser(file_name)\n",
    "    headers = []\n",
    "    sequences = []\n",
    "    for k, v in d.items():\n",
    "        new_frame = get_frame(v, frame)\n",
    "        headers.append(k)\n",
    "        sequences.append(new_frame)\n",
    "    save_fasta(headers, sequences, new_file_name)\n",
    "\n",
    "\n",
    "save_other_frame(\"data/dna_example_1.fasta\", \"dna_example_1_frame-3r\", \"3r\")"
   ]
  }
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