Repository 'tassel5'
hg clone https://toolshed.g2.bx.psu.edu/repos/dereeper/tassel5

Changeset 20:8831e7141a41 (2024-10-22)
Previous changeset 19:55cb63deadfe (2024-10-22)
Commit message:
Uploaded
added:
test-data/Allele_effects_output.txt
test-data/Best_K_Output2
test-data/input.vcf
test-data/phenotyping_xantho.tsv
test-data/statistics_output.txt
removed:
tassel5.zip
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diff -r 55cb63deadfe -r 8831e7141a41 tassel5.zip
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Binary file tassel5.zip has changed
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diff -r 55cb63deadfe -r 8831e7141a41 test-data/Allele_effects_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Allele_effects_output.txt Tue Oct 22 09:47:46 2024 +0000
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diff -r 55cb63deadfe -r 8831e7141a41 test-data/Best_K_Output2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Best_K_Output2 Tue Oct 22 09:47:46 2024 +0000
b
b'@@ -0,0 +1,260 @@\n+<Covariate>\n+<Trait>\tQ1\tQ2\tQ3\tQ4\tQ5\n+B184\t0.540305\t0.297278\t0.0406719\t9.9991E-05\t0.121645\n+IRIS-313-10045\t0.610036\t0.015795\t0.0680474\t0.261366\t0.0447553\n+IRIS-313-10177\t0.718781\t0.226298\t0.0120862\t9.9991E-05\t0.0427341\n+IRIS-313-10221\t0.681027\t0.270315\t9.9982E-05\t9.9982E-05\t0.0484575\n+IRIS-313-10271\t0.537776\t9.9973E-05\t9.9973E-05\t9.9973E-05\t0.461925\n+IRIS-313-10509\t0.796875\t0.0214879\t0.119214\t9.9991E-05\t0.0623235\n+IRIS-313-10525\t0.556451\t9.99729E-05\t0.443249\t9.99729E-05\t9.99729E-05\n+IRIS-313-10723\t0.611087\t0.00819447\t9.9991E-05\t0.336137\t0.0444817\n+IRIS-313-10725\t0.51066\t9.9973E-05\t9.9973E-05\t0.48904\t9.9973E-05\n+IRIS-313-10728\t0.770601\t0.00671553\t9.9982E-05\t0.222484\t9.9982E-05\n+IRIS-313-10762\t0.615624\t0.0949002\t0.289276\t9.99819E-05\t9.99819E-05\n+IRIS-313-10825\t0.615143\t9.99822E-05\t0.134832\t0.249825\t9.99822E-05\n+IRIS-313-10897\t0.959979\t9.9973E-05\t0.0397212\t9.9973E-05\t9.9973E-05\n+IRIS-313-10898\t0.915803\t0.0309356\t9.9991E-05\t0.0144913\t0.0386697\n+IRIS-313-10924\t0.604983\t0.279318\t0.0177384\t0.0978611\t9.9991E-05\n+IRIS-313-10942\t0.574522\t9.99729E-05\t0.425178\t9.99729E-05\t9.99729E-05\n+IRIS-313-10966\t0.553424\t0.30961\t9.9982E-05\t9.9982E-05\t0.136765\n+IRIS-313-10990\t0.651783\t0.227902\t0.120115\t9.99819E-05\t9.99819E-05\n+IRIS-313-10995\t0.734099\t0.0152736\t0.099866\t0.144191\t0.00656969\n+IRIS-313-11130\t0.56965\t0.0982943\t0.0709538\t0.198969\t0.062133\n+IRIS-313-11160\t0.514377\t0.0598015\t0.370615\t0.0441335\t0.0110732\n+IRIS-313-11206\t0.540715\t9.9991E-05\t0.235672\t0.153687\t0.0698264\n+IRIS-313-11330\t0.910599\t0.0628614\t9.9982E-05\t9.9982E-05\t0.0263394\n+IRIS-313-11403\t0.579254\t0.242269\t0.0943379\t0.0568279\t0.0273111\n+IRIS-313-11405\t0.635451\t9.99823E-05\t0.290828\t0.0735206\t9.99823E-05\n+IRIS-313-11406\t0.951581\t0.0344377\t9.9982E-05\t9.9982E-05\t0.0137812\n+IRIS-313-11523\t0.859188\t0.0261163\t9.9991E-05\t0.112706\t0.00188981\n+IRIS-313-11525\t0.840514\t0.050368\t9.9991E-05\t0.0589065\t0.050112\n+IRIS-313-11551\t0.718669\t9.9982E-05\t0.163079\t0.118052\t9.9982E-05\n+IRIS-313-11757\t0.938243\t9.9982E-05\t9.9982E-05\t0.0377918\t0.0237654\n+IRIS-313-11758\t0.544706\t9.9982E-05\t0.0401812\t0.414913\t9.9982E-05\n+IRIS-313-11773\t0.836322\t0.0204607\t9.9982E-05\t0.143017\t9.9982E-05\n+IRIS-313-11783\t0.776524\t9.99819E-05\t0.00552584\t0.21775\t9.99819E-05\n+IRIS-313-11812\t0.924444\t9.9982E-05\t9.9982E-05\t0.0125611\t0.0627951\n+IRIS-313-11895\t0.888837\t9.9982E-05\t0.0955285\t9.9982E-05\t0.0154343\n+IRIS-313-11912\t0.620701\t0.00513352\t0.286665\t0.0874003\t9.9991E-05\n+IRIS-313-11983\t0.69007\t9.9991E-05\t0.000568757\t0.286034\t0.0232279\n+IRIS-313-11997\t0.901006\t0.0498149\t9.9991E-05\t0.0179961\t0.0310827\n+IRIS-313-12017\t0.619588\t0.218723\t0.155522\t0.00606723\t9.9991E-05\n+IRIS-313-12027\t0.570625\t0.145124\t0.284051\t9.9982E-05\t9.9982E-05\n+IRIS-313-12078\t0.594355\t0.207523\t9.9991E-05\t0.135765\t0.062257\n+IRIS-313-12109\t0.90941\t9.9982E-05\t9.9982E-05\t0.046338\t0.0440522\n+IRIS-313-12142\t0.963316\t9.9982E-05\t0.0222411\t9.9982E-05\t0.014243\n+IRIS-313-12147\t0.800304\t0.0163974\t0.0262485\t0.0475677\t0.109483\n+IRIS-313-12148\t0.978707\t9.9973E-05\t0.0209927\t9.9973E-05\t9.9973E-05\n+IRIS-313-12210\t0.62919\t0.237062\t0.0587454\t9.9991E-05\t0.074902\n+IRIS-313-12246\t0.855401\t9.9982E-05\t9.9982E-05\t0.0215931\t0.122806\n+IRIS-313-7719\t0.541712\t9.9982E-05\t9.9982E-05\t0.0541538\t0.403935\n+IRIS-313-8312\t0.552157\t9.99729E-05\t0.447544\t9.99729E-05\t9.99729E-05\n+IRIS-313-8909\t0.89388\t0.0249838\t9.9982E-05\t9.9982E-05\t0.0809364\n+IRIS-313-9117\t0.505664\t0.0988019\t0.395334\t9.9982E-05\t9.9982E-05\n+IRIS-313-9294\t0.668616\t9.99819E-05\t9.99819E-05\t0.318838\t0.0123459\n+B028\t0.00827815\t0.55607\t0.116782\t0.115165\t0.203705\n+IRIS-313-10047\t9.99729E-05\t0.516137\t9.99729E-05\t9.99729E-05\t0.483563\n+IRIS-313-10103\t0.271882\t0.504528\t9.9991E-05\t0.166467\t0.0570227\n+IRIS-313-10224\t0.073999\t0.784966\t0.0171295\t0.123805\t9.9991E-05\n+IRIS-313-10449\t0.161662\t0.745237\t0.0349848\t9.9991E-05\t0.0580168\n+IRIS-313-10458\t0.164823\t0.818608\t0.0163692\t9.9982E-05\t9.9982E-05\n+IRIS-313-10484\t9.99737E-05\t0.799992\t0.199708\t9.99737E-05\t9.99737E-05\n+IRIS-313-10502\t0.0302358\t0.792189\t0.0303828\t0.0576441\t0.0895486\n+IRIS-313-10515'..b'S-313-11233\t0.213205\t9.99819E-05\t0.177055\t9.99819E-05\t0.60954\n+IRIS-313-11357\t9.9991E-05\t0.162508\t0.0752261\t0.0751235\t0.687042\n+IRIS-313-11437\t0.126312\t9.9982E-05\t0.148306\t9.9982E-05\t0.725182\n+IRIS-313-11480\t9.997E-05\t9.997E-05\t9.997E-05\t9.997E-05\t0.9996\n+IRIS-313-11513\t9.99819E-05\t0.0405992\t0.00511816\t9.99819E-05\t0.954083\n+IRIS-313-11643\t9.9991E-05\t0.0199138\t0.114522\t0.290474\t0.574991\n+IRIS-313-11714\t9.9991E-05\t0.138962\t0.224365\t0.114684\t0.52189\n+IRIS-313-11784\t0.073027\t0.0151978\t0.374035\t9.9991E-05\t0.53764\n+IRIS-313-11930\t0.179013\t9.9991E-05\t0.135729\t0.0218874\t0.663271\n+IRIS-313-11937\t9.9991E-05\t0.194752\t0.0513599\t0.0881751\t0.665613\n+IRIS-313-11941\t0.00923075\t9.9991E-05\t0.0134894\t0.077459\t0.899721\n+IRIS-313-11960\t0.0491336\t9.9991E-05\t0.120646\t0.110899\t0.719221\n+IRIS-313-12135\t0.170725\t0.0413305\t0.142539\t0.0526395\t0.592765\n+IRIS-313-12234\t9.99729E-05\t0.02197\t9.99729E-05\t9.99729E-05\t0.97773\n+IRIS-313-7636\t0.0603104\t9.99819E-05\t0.333077\t9.99819E-05\t0.606412\n+IRIS-313-8514\t9.9991E-05\t0.011053\t0.13634\t0.0364248\t0.816082\n+IRIS-313-8621\t0.218029\t9.9991E-05\t0.000206847\t0.191274\t0.59039\n+IRIS-313-8732\t0.0315744\t0.0532376\t9.9982E-05\t9.9982E-05\t0.914988\n+IRIS-313-9227\t9.99819E-05\t0.0969773\t0.0106578\t9.99819E-05\t0.892165\n+IRIS-313-9566\t9.99729E-05\t9.99729E-05\t9.99729E-05\t0.209848\t0.789852\n+IRIS-313-9922\t9.99729E-05\t9.99729E-05\t0.495101\t9.99729E-05\t0.504599\n+IRIS-313-9966\t0.103952\t9.99819E-05\t0.372912\t9.99819E-05\t0.522936\n+B035\t0.291622\t9.9982E-05\t0.22799\t9.9982E-05\t0.480188\n+B051\t0.0673927\t0.125943\t0.273292\t0.108758\t0.424614\n+CX124\t0.0762836\t0.0647638\t0.453315\t0.0864127\t0.319225\n+CX228\t9.9991E-05\t0.469991\t0.0845465\t0.157842\t0.287521\n+CX250\t0.332606\t9.9991E-05\t0.165591\t0.0675294\t0.434174\n+CX268\t0.0466932\t0.21108\t0.148852\t0.12632\t0.467055\n+CX274\t0.487565\t0.0589251\t0.146283\t9.9991E-05\t0.307126\n+CX278\t0.011722\t0.360938\t0.205763\t0.0816023\t0.339974\n+CX286\t0.0812969\t0.0803312\t0.230997\t0.132805\t0.47457\n+CX288\t0.141244\t0.290669\t0.0635215\t0.109282\t0.395282\n+CX291\t0.263568\t0.0241847\t0.235208\t0.086418\t0.390622\n+CX51\t0.276837\t0.449073\t0.0867963\t0.0526411\t0.134652\n+CX52\t0.200127\t0.249455\t0.106741\t0.174998\t0.268679\n+CX85\t0.131758\t0.105345\t0.153439\t0.139027\t0.470431\n+IRIS-313-10010\t0.280118\t0.0441077\t0.0915582\t0.496595\t0.0876211\n+IRIS-313-10077\t0.488517\t0.00345602\t0.180636\t0.268279\t0.0591125\n+IRIS-313-10238\t0.234358\t0.193981\t0.198596\t0.0780773\t0.294988\n+IRIS-313-10268\t0.20434\t9.9991E-05\t0.205739\t0.0979889\t0.491832\n+IRIS-313-10301\t0.294492\t0.0308439\t0.208786\t9.9991E-05\t0.465778\n+IRIS-313-10314\t0.0884061\t0.11604\t0.36533\t0.0188426\t0.411382\n+IRIS-313-10333\t0.0498105\t0.050366\t0.432888\t0.0284066\t0.438529\n+IRIS-313-10334\t0.0535691\t0.0517596\t0.428425\t0.029949\t0.436297\n+IRIS-313-10516\t0.389955\t9.9982E-05\t0.329738\t0.280106\t9.9982E-05\n+IRIS-313-10572\t0.198939\t0.190868\t0.351016\t0.259076\t9.99911E-05\n+IRIS-313-10575\t0.383323\t0.256086\t0.114047\t0.167497\t0.0790468\n+IRIS-313-10754\t9.99819E-05\t0.237637\t0.410033\t9.99819E-05\t0.352131\n+IRIS-313-11108\t0.481109\t0.0528191\t0.441387\t0.0245857\t9.9991E-05\n+IRIS-313-11394\t0.310628\t0.0423406\t0.441847\t0.0653139\t0.13987\n+IRIS-313-11433\t0.0140163\t0.418468\t9.9991E-05\t0.0962605\t0.471156\n+IRIS-313-11449\t0.3168\t0.00268216\t0.279627\t0.384183\t0.016707\n+IRIS-313-11510\t0.100359\t0.115677\t0.447188\t0.145328\t0.191447\n+IRIS-313-11750\t0.232015\t0.226945\t0.0109956\t0.0305781\t0.499467\n+IRIS-313-11916\t0.26406\t0.174903\t0.119854\t0.437008\t0.00417429\n+IRIS-313-12186\t0.237803\t0.471858\t0.00746885\t0.192328\t0.0905419\n+IRIS-313-8205\t0.167448\t0.159683\t0.250146\t0.1403\t0.282423\n+IRIS-313-8699\t0.442322\t0.0781333\t0.0639307\t0.29295\t0.122664\n+IRIS-313-8930\t0.0689\t0.162124\t0.382518\t0.16195\t0.224507\n+IRIS-313-9072\t0.330967\t0.0851478\t0.0892837\t0.434697\t0.0599043\n+IRIS-313-9433\t0.490107\t9.9991E-05\t0.0882312\t0.310845\t0.110717\n+IRIS-313-9572\t0.203297\t0.216733\t0.143725\t0.33932\t0.096925\n+IRIS-313-9825\t0.484253\t9.99822E-05\t0.0326484\t0.482898\t9.99822E-05\n+IRIS-313-9935\t0.382164\t9.9991E-05\t0.112535\t0.486055\t0.0191461\n+IRIS-313-9940\t0.0770131\t9.9991E-05\t0.494699\t0.0117236\t0.416464\n'
b
diff -r 55cb63deadfe -r 8831e7141a41 test-data/input.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.vcf Tue Oct 22 09:47:46 2024 +0000
b
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b
diff -r 55cb63deadfe -r 8831e7141a41 test-data/phenotyping_xantho.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phenotyping_xantho.tsv Tue Oct 22 09:47:46 2024 +0000
b
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b
diff -r 55cb63deadfe -r 8831e7141a41 test-data/statistics_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/statistics_output.txt Tue Oct 22 09:47:46 2024 +0000
b
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