view commons/tools/tests/Test_F_FilterAlign.py @ 31:0ab839023fe4

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from commons.core.utils.FileUtils import FileUtils
import unittest
import os

class Test_F_FilterAlign(unittest.TestCase):

    def test_as_script(self):
        alignFileName = "batch.fa.align"
        self._writeAlignFile(alignFileName)
        expFileName = "exp.filtered"
        self._writeExpFile(expFileName)
        obsFileName = "batch.fa.align.filtered"
        cmd = "FilterAlign.py"
        cmd += " -i %s" % alignFileName
        cmd += " -S 100"
        cmd += " -v 1"
        os.system(cmd)
        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
        os.remove(alignFileName)
        os.remove(expFileName)
        os.remove(obsFileName)
        
    def _writeExpFile(self, fileName):
        f = open(fileName, "w")
        f.write("chunk09914\t2257\t2722\trefTE_747\t2614\t2169\t0\t249\t77.5463\n")
        f.write("chunk09914\t3114\t4494\trefTE_747\t1598\t228\t0\t571\t78.0453\n")
        f.write("chunk09914\t2251\t4816\trefTE_759\t173\t2769\t0\t3203\t90.5966\n")
        f.write("chunk09914\t3019\t3698\trefTE_764\t49\t735\t0\t343\t78.3912\n")
        f.write("chunk09914\t4102\t4530\trefTE_764\t1191\t1603\t0\t154\t83.0601\n")
        f.write("chunk09914\t4603\t4864\trefTE_779\t291\t24\t6.5e-39\t135\t80.9917\n")
        f.write("chunk09914\t4642\t4909\trefTE_787\t56\t326\t0\t132\t79.0323\n")
        f.write("chunk09914\t5086\t6724\trefTE_787\t532\t2194\t0\t218\t71.4668\n")
        f.write("chunk09914\t6180\t6594\trefTE_812\t2516\t2949\t1.6e-32\t125\t72.5441\n")
        f.write("chunk09914\t2349\t2723\trefTE_818\t1034\t663\t0\t347\t80.0539\n")
        f.write("chunk09914\t2412\t2727\trefTE_818\t1169\t1482\t0\t278\t78.5942\n")
        f.write("chunk09914\t3853\t5302\trefTE_828\t3133\t1713\t0\t417\t77.8644\n")
        f.write("chunk09914\t5486\t6724\trefTE_828\t1715\t454\t0\t584\t73.8655\n")
        f.write("chunk09914\t849\t1203\trefTE_838\t83\t449\t0\t493\t95.7386\n")
        f.write("chunk09914\t3355\t4471\trefTE_861\t2024\t3183\t0\t260\t77.1289\n")
        f.write("chunk09914\t2263\t4696\trefTE_866\t19\t2476\t0\t3136\t91.1287\n")
        f.write("chunk09914\t4803\t5747\trefTE_866\t2479\t3429\t0\t1352\t93.1217\n")
        f.write("chunk09914\t4134\t4702\trefTE_880\t1685\t1129\t7.8e-35\t126\t80.7851\n")
        f.write("chunk09914\t3598\t4029\trefTE_904\t666\t1122\t0\t414\t84.7418\n")
        f.write("chunk09914\t3887\t4480\trefTE_904\t1030\t1635\t0\t384\t82.6087\n")
        f.write("chunk09914\t2257\t2722\trefTE_908\t1005\t551\t0\t240\t78.5377\n")
        f.write("chunk09914\t6180\t6594\trefTE_914\t1420\t987\t8.6e-30\t125\t72.5441\n")
        f.write("chunk09914\t4144\t6724\trefTE_931\t3801\t1202\t0\t1057\t74.7937\n")
        f.write("chunk09914\t848\t1204\trefTE_966\t370\t1\t0\t522\t98.0282\n")
        f.write("chunk09914\t854\t1145\trefTE_966\t5130\t4829\t0\t411\t95.8763\n")
        f.write("chunk09914\t4142\t4487\trefTE_969\t455\t130\t4.2039e-45\t161\t81.1881\n")
        f.write("chunk09914\t848\t1218\trefTE_980\t1182\t814\t0\t431\t92.1127\n")
        f.write("chunk09914\t4093\t4489\trefTE_999\t5850\t5485\t3.6e-39\t142\t81.0651\n")
        f.write("chunk09914\t2257\t2722\trefTE_1006\t2472\t2025\t0\t257\t77.4193\n")
        f.write("chunk09914\t3755\t4491\trefTE_1006\t941\t230\t0\t188\t80.0948\n")
        f.write("chunk09914\t5060\t6724\trefTE_1006\t7451\t5776\t0\t711\t72.3792\n")
        f.write("chunk09914\t2251\t3361\trefTE_1015\t7278\t8364\t0\t1514\t86.8087\n")
        f.write("chunk09914\t2780\t6724\trefTE_1015\t1\t3962\t0\t5370\t91.9552\n")
        f.write("chunk09914\t3383\t4672\trefTE_1015\t8150\t9445\t0\t1746\t92.1217\n")
        f.write("chunk09914\t6228\t6594\trefTE_1018\t5554\t5920\t6.2e-22\t106\t73.3138\n")
        f.close()
        
    def _writeAlignFile(self, fileName):
        f = open(fileName, "w")
        f.write("chunk09914\t5038\t5133\trefTE_745\t288\t389\t1.3e-15\t38\t86.747\n")
        f.write("chunk09914\t6415\t6574\trefTE_745\t605\t761\t1.3e-15\t76\t78.9116\n")
        f.write("chunk09914\t2257\t2722\trefTE_747\t2614\t2169\t3.8e-165\t249\t77.5463\n")
        f.write("chunk09914\t3114\t4494\trefTE_747\t1598\t228\t3.8e-165\t571\t78.0453\n")
        f.write("chunk09914\t2251\t4816\trefTE_759\t173\t2769\t0\t3203\t90.5966\n")
        f.write("chunk09914\t3019\t3698\trefTE_764\t49\t735\t3.4e-133\t343\t78.3912\n")
        f.write("chunk09914\t4102\t4530\trefTE_764\t1191\t1603\t3.4e-133\t154\t83.0601\n")
        f.write("chunk09914\t4640\t4702\trefTE_764\t1676\t1738\t3.4e-133\t39\t86.2069\n")
        f.write("chunk09914\t1436\t1549\trefTE_779\t749\t628\t3.9e-33\t38\t75.7009\n")
        f.write("chunk09914\t3992\t4156\trefTE_779\t958\t743\t2.6e-34\t42\t85.4305\n")
        f.write("chunk09914\t4050\t4229\trefTE_779\t782\t602\t6.5e-39\t57\t82.6923\n")
        f.write("chunk09914\t4430\t4499\trefTE_779\t1029\t952\t1.2e-33\t39\t83.3333\n")
        f.write("chunk09914\t4603\t4864\trefTE_779\t291\t24\t6.5e-39\t135\t80.9917\n")
        f.write("chunk09914\t4642\t4909\trefTE_787\t56\t326\t4e-86\t132\t79.0323\n")
        f.write("chunk09914\t5086\t6724\trefTE_787\t532\t2194\t4e-86\t218\t71.4668\n")
        f.write("chunk09914\t4689\t4718\trefTE_812\t828\t855\t1.6e-32\t37\t92.8571\n")
        f.write("chunk09914\t6178\t6204\trefTE_812\t1111\t1138\t1.6e-32\t36\t92.5926\n")
        f.write("chunk09914\t6180\t6594\trefTE_812\t2516\t2949\t1.6e-32\t125\t72.5441\n")
        f.write("chunk09914\t2349\t2723\trefTE_818\t1034\t663\t2e-97\t347\t80.0539\n")
        f.write("chunk09914\t2412\t2727\trefTE_818\t1169\t1482\t1.1e-73\t278\t78.5942\n")
        f.write("chunk09914\t3315\t3420\trefTE_818\t423\t318\t2e-97\t41\t74\n")
        f.write("chunk09914\t3339\t3429\trefTE_818\t153\t49\t1.7e-96\t38\t82.5581\n")
        f.write("chunk09914\t3853\t5302\trefTE_828\t3133\t1713\t1.6e-281\t417\t77.8644\n")
        f.write("chunk09914\t5486\t6724\trefTE_828\t1715\t454\t1.6e-281\t584\t73.8655\n")
        f.write("chunk09914\t2593\t2700\trefTE_831\t905\t798\t1.2e-15\t85\t75\n")
        f.write("chunk09914\t849\t1203\trefTE_838\t83\t449\t2.6e-138\t493\t95.7386\n")
        f.write("chunk09914\t5276\t5639\trefTE_842\t725\t1094\t1.7e-16\t47\t71.8563\n")
        f.write("chunk09914\t6223\t6594\trefTE_842\t1689\t2058\t1.7e-16\t70\t73.8602\n")
        f.write("chunk09914\t6180\t6594\trefTE_844\t3220\t2788\t3e-19\t97\t71.5013\n")
        f.write("chunk09914\t6415\t6593\trefTE_847\t3137\t2959\t2e-15\t85\t74.4186\n")
        f.write("chunk09914\t4691\t4762\trefTE_852\t2829\t2755\t1.9e-21\t36\t82.0895\n")
        f.write("chunk09914\t6172\t6594\trefTE_852\t1201\t770\t1.9e-21\t97\t71.2121\n")
        f.write("chunk09914\t2441\t2723\trefTE_861\t995\t1282\t3.9e-54\t78\t75.3906\n")
        f.write("chunk09914\t3323\t3437\trefTE_861\t1683\t1811\t3.9e-54\t36\t81.3084\n")
        f.write("chunk09914\t3355\t4471\trefTE_861\t2024\t3183\t3.9e-54\t260\t77.1289\n")
        f.write("chunk09914\t4602\t4701\trefTE_861\t3281\t3372\t3.9e-54\t39\t85.7143\n")
        f.write("chunk09914\t360\t470\trefTE_864\t2853\t2962\t6.3e-17\t38\t77.2277\n")
        f.write("chunk09914\t4200\t4472\trefTE_864\t3062\t3320\t6.3e-17\t81\t75.2066\n")
        f.write("chunk09914\t2594\t2736\trefTE_865\t3\t145\t1.3e-26\t62\t71.7391\n")
        f.write("chunk09914\t3531\t3622\trefTE_865\t727\t810\t1.3e-26\t38\t80\n")
        f.write("chunk09914\t4025\t4484\trefTE_865\t2086\t2534\t1.3e-26\t79\t78.7179\n")
        f.write("chunk09914\t2263\t4696\trefTE_866\t19\t2476\t0\t3136\t91.1287\n")
        f.write("chunk09914\t4803\t5747\trefTE_866\t2479\t3429\t0\t1352\t93.1217\n")
        f.write("chunk09914\t646\t733\trefTE_870\t3379\t3466\t6.1e-19\t96\t79.5455\n")
        f.write("chunk09914\t6272\t6716\trefTE_875\t2153\t1701\t3.7e-13\t77\t73.7624\n")
        f.write("chunk09914\t646\t737\trefTE_877\t3412\t3502\t2.2e-18\t94\t82.2222\n")
        f.write("chunk09914\t3596\t3756\trefTE_880\t2230\t2079\t7.8e-35\t53\t79.2857\n")
        f.write("chunk09914\t4090\t4521\trefTE_880\t1702\t1261\t4.1e-24\t90\t81.3699\n")
        f.write("chunk09914\t4134\t4702\trefTE_880\t1685\t1129\t7.8e-35\t126\t80.7851\n")
        f.write("chunk09914\t2569\t2725\trefTE_885\t789\t935\t6.6e-18\t73\t76.9231\n")
        f.write("chunk09914\t2583\t2699\trefTE_885\t118\t1\t4.4e-17\t90\t81.25\n")
        f.write("chunk09914\t3507\t3758\trefTE_885\t1631\t1887\t6.6e-18\t49\t77.6786\n")
        f.write("chunk09914\t3598\t4029\trefTE_904\t666\t1122\t3e-117\t414\t84.7418\n")
        f.write("chunk09914\t3841\t3924\trefTE_904\t1044\t1130\t3.1e-11\t60\t82.2785\n")
        f.write("chunk09914\t3887\t4480\trefTE_904\t1030\t1635\t3.9e-108\t384\t82.6087\n")
        f.write("chunk09914\t4660\t4708\trefTE_904\t1763\t1813\t3e-117\t40\t79.5918\n")
        f.write("chunk09914\t2257\t2722\trefTE_908\t1005\t551\t3.9e-62\t240\t78.5377\n")
        f.write("chunk09914\t4689\t4718\trefTE_914\t3130\t3103\t8.6e-30\t37\t92.8571\n")
        f.write("chunk09914\t6180\t6594\trefTE_914\t1420\t987\t8.6e-30\t125\t72.5441\n")
        f.write("chunk09914\t4691\t4755\trefTE_930\t2120\t2187\t2.3e-14\t39\t86.6667\n")
        f.write("chunk09914\t6172\t6506\trefTE_930\t3738\t4087\t2.3e-14\t71\t72.293\n")
        f.write("chunk09914\t3755\t3945\trefTE_931\t4127\t3947\t0\t45\t79.3939\n")
        f.write("chunk09914\t4144\t6724\trefTE_931\t3801\t1202\t0\t1057\t74.7937\n")
        f.write("chunk09914\t4692\t4772\trefTE_962\t2382\t2453\t1.5e-16\t39\t85.0746\n")
        f.write("chunk09914\t6178\t6560\trefTE_962\t3929\t4309\t1.5e-16\t79\t70.5882\n")
        f.write("chunk09914\t848\t1204\trefTE_966\t370\t1\t4e-147\t522\t98.0282\n")
        f.write("chunk09914\t854\t1145\trefTE_966\t5130\t4829\t1.5e-115\t411\t95.8763\n")
        f.write("chunk09914\t1139\t1203\trefTE_966\t4770\t4681\t1.5e-115\t38\t87.5\n")
        f.write("chunk09914\t646\t734\trefTE_967\t4583\t4671\t4.8e-16\t87\t76.4045\n")
        f.write("chunk09914\t3565\t3698\trefTE_969\t1106\t990\t4.3e-45\t53\t79.646\n")
        f.write("chunk09914\t4142\t4487\trefTE_969\t455\t130\t4.3e-45\t161\t81.1881\n")
        f.write("chunk09914\t848\t1218\trefTE_980\t1182\t814\t6.8e-120\t431\t92.1127\n")
        f.write("chunk09914\t4691\t4762\trefTE_986\t3059\t3133\t3.3e-21\t36\t82.0895\n")
        f.write("chunk09914\t6172\t6594\trefTE_986\t4689\t5120\t3.3e-21\t97\t71.2121\n")
        f.write("chunk09914\t149\t280\trefTE_987\t3872\t3721\t2.8e-18\t38\t79.2\n")
        f.write("chunk09914\t4689\t4769\trefTE_987\t3186\t3102\t2.8e-18\t37\t83.5616\n")
        f.write("chunk09914\t6178\t6594\trefTE_987\t1600\t1188\t2.8e-18\t77\t72.0317\n")
        f.write("chunk09914\t4108\t4241\trefTE_991\t2079\t2237\t1.2e-12\t62\t82.1705\n")
        f.write("chunk09914\t4602\t4701\trefTE_991\t2535\t2634\t1.2e-12\t43\t78.022\n")
        f.write("chunk09914\t3596\t3757\trefTE_999\t6434\t6307\t3.6e-39\t52\t85.124\n")
        f.write("chunk09914\t4093\t4489\trefTE_999\t5850\t5485\t3.6e-39\t142\t81.0651\n")
        f.write("chunk09914\t4348\t4702\trefTE_999\t5619\t5295\t5.9e-13\t54\t79.7251\n")
        f.write("chunk09914\t4541\t4805\trefTE_1002\t3207\t2973\t6.8e-27\t57\t85.5769\n")
        f.write("chunk09914\t6178\t6723\trefTE_1002\t1494\t946\t6.8e-27\t96\t75.7764\n")
        f.write("chunk09914\t4085\t4179\trefTE_1004\t3933\t4033\t1.5e-17\t47\t80\n")
        f.write("chunk09914\t4690\t4718\trefTE_1004\t4126\t4153\t1.5e-17\t38\t92.8571\n")
        f.write("chunk09914\t6262\t6594\trefTE_1004\t5242\t5574\t1.5e-17\t65\t70.2265\n")
        f.write("chunk09914\t2257\t2722\trefTE_1006\t2472\t2025\t2.5e-134\t257\t77.4193\n")
        f.write("chunk09914\t3134\t3382\trefTE_1006\t1450\t1199\t2.9e-118\t45\t75.7991\n")
        f.write("chunk09914\t3331\t3661\trefTE_1006\t1468\t1146\t2.5e-134\t98\t78.2313\n")
        f.write("chunk09914\t3755\t4491\trefTE_1006\t941\t230\t2.5e-134\t188\t80.0948\n")
        f.write("chunk09914\t5060\t6724\trefTE_1006\t7451\t5776\t3.8e-204\t711\t72.3792\n")
        f.write("chunk09914\t2670\t2723\trefTE_1009\t6642\t6591\t7.1e-18\t39\t86\n")
        f.write("chunk09914\t3328\t3647\trefTE_1009\t5826\t5508\t7.1e-18\t84\t75\n")
        f.write("chunk09914\t6\t130\trefTE_1011\t3884\t3994\t1.6e-11\t38\t76.6355\n")
        f.write("chunk09914\t4690\t4741\trefTE_1011\t4997\t5046\t1.6e-11\t37\t91.1111\n")
        f.write("chunk09914\t6180\t6716\trefTE_1011\t6676\t7235\t1.6e-11\t55\t71.2274\n")
        f.write("chunk09914\t2251\t3361\trefTE_1015\t7278\t8364\t0\t1514\t86.8087\n")
        f.write("chunk09914\t2780\t6724\trefTE_1015\t1\t3962\t0\t5370\t91.9552\n")
        f.write("chunk09914\t3383\t4672\trefTE_1015\t8150\t9445\t0\t1746\t92.1217\n")
        f.write("chunk09914\t6228\t6594\trefTE_1018\t5554\t5920\t6.2e-22\t106\t73.3138\n")
        f.close()

if __name__ == "__main__":
    unittest.main()