| Previous changeset 2:ea2cccb9f73e (2023-01-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 58587e05f604590c70550e13fc51b7425e916ed4 |
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modified:
macros.xml predict.py virhunter.xml |
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added:
test-data/predicted.tsv test-data/predicted_fragments.tsv |
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removed:
test-data/predicted.csv test-data/predicted_fragments.csv |
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| diff -r ea2cccb9f73e -r 302332b914ef macros.xml --- a/macros.xml Thu Jan 05 14:27:54 2023 +0000 +++ b/macros.xml Sat Jan 14 21:08:33 2023 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.0.0</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <xml name="requirements"> <requirements> <requirement type="package" version="1.23.3">numpy</requirement> |
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| diff -r ea2cccb9f73e -r 302332b914ef predict.py --- a/predict.py Thu Jan 05 14:27:54 2023 +0000 +++ b/predict.py Sat Jan 14 21:08:33 2023 +0000 |
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| @@ -153,7 +153,6 @@ length=l_, use_10=use_10 ) - print(df) df = predict_rf( df=df, rf_weights_path=weights, @@ -168,14 +167,14 @@ df_500 = dfs_fr[0][(dfs_fr[0]['length'] >= limit) & (dfs_fr[0]['length'] < 1500)] df_1000 = dfs_fr[1][(dfs_fr[1]['length'] >= 1500)] df = pd.concat([df_1000, df_500], ignore_index=True) - pred_fr = Path(out_path, 'predicted_fragments.csv') - df.to_csv(pred_fr) + pred_fr = Path(out_path, 'predicted_fragments.tsv') + df.to_csv(pred_fr, sep='\t') df_500 = dfs_cont[0][(dfs_cont[0]['length'] >= limit) & (dfs_cont[0]['length'] < 1500)] df_1000 = dfs_cont[1][(dfs_cont[1]['length'] >= 1500)] df = pd.concat([df_1000, df_500], ignore_index=True) - pred_contigs = Path(out_path, 'predicted.csv') - df.to_csv(pred_contigs) + pred_contigs = Path(out_path, 'predicted.tsv') + df.to_csv(pred_contigs, sep='\t') if return_viral: viral_ids = list(df[df["decision"] == "virus"]["id"]) |
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| diff -r ea2cccb9f73e -r 302332b914ef test-data/predicted.csv --- a/test-data/predicted.csv Thu Jan 05 14:27:54 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,274 +0,0 @@\n-,length,id,# viral fragments,# plant fragments,# bacterial fragments,decision,# viral / # total,# viral / # total * length\n-0,19251,KY110737.1,30,2,6,virus,0.789,15189.039\n-1,18478,KY707825.2,24,3,9,virus,0.667,12324.826000000001\n-2,10427,AM267479.1,20,0,0,virus,1.0,10427.0\n-3,9802,MT533611.1,19,0,0,virus,1.0,9802.0\n-4,9798,LC537538.1,19,0,0,virus,1.0,9798.0\n-5,9736,LC600465.1,19,0,0,virus,1.0,9736.0\n-6,9736,LC494681.1,19,0,0,virus,1.0,9736.0\n-7,9445,JN936438.1,18,0,0,virus,1.0,9445.0\n-8,11892,LC602461.1,18,5,0,virus,0.783,9311.436\n-9,9757,MK777994.1,18,1,0,virus,0.947,9239.878999999999\n-10,9663,LC038073.1,18,1,0,virus,0.947,9150.860999999999\n-11,9429,MK649741.1,17,1,0,virus,0.944,8900.975999999999\n-12,9798,LC537503.1,17,0,2,virus,0.895,8769.210000000001\n-13,8421,MN059369.1,16,0,0,virus,1.0,8421.0\n-14,9798,AB747297.1,16,0,3,virus,0.842,8249.916\n-15,8745,NC_008169.1,16,0,1,virus,0.941,8229.045\n-16,10487,KX884756.1,15,5,0,virus,0.75,7865.25\n-17,9287,MZ148041.1,15,3,0,virus,0.833,7736.071\n-18,8745,MT554537.1,15,0,2,virus,0.882,7713.09\n-19,8366,MN059208.1,14,1,1,virus,0.875,7320.25\n-20,7242,AJ534983.1,14,0,0,virus,1.0,7242.0\n-21,7702,KX008574.1,14,1,0,virus,0.933,7185.966\n-22,8644,MN059273.1,14,0,3,virus,0.824,7122.656\n-23,7343,KX034904.1,13,1,0,virus,0.929,6821.647\n-24,7341,KX034878.1,13,1,0,virus,0.929,6819.789000000001\n-25,6791,JN710440.1,13,0,0,virus,1.0,6791.0\n-26,6436,MT752813.1,12,0,0,virus,1.0,6436.0\n-27,6436,MT752690.1,12,0,0,virus,1.0,6436.0\n-28,6436,MT752919.1,12,0,0,virus,1.0,6436.0\n-29,6395,HE818411.1,12,0,0,virus,1.0,6395.0\n-30,6355,EF469769.1,12,0,0,virus,1.0,6355.0\n-31,6226,LC125633.1,12,0,0,virus,1.0,6226.0\n-32,7466,MN504765.1,11,1,2,virus,0.786,5868.276\n-33,6383,MF002491.1,11,1,0,virus,0.917,5853.211\n-34,8361,MZ148109.1,11,5,0,virus,0.688,5752.3679999999995\n-35,5664,LT991639.1,11,0,0,virus,1.0,5664.0\n-36,6549,MT317167.1,11,2,0,virus,0.846,5540.454\n-37,7010,BK011046.1,11,3,0,virus,0.786,5509.860000000001\n-38,5266,MN497809.1,10,0,0,virus,1.0,5266.0\n-39,5078,KY769710.1,10,0,0,virus,1.0,5078.0\n-40,7377,KC847061.1,9,5,0,virus,0.643,4743.411\n-41,8434,KF030878.2,9,7,0,virus,0.562,4739.908\n-42,5398,MT892660.1,8,0,2,virus,0.8,4318.400000000001\n-43,4224,EF155982.1,8,0,0,virus,1.0,4224.0\n-44,4059,MN101211.1,8,0,0,virus,1.0,4059.0\n-45,8607,MW629381.1,7,10,0,plant,0.412,3546.084\n-46,3334,LC066453.1,6,0,0,virus,1.0,3334.0\n-47,3449,MN160358.1,5,1,0,virus,0.833,2873.017\n-48,2824,NC_015324.1,5,0,0,virus,1.0,2824.0\n-49,2797,JF909142.1,5,0,0,virus,1.0,2797.0\n-50,2789,JX025360.1,5,0,0,virus,1.0,2789.0\n-51,2781,MG250124.1,5,0,0,virus,1.0,2781.0\n-52,2781,KC106643.1,5,0,0,virus,1.0,2781.0\n-53,2781,KX024650.1,5,0,0,virus,1.0,2781.0\n-54,2778,GU180085.1,5,0,0,virus,1.0,2778.0\n-55,2773,LN846605.1,5,0,0,virus,1.0,2773.0\n-56,2768,JN604500.1,5,0,0,virus,1.0,2768.0\n-57,2767,KU569582.1,5,0,0,virus,1.0,2767.0\n-58,2762,FN554528.1,5,0,0,virus,1.0,2762.0\n-59,2761,MK757212.1,5,0,0,virus,1.0,2761.0\n-60,2761,NC_023312.1,5,0,0,virus,1.0,2761.0\n-61,2751,AJ558124.1,5,0,0,virus,1.0,2751.0\n-62,2750,KJ536097.1,5,0,0,virus,1.0,2750.0\n-63,2749,KJ473695.1,5,0,0,virus,1.0,2749.0\n-64,2743,MT298220.1,5,0,0,virus,1.0,2743.0\n-65,2741,KC019309.1,5,0,0,virus,1.0,2741.0\n-66,2739,JN082236.1,5,0,0,virus,1.0,2739.0\n-67,2738,MH577756.1,5,0,0,virus,1.0,2738.0\n-68,2738,MH577693.1,5,0,0,virus,1.0,2738.0\n-69,2738,AY184487.3,5,0,0,virus,1.0,2738.0\n-70,2737,MN630281.1,5,0,0,virus,1.0,2737.0\n-71,2736,KX302711.1,5,0,0,virus,1.0,2736.0\n-72,2732,AJ558125.1,5,0,0,virus,1.0,2732.0\n-73,2724,HE979787.1,5,0,0,virus,1.0,2724.0\n-74,3808,HM125550.1,5,0,2,virus,0.714,2718.912\n-75,2705,KM229922.1,5,0,0,virus,1.0,2705.0\n-76,2698,HQ264186.1,5,0,0,virus,1.0,2698.0\n-77,2693,MW426877.1,5,0,0,virus,1.0,2693.0\n-78,2690,MT592862.1,5,0,0,virus,1.0,2690.0\n-79,2662,BK010711.1,5,0,0,virus,1.0,2662.0\n-80,2659,NC_055586.1,5,0,0,virus,1.0,2659.0\n-81,2640,MW273384.1,5,0,0,virus,1.0,2640.0\n-82,2638,JX857691.1,5,0,0,virus,1.0,2638.0\n-83,3164,MH999327.1,5,1,0,virus,0.833,2635.612\n-84,2630,E'..b'1,3,0,0,virus,1.0,909.0\n-185,1200,GU904131.1,3,1,0,virus,0.75,900.0\n-186,900,EU196425.1,3,0,0,virus,1.0,900.0\n-187,894,MH974475.1,3,0,0,virus,1.0,894.0\n-188,885,MF773983.1,3,0,0,virus,1.0,885.0\n-189,873,KC985038.1,3,0,0,virus,1.0,873.0\n-190,872,MT656393.1,3,0,0,virus,1.0,872.0\n-191,872,MT656427.1,3,0,0,virus,1.0,872.0\n-192,871,KR076680.1,3,0,0,virus,1.0,871.0\n-193,867,DQ364987.1,3,0,0,virus,1.0,867.0\n-194,1419,AY366417.1,3,2,0,virus,0.6,851.4\n-195,849,HM768172.1,3,0,0,virus,1.0,849.0\n-196,1132,MK929579.1,3,1,0,virus,0.75,849.0\n-197,849,HM768183.1,3,0,0,virus,1.0,849.0\n-198,846,MN814413.1,3,0,0,virus,1.0,846.0\n-199,1410,AB457617.1,3,2,0,virus,0.6,846.0\n-200,837,KU743350.1,3,0,0,virus,1.0,837.0\n-201,1374,KJ789902.1,3,2,0,virus,0.6,824.4\n-202,1370,KY271069.1,3,2,0,virus,0.6,822.0\n-203,822,JQ361098.1,3,0,0,virus,1.0,822.0\n-204,821,MG717790.1,3,0,0,virus,1.0,821.0\n-205,1366,LN831969.1,3,2,0,virus,0.6,819.6\n-206,1086,KF710809.1,3,0,1,virus,0.75,814.5\n-207,1086,KF710849.1,3,0,1,virus,0.75,814.5\n-208,1086,KM607344.1,3,1,0,virus,0.75,814.5\n-209,810,JQ619096.1,3,0,0,virus,1.0,810.0\n-210,810,JQ619105.1,3,0,0,virus,1.0,810.0\n-211,1075,FJ859737.1,3,1,0,virus,0.75,806.25\n-212,803,KC282369.1,3,0,0,virus,1.0,803.0\n-213,801,JQ954315.1,3,0,0,virus,1.0,801.0\n-214,795,MN955028.1,3,0,0,virus,1.0,795.0\n-215,794,KX130921.1,3,0,0,virus,1.0,794.0\n-216,1058,FJ463044.1,3,1,0,virus,0.75,793.5\n-217,787,AM113814.1,3,0,0,virus,1.0,787.0\n-218,1048,KM607216.1,3,1,0,virus,0.75,786.0\n-219,1040,KM607230.1,3,1,0,virus,0.75,780.0\n-220,777,HM180089.1,3,0,0,virus,1.0,777.0\n-221,777,KJ494928.1,3,0,0,virus,1.0,777.0\n-222,777,KU297996.1,3,0,0,virus,1.0,777.0\n-223,776,MT037061.1,3,0,0,virus,1.0,776.0\n-224,1032,MH746956.1,3,1,0,virus,0.75,774.0\n-225,774,FR693101.1,3,0,0,virus,1.0,774.0\n-226,1028,KF711199.1,3,1,0,virus,0.75,771.0\n-227,771,KM275602.1,3,0,0,virus,1.0,771.0\n-228,1028,KF711263.1,3,1,0,virus,0.75,771.0\n-229,771,JF825866.1,3,0,0,virus,1.0,771.0\n-230,1264,KX119438.1,3,2,0,virus,0.6,758.4\n-231,751,KF156666.1,3,0,0,virus,1.0,751.0\n-232,999,FJ262095.1,2,1,0,virus,0.667,666.3330000000001\n-233,999,FJ262061.1,2,1,0,virus,0.667,666.3330000000001\n-234,976,LC465418.1,2,1,0,virus,0.667,650.9920000000001\n-235,956,KR065439.1,2,1,0,virus,0.667,637.652\n-236,917,MK445316.1,2,0,1,virus,0.667,611.639\n-237,1200,KJ849141.1,2,2,0,bacteria,0.5,600.0\n-238,890,HQ335265.1,2,1,0,virus,0.667,593.63\n-239,881,AJ884700.1,2,0,1,virus,0.667,587.6270000000001\n-240,1164,KP233027.1,2,1,1,virus,0.5,582.0\n-241,859,KF525380.1,2,1,0,virus,0.667,572.9530000000001\n-242,1421,AY839627.1,2,3,0,plant,0.4,568.4\n-243,836,LC223336.1,2,0,1,virus,0.667,557.6120000000001\n-244,1372,MH643738.1,2,3,0,plant,0.4,548.8000000000001\n-245,1365,MN240344.1,2,3,0,plant,0.4,546.0\n-246,1342,FN806780.1,2,3,0,plant,0.4,536.8000000000001\n-247,1061,KM607850.1,2,1,1,virus,0.5,530.5\n-248,1060,KM607802.1,2,2,0,bacteria,0.5,530.0\n-249,784,AM494507.1,2,1,0,virus,0.667,522.928\n-250,1037,KM607814.1,2,1,1,virus,0.5,518.5\n-251,1035,KY473725.1,2,2,0,bacteria,0.5,517.5\n-252,768,MH182699.1,2,1,0,virus,0.667,512.2560000000001\n-253,1023,JF828185.1,2,2,0,bacteria,0.5,511.5\n-254,756,MH686308.1,2,0,1,virus,0.667,504.252\n-255,1003,KX431385.1,2,2,0,bacteria,0.5,501.5\n-256,975,KP866939.1,1,0,2,bacteria,0.333,324.675\n-257,960,KF010516.1,1,0,2,bacteria,0.333,319.68\n-258,945,KX418448.1,1,2,0,plant,0.333,314.685\n-259,942,JF795548.1,1,2,0,plant,0.333,313.68600000000004\n-260,939,KP232980.1,1,0,2,bacteria,0.333,312.687\n-261,1369,KM880104.1,1,4,0,plant,0.2,273.8\n-262,1367,LT600712.1,1,4,0,plant,0.2,273.40000000000003\n-263,1083,KM607376.1,1,2,1,plant,0.25,270.75\n-264,1346,LT674474.1,1,4,0,plant,0.2,269.2\n-265,756,MW519386.1,1,2,0,plant,0.333,251.74800000000002\n-266,1256,AM041944.1,1,4,0,plant,0.2,251.20000000000002\n-267,1179,AJ493270.1,0,4,0,plant,0.0,0.0\n-268,833,MK876224.1,0,3,0,plant,0.0,0.0\n-269,1216,AB697885.1,0,4,0,plant,0.0,0.0\n-270,822,MF043148.1,0,0,3,bacteria,0.0,0.0\n-271,960,KC969470.1,0,3,0,plant,0.0,0.0\n-272,756,MW519383.1,0,3,0,plant,0.0,0.0\n' 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| diff -r ea2cccb9f73e -r 302332b914ef test-data/predicted.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/predicted.tsv Sat Jan 14 21:08:33 2023 +0000 |
| b |
| b'@@ -0,0 +1,274 @@\n+\tlength\tid\t# viral fragments\t# plant fragments\t# bacterial fragments\tdecision\t# viral / # total\t# viral / # total * length\n+0\t19251\tKY110737.1\t30\t2\t6\tvirus\t0.789\t15189.039\n+1\t18478\tKY707825.2\t24\t3\t9\tvirus\t0.667\t12324.826000000001\n+2\t10427\tAM267479.1\t20\t0\t0\tvirus\t1.0\t10427.0\n+3\t9802\tMT533611.1\t19\t0\t0\tvirus\t1.0\t9802.0\n+4\t9798\tLC537538.1\t19\t0\t0\tvirus\t1.0\t9798.0\n+5\t9736\tLC600465.1\t19\t0\t0\tvirus\t1.0\t9736.0\n+6\t9736\tLC494681.1\t19\t0\t0\tvirus\t1.0\t9736.0\n+7\t9445\tJN936438.1\t18\t0\t0\tvirus\t1.0\t9445.0\n+8\t11892\tLC602461.1\t18\t5\t0\tvirus\t0.783\t9311.436\n+9\t9757\tMK777994.1\t18\t1\t0\tvirus\t0.947\t9239.878999999999\n+10\t9663\tLC038073.1\t18\t1\t0\tvirus\t0.947\t9150.860999999999\n+11\t9429\tMK649741.1\t17\t1\t0\tvirus\t0.944\t8900.975999999999\n+12\t9798\tLC537503.1\t17\t0\t2\tvirus\t0.895\t8769.210000000001\n+13\t8421\tMN059369.1\t16\t0\t0\tvirus\t1.0\t8421.0\n+14\t9798\tAB747297.1\t16\t0\t3\tvirus\t0.842\t8249.916\n+15\t8745\tNC_008169.1\t16\t0\t1\tvirus\t0.941\t8229.045\n+16\t10487\tKX884756.1\t15\t5\t0\tvirus\t0.75\t7865.25\n+17\t9287\tMZ148041.1\t15\t3\t0\tvirus\t0.833\t7736.071\n+18\t8745\tMT554537.1\t15\t0\t2\tvirus\t0.882\t7713.09\n+19\t8366\tMN059208.1\t14\t1\t1\tvirus\t0.875\t7320.25\n+20\t7242\tAJ534983.1\t14\t0\t0\tvirus\t1.0\t7242.0\n+21\t7702\tKX008574.1\t14\t1\t0\tvirus\t0.933\t7185.966\n+22\t8644\tMN059273.1\t14\t0\t3\tvirus\t0.824\t7122.656\n+23\t7343\tKX034904.1\t13\t1\t0\tvirus\t0.929\t6821.647\n+24\t7341\tKX034878.1\t13\t1\t0\tvirus\t0.929\t6819.789000000001\n+25\t6791\tJN710440.1\t13\t0\t0\tvirus\t1.0\t6791.0\n+26\t6436\tMT752813.1\t12\t0\t0\tvirus\t1.0\t6436.0\n+27\t6436\tMT752690.1\t12\t0\t0\tvirus\t1.0\t6436.0\n+28\t6436\tMT752919.1\t12\t0\t0\tvirus\t1.0\t6436.0\n+29\t6395\tHE818411.1\t12\t0\t0\tvirus\t1.0\t6395.0\n+30\t6355\tEF469769.1\t12\t0\t0\tvirus\t1.0\t6355.0\n+31\t6226\tLC125633.1\t12\t0\t0\tvirus\t1.0\t6226.0\n+32\t7466\tMN504765.1\t11\t1\t2\tvirus\t0.786\t5868.276\n+33\t6383\tMF002491.1\t11\t1\t0\tvirus\t0.917\t5853.211\n+34\t8361\tMZ148109.1\t11\t5\t0\tvirus\t0.688\t5752.3679999999995\n+35\t5664\tLT991639.1\t11\t0\t0\tvirus\t1.0\t5664.0\n+36\t6549\tMT317167.1\t11\t2\t0\tvirus\t0.846\t5540.454\n+37\t7010\tBK011046.1\t11\t3\t0\tvirus\t0.786\t5509.860000000001\n+38\t5266\tMN497809.1\t10\t0\t0\tvirus\t1.0\t5266.0\n+39\t5078\tKY769710.1\t10\t0\t0\tvirus\t1.0\t5078.0\n+40\t7377\tKC847061.1\t9\t5\t0\tvirus\t0.643\t4743.411\n+41\t8434\tKF030878.2\t9\t7\t0\tvirus\t0.562\t4739.908\n+42\t5398\tMT892660.1\t8\t0\t2\tvirus\t0.8\t4318.400000000001\n+43\t4224\tEF155982.1\t8\t0\t0\tvirus\t1.0\t4224.0\n+44\t4059\tMN101211.1\t8\t0\t0\tvirus\t1.0\t4059.0\n+45\t8607\tMW629381.1\t7\t10\t0\tplant\t0.412\t3546.084\n+46\t3334\tLC066453.1\t6\t0\t0\tvirus\t1.0\t3334.0\n+47\t3449\tMN160358.1\t5\t1\t0\tvirus\t0.833\t2873.017\n+48\t2824\tNC_015324.1\t5\t0\t0\tvirus\t1.0\t2824.0\n+49\t2797\tJF909142.1\t5\t0\t0\tvirus\t1.0\t2797.0\n+50\t2789\tJX025360.1\t5\t0\t0\tvirus\t1.0\t2789.0\n+51\t2781\tMG250124.1\t5\t0\t0\tvirus\t1.0\t2781.0\n+52\t2781\tKC106643.1\t5\t0\t0\tvirus\t1.0\t2781.0\n+53\t2781\tKX024650.1\t5\t0\t0\tvirus\t1.0\t2781.0\n+54\t2778\tGU180085.1\t5\t0\t0\tvirus\t1.0\t2778.0\n+55\t2773\tLN846605.1\t5\t0\t0\tvirus\t1.0\t2773.0\n+56\t2768\tJN604500.1\t5\t0\t0\tvirus\t1.0\t2768.0\n+57\t2767\tKU569582.1\t5\t0\t0\tvirus\t1.0\t2767.0\n+58\t2762\tFN554528.1\t5\t0\t0\tvirus\t1.0\t2762.0\n+59\t2761\tMK757212.1\t5\t0\t0\tvirus\t1.0\t2761.0\n+60\t2761\tNC_023312.1\t5\t0\t0\tvirus\t1.0\t2761.0\n+61\t2751\tAJ558124.1\t5\t0\t0\tvirus\t1.0\t2751.0\n+62\t2750\tKJ536097.1\t5\t0\t0\tvirus\t1.0\t2750.0\n+63\t2749\tKJ473695.1\t5\t0\t0\tvirus\t1.0\t2749.0\n+64\t2743\tMT298220.1\t5\t0\t0\tvirus\t1.0\t2743.0\n+65\t2741\tKC019309.1\t5\t0\t0\tvirus\t1.0\t2741.0\n+66\t2739\tJN082236.1\t5\t0\t0\tvirus\t1.0\t2739.0\n+67\t2738\tMH577756.1\t5\t0\t0\tvirus\t1.0\t2738.0\n+68\t2738\tMH577693.1\t5\t0\t0\tvirus\t1.0\t2738.0\n+69\t2738\tAY184487.3\t5\t0\t0\tvirus\t1.0\t2738.0\n+70\t2737\tMN630281.1\t5\t0\t0\tvirus\t1.0\t2737.0\n+71\t2736\tKX302711.1\t5\t0\t0\tvirus\t1.0\t2736.0\n+72\t2732\tAJ558125.1\t5\t0\t0\tvirus\t1.0\t2732.0\n+73\t2724\tHE979787.1\t5\t0\t0\tvirus\t1.0\t2724.0\n+74\t3808\tHM125550.1\t5\t0\t2\tvirus\t0.714\t2718.912\n+75\t2705\tKM229922.1\t5\t0\t0\tvirus\t1.0\t2705.0\n+76\t2698\tHQ264186.1\t5\t0\t0\tvirus\t1.0\t2698.0\n+77\t2693\tMW426877.1\t5\t0\t0\tvirus\t1.0\t2693.0\n+78\t2690\tMT592862.1\t5\t0\t0\tvirus\t1.0\t2690.0\n+79\t2662\tBK010711.1\t5\t0\t0\tvirus\t1.0\t2662.0\n+80\t2659\tNC_055586.1\t5\t0\t0\tvirus\t1.0\t2659.0\n+81\t2640\tMW273384.1\t5\t0\t0\tvirus\t1.0\t2640.0\n+82\t2638\tJX857691.1\t5\t0\t0\tvirus\t1.0\t2638.0\n+83\t3164\tMH999327.1\t5\t1\t0\tvirus\t0.833\t2635.612\n+84\t2630\tE'..b'1\t3\t0\t0\tvirus\t1.0\t909.0\n+185\t1200\tGU904131.1\t3\t1\t0\tvirus\t0.75\t900.0\n+186\t900\tEU196425.1\t3\t0\t0\tvirus\t1.0\t900.0\n+187\t894\tMH974475.1\t3\t0\t0\tvirus\t1.0\t894.0\n+188\t885\tMF773983.1\t3\t0\t0\tvirus\t1.0\t885.0\n+189\t873\tKC985038.1\t3\t0\t0\tvirus\t1.0\t873.0\n+190\t872\tMT656393.1\t3\t0\t0\tvirus\t1.0\t872.0\n+191\t872\tMT656427.1\t3\t0\t0\tvirus\t1.0\t872.0\n+192\t871\tKR076680.1\t3\t0\t0\tvirus\t1.0\t871.0\n+193\t867\tDQ364987.1\t3\t0\t0\tvirus\t1.0\t867.0\n+194\t1419\tAY366417.1\t3\t2\t0\tvirus\t0.6\t851.4\n+195\t849\tHM768172.1\t3\t0\t0\tvirus\t1.0\t849.0\n+196\t1132\tMK929579.1\t3\t1\t0\tvirus\t0.75\t849.0\n+197\t849\tHM768183.1\t3\t0\t0\tvirus\t1.0\t849.0\n+198\t846\tMN814413.1\t3\t0\t0\tvirus\t1.0\t846.0\n+199\t1410\tAB457617.1\t3\t2\t0\tvirus\t0.6\t846.0\n+200\t837\tKU743350.1\t3\t0\t0\tvirus\t1.0\t837.0\n+201\t1374\tKJ789902.1\t3\t2\t0\tvirus\t0.6\t824.4\n+202\t1370\tKY271069.1\t3\t2\t0\tvirus\t0.6\t822.0\n+203\t822\tJQ361098.1\t3\t0\t0\tvirus\t1.0\t822.0\n+204\t821\tMG717790.1\t3\t0\t0\tvirus\t1.0\t821.0\n+205\t1366\tLN831969.1\t3\t2\t0\tvirus\t0.6\t819.6\n+206\t1086\tKF710809.1\t3\t0\t1\tvirus\t0.75\t814.5\n+207\t1086\tKF710849.1\t3\t0\t1\tvirus\t0.75\t814.5\n+208\t1086\tKM607344.1\t3\t1\t0\tvirus\t0.75\t814.5\n+209\t810\tJQ619096.1\t3\t0\t0\tvirus\t1.0\t810.0\n+210\t810\tJQ619105.1\t3\t0\t0\tvirus\t1.0\t810.0\n+211\t1075\tFJ859737.1\t3\t1\t0\tvirus\t0.75\t806.25\n+212\t803\tKC282369.1\t3\t0\t0\tvirus\t1.0\t803.0\n+213\t801\tJQ954315.1\t3\t0\t0\tvirus\t1.0\t801.0\n+214\t795\tMN955028.1\t3\t0\t0\tvirus\t1.0\t795.0\n+215\t794\tKX130921.1\t3\t0\t0\tvirus\t1.0\t794.0\n+216\t1058\tFJ463044.1\t3\t1\t0\tvirus\t0.75\t793.5\n+217\t787\tAM113814.1\t3\t0\t0\tvirus\t1.0\t787.0\n+218\t1048\tKM607216.1\t3\t1\t0\tvirus\t0.75\t786.0\n+219\t1040\tKM607230.1\t3\t1\t0\tvirus\t0.75\t780.0\n+220\t777\tHM180089.1\t3\t0\t0\tvirus\t1.0\t777.0\n+221\t777\tKJ494928.1\t3\t0\t0\tvirus\t1.0\t777.0\n+222\t777\tKU297996.1\t3\t0\t0\tvirus\t1.0\t777.0\n+223\t776\tMT037061.1\t3\t0\t0\tvirus\t1.0\t776.0\n+224\t1032\tMH746956.1\t3\t1\t0\tvirus\t0.75\t774.0\n+225\t774\tFR693101.1\t3\t0\t0\tvirus\t1.0\t774.0\n+226\t1028\tKF711199.1\t3\t1\t0\tvirus\t0.75\t771.0\n+227\t771\tKM275602.1\t3\t0\t0\tvirus\t1.0\t771.0\n+228\t1028\tKF711263.1\t3\t1\t0\tvirus\t0.75\t771.0\n+229\t771\tJF825866.1\t3\t0\t0\tvirus\t1.0\t771.0\n+230\t1264\tKX119438.1\t3\t2\t0\tvirus\t0.6\t758.4\n+231\t751\tKF156666.1\t3\t0\t0\tvirus\t1.0\t751.0\n+232\t999\tFJ262095.1\t2\t1\t0\tvirus\t0.667\t666.3330000000001\n+233\t999\tFJ262061.1\t2\t1\t0\tvirus\t0.667\t666.3330000000001\n+234\t976\tLC465418.1\t2\t1\t0\tvirus\t0.667\t650.9920000000001\n+235\t956\tKR065439.1\t2\t1\t0\tvirus\t0.667\t637.652\n+236\t917\tMK445316.1\t2\t0\t1\tvirus\t0.667\t611.639\n+237\t1200\tKJ849141.1\t2\t2\t0\tbacteria\t0.5\t600.0\n+238\t890\tHQ335265.1\t2\t1\t0\tvirus\t0.667\t593.63\n+239\t881\tAJ884700.1\t2\t0\t1\tvirus\t0.667\t587.6270000000001\n+240\t1164\tKP233027.1\t2\t1\t1\tvirus\t0.5\t582.0\n+241\t859\tKF525380.1\t2\t1\t0\tvirus\t0.667\t572.9530000000001\n+242\t1421\tAY839627.1\t2\t3\t0\tplant\t0.4\t568.4\n+243\t836\tLC223336.1\t2\t0\t1\tvirus\t0.667\t557.6120000000001\n+244\t1372\tMH643738.1\t2\t3\t0\tplant\t0.4\t548.8000000000001\n+245\t1365\tMN240344.1\t2\t3\t0\tplant\t0.4\t546.0\n+246\t1342\tFN806780.1\t2\t3\t0\tplant\t0.4\t536.8000000000001\n+247\t1061\tKM607850.1\t2\t1\t1\tvirus\t0.5\t530.5\n+248\t1060\tKM607802.1\t2\t2\t0\tbacteria\t0.5\t530.0\n+249\t784\tAM494507.1\t2\t1\t0\tvirus\t0.667\t522.928\n+250\t1037\tKM607814.1\t2\t1\t1\tvirus\t0.5\t518.5\n+251\t1035\tKY473725.1\t2\t2\t0\tbacteria\t0.5\t517.5\n+252\t768\tMH182699.1\t2\t1\t0\tvirus\t0.667\t512.2560000000001\n+253\t1023\tJF828185.1\t2\t2\t0\tbacteria\t0.5\t511.5\n+254\t756\tMH686308.1\t2\t0\t1\tvirus\t0.667\t504.252\n+255\t1003\tKX431385.1\t2\t2\t0\tbacteria\t0.5\t501.5\n+256\t975\tKP866939.1\t1\t0\t2\tbacteria\t0.333\t324.675\n+257\t960\tKF010516.1\t1\t0\t2\tbacteria\t0.333\t319.68\n+258\t945\tKX418448.1\t1\t2\t0\tplant\t0.333\t314.685\n+259\t942\tJF795548.1\t1\t2\t0\tplant\t0.333\t313.68600000000004\n+260\t939\tKP232980.1\t1\t0\t2\tbacteria\t0.333\t312.687\n+261\t1369\tKM880104.1\t1\t4\t0\tplant\t0.2\t273.8\n+262\t1367\tLT600712.1\t1\t4\t0\tplant\t0.2\t273.40000000000003\n+263\t1083\tKM607376.1\t1\t2\t1\tplant\t0.25\t270.75\n+264\t1346\tLT674474.1\t1\t4\t0\tplant\t0.2\t269.2\n+265\t756\tMW519386.1\t1\t2\t0\tplant\t0.333\t251.74800000000002\n+266\t1256\tAM041944.1\t1\t4\t0\tplant\t0.2\t251.20000000000002\n+267\t1179\tAJ493270.1\t0\t4\t0\tplant\t0.0\t0.0\n+268\t833\tMK876224.1\t0\t3\t0\tplant\t0.0\t0.0\n+269\t1216\tAB697885.1\t0\t4\t0\tplant\t0.0\t0.0\n+270\t822\tMF043148.1\t0\t0\t3\tbacteria\t0.0\t0.0\n+271\t960\tKC969470.1\t0\t3\t0\tplant\t0.0\t0.0\n+272\t756\tMW519383.1\t0\t3\t0\tplant\t0.0\t0.0\n' |
| b |
| diff -r ea2cccb9f73e -r 302332b914ef test-data/predicted_fragments.csv --- a/test-data/predicted_fragments.csv Thu Jan 05 14:27:54 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1730 +0,0 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|
| b |
| diff -r ea2cccb9f73e -r 302332b914ef test-data/predicted_fragments.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/predicted_fragments.tsv Sat Jan 14 21:08:33 2023 +0000 |
| b |
| b'@@ -0,0 +1,1730 @@\n+\tid\tlength\tfragment\tpred_plant_5\tpred_vir_5\tpred_bact_5\tpred_plant_7\tpred_vir_7\tpred_bact_7\tRF_decision\tRF_pred_plant\tRF_pred_vir\tRF_pred_bact\n+0\tMT921846.1\t2971\t0\t0.716\t0.252\t0.032\t0.129\t0.799\t0.072\tvirus\t0.19\t0.782\t0.028\n+1\tMT921846.1\t2971\t1\t0.681\t0.287\t0.033\t0.263\t0.684\t0.053\tvirus\t0.221\t0.772\t0.007\n+2\tMT921846.1\t2971\t2\t0.741\t0.224\t0.036\t0.789\t0.181\t0.029\tplant\t0.878\t0.065\t0.057\n+3\tMT921846.1\t2971\t3\t0.754\t0.208\t0.038\t0.783\t0.154\t0.063\tplant\t0.878\t0.065\t0.057\n+4\tMT921846.1\t2971\t4\t0.513\t0.414\t0.073\t0.269\t0.601\t0.13\tvirus\t0.324\t0.584\t0.091\n+5\tMF540775.1\t3929\t0\t0.896\t0.093\t0.011\t0.884\t0.112\t0.004\tplant\t0.855\t0.028\t0.117\n+6\tMF540775.1\t3929\t1\t0.843\t0.14\t0.016\t0.806\t0.186\t0.009\tplant\t0.85\t0.053\t0.098\n+7\tMF540775.1\t3929\t2\t0.879\t0.108\t0.013\t0.765\t0.211\t0.024\tplant\t0.705\t0.039\t0.256\n+8\tMF540775.1\t3929\t3\t0.824\t0.158\t0.017\t0.698\t0.257\t0.045\tplant\t0.804\t0.129\t0.066\n+9\tMF540775.1\t3929\t4\t0.748\t0.223\t0.029\t0.562\t0.38\t0.058\tplant\t0.765\t0.136\t0.099\n+10\tMF540775.1\t3929\t5\t0.836\t0.15\t0.015\t0.675\t0.31\t0.015\tplant\t0.804\t0.129\t0.066\n+11\tMF540775.1\t3929\t6\t0.857\t0.129\t0.015\t0.584\t0.398\t0.018\tplant\t0.753\t0.162\t0.085\n+12\tBK011046.1\t7010\t0\t0.526\t0.424\t0.05\t0.221\t0.728\t0.051\tvirus\t0.303\t0.692\t0.004\n+13\tBK011046.1\t7010\t1\t0.464\t0.486\t0.05\t0.243\t0.707\t0.05\tvirus\t0.28\t0.713\t0.007\n+14\tBK011046.1\t7010\t2\t0.282\t0.605\t0.112\t0.181\t0.702\t0.117\tvirus\t0.04\t0.919\t0.041\n+15\tBK011046.1\t7010\t3\t0.315\t0.585\t0.1\t0.343\t0.632\t0.025\tvirus\t0.424\t0.543\t0.032\n+16\tBK011046.1\t7010\t4\t0.539\t0.413\t0.048\t0.561\t0.435\t0.004\tplant\t0.855\t0.093\t0.052\n+17\tBK011046.1\t7010\t5\t0.449\t0.477\t0.075\t0.423\t0.555\t0.022\tplant\t0.602\t0.327\t0.071\n+18\tBK011046.1\t7010\t6\t0.442\t0.482\t0.076\t0.398\t0.571\t0.031\tplant\t0.565\t0.347\t0.088\n+19\tBK011046.1\t7010\t7\t0.392\t0.493\t0.115\t0.189\t0.745\t0.065\tvirus\t0.103\t0.883\t0.013\n+20\tBK011046.1\t7010\t8\t0.506\t0.396\t0.098\t0.203\t0.717\t0.08\tvirus\t0.316\t0.671\t0.013\n+21\tBK011046.1\t7010\t9\t0.427\t0.49\t0.083\t0.177\t0.731\t0.092\tvirus\t0.152\t0.829\t0.019\n+22\tBK011046.1\t7010\t10\t0.389\t0.509\t0.101\t0.26\t0.672\t0.067\tvirus\t0.233\t0.759\t0.008\n+23\tBK011046.1\t7010\t11\t0.224\t0.642\t0.134\t0.115\t0.791\t0.094\tvirus\t0.034\t0.951\t0.014\n+24\tBK011046.1\t7010\t12\t0.267\t0.598\t0.135\t0.156\t0.72\t0.125\tvirus\t0.04\t0.919\t0.041\n+25\tBK011046.1\t7010\t13\t0.253\t0.607\t0.139\t0.161\t0.711\t0.128\tvirus\t0.04\t0.919\t0.041\n+26\tNC_055544.1\t2626\t0\t0.098\t0.568\t0.334\t0.033\t0.855\t0.112\tvirus\t0.026\t0.96\t0.013\n+27\tNC_055544.1\t2626\t1\t0.214\t0.687\t0.099\t0.06\t0.893\t0.047\tvirus\t0.029\t0.957\t0.014\n+28\tNC_055544.1\t2626\t2\t0.208\t0.713\t0.079\t0.045\t0.93\t0.024\tvirus\t0.029\t0.957\t0.014\n+29\tNC_055544.1\t2626\t3\t0.262\t0.625\t0.113\t0.04\t0.886\t0.074\tvirus\t0.029\t0.957\t0.014\n+30\tNC_055544.1\t2626\t4\t0.322\t0.6\t0.078\t0.065\t0.908\t0.027\tvirus\t0.041\t0.946\t0.013\n+31\tJX857691.1\t2638\t0\t0.146\t0.588\t0.266\t0.066\t0.892\t0.042\tvirus\t0.033\t0.952\t0.014\n+32\tJX857691.1\t2638\t1\t0.334\t0.606\t0.06\t0.119\t0.866\t0.015\tvirus\t0.047\t0.94\t0.013\n+33\tJX857691.1\t2638\t2\t0.149\t0.757\t0.095\t0.077\t0.904\t0.018\tvirus\t0.033\t0.952\t0.014\n+34\tJX857691.1\t2638\t3\t0.169\t0.663\t0.168\t0.067\t0.828\t0.106\tvirus\t0.034\t0.949\t0.017\n+35\tJX857691.1\t2638\t4\t0.274\t0.611\t0.115\t0.112\t0.869\t0.019\tvirus\t0.034\t0.951\t0.014\n+36\tLC125633.1\t6226\t0\t0.111\t0.533\t0.356\t0.078\t0.839\t0.083\tvirus\t0.044\t0.924\t0.032\n+37\tLC125633.1\t6226\t1\t0.236\t0.645\t0.119\t0.144\t0.821\t0.035\tvirus\t0.034\t0.951\t0.014\n+38\tLC125633.1\t6226\t2\t0.134\t0.606\t0.26\t0.14\t0.825\t0.035\tvirus\t0.039\t0.946\t0.014\n+39\tLC125633.1\t6226\t3\t0.233\t0.581\t0.186\t0.103\t0.841\t0.055\tvirus\t0.034\t0.949\t0.017\n+40\tLC125633.1\t6226\t4\t0.202\t0.631\t0.167\t0.069\t0.85\t0.081\tvirus\t0.029\t0.957\t0.014\n+41\tLC125633.1\t6226\t5\t0.191\t0.593\t0.216\t0.202\t0.736\t0.062\tvirus\t0.209\t0.779\t0.012\n+42\tLC125633.1\t6226\t6\t0.345\t0.54\t0.115\t0.314\t0.629\t0.057\tvirus\t0.232\t0.704\t0.064\n+43\tLC125633.1\t6226\t7\t0.07\t0.424\t0.507\t0.046\t0.702\t0.252\tvirus\t0.066\t0.79\t0.144\n+44\tLC125633.1\t6226\t8\t0.068\t0.478\t0.454\t0.025\t0.677\t0.298\tvirus\t0.04\t0.88\t0.081\n+45\tLC125633.1\t6226\t9\t0.136\t0.399\t0.465\t0.122\t0.845\t0.033\tvirus\t0.084\t0.885\t0.031\n+46\tLC125633.1\t6226\t10\t0.068\t0.435\t0.498\t0.127\t0.777\t0.097\tvirus\t0.058\t0.856\t0.087\n+47\tLC125633.1\t622'..b'virus\t0.015\t0.975\t0.01\n+1681\tKC007531.1\t1293\t4\t0.056\t0.928\t0.016\t0.147\t0.849\t0.004\tvirus\t0.013\t0.983\t0.004\n+1682\tMK098183.1\t1350\t0\t0.112\t0.866\t0.021\t0.218\t0.767\t0.015\tvirus\t0.036\t0.937\t0.027\n+1683\tMK098183.1\t1350\t1\t0.081\t0.914\t0.005\t0.132\t0.866\t0.002\tvirus\t0.007\t0.982\t0.012\n+1684\tMK098183.1\t1350\t2\t0.29\t0.698\t0.012\t0.676\t0.315\t0.009\tplant\t0.637\t0.307\t0.056\n+1685\tMK098183.1\t1350\t3\t0.152\t0.842\t0.006\t0.342\t0.63\t0.028\tvirus\t0.273\t0.627\t0.1\n+1686\tMK098183.1\t1350\t4\t0.069\t0.924\t0.006\t0.307\t0.67\t0.023\tvirus\t0.154\t0.815\t0.03\n+1687\tMN814413.1\t846\t0\t0.093\t0.864\t0.043\t0.112\t0.839\t0.05\tvirus\t0.015\t0.973\t0.012\n+1688\tMN814413.1\t846\t1\t0.264\t0.72\t0.015\t0.051\t0.938\t0.011\tvirus\t0.105\t0.862\t0.033\n+1689\tMN814413.1\t846\t2\t0.192\t0.802\t0.005\t0.056\t0.939\t0.005\tvirus\t0.022\t0.968\t0.01\n+1690\tFJ859737.1\t1075\t0\t0.136\t0.271\t0.593\t0.231\t0.534\t0.235\tvirus\t0.176\t0.606\t0.217\n+1691\tFJ859737.1\t1075\t1\t0.34\t0.637\t0.023\t0.261\t0.728\t0.011\tvirus\t0.28\t0.707\t0.012\n+1692\tFJ859737.1\t1075\t2\t0.176\t0.812\t0.011\t0.439\t0.553\t0.008\tplant\t0.514\t0.478\t0.008\n+1693\tFJ859737.1\t1075\t3\t0.101\t0.892\t0.007\t0.191\t0.806\t0.003\tvirus\t0.033\t0.952\t0.015\n+1694\tKX420987.1\t938\t0\t0.028\t0.967\t0.005\t0.047\t0.946\t0.007\tvirus\t0.003\t0.995\t0.002\n+1695\tKX420987.1\t938\t1\t0.024\t0.963\t0.013\t0.031\t0.94\t0.029\tvirus\t0.003\t0.987\t0.01\n+1696\tKX420987.1\t938\t2\t0.045\t0.889\t0.065\t0.06\t0.871\t0.069\tvirus\t0.005\t0.987\t0.008\n+1697\tKX418448.1\t945\t0\t0.506\t0.482\t0.012\t0.326\t0.669\t0.005\tvirus\t0.417\t0.56\t0.023\n+1698\tKX418448.1\t945\t1\t0.7\t0.295\t0.005\t0.808\t0.191\t0.001\tplant\t0.811\t0.126\t0.063\n+1699\tKX418448.1\t945\t2\t0.349\t0.646\t0.005\t0.666\t0.332\t0.002\tplant\t0.663\t0.312\t0.026\n+1700\tKC985038.1\t873\t0\t0.12\t0.796\t0.084\t0.414\t0.503\t0.083\tvirus\t0.459\t0.479\t0.062\n+1701\tKC985038.1\t873\t1\t0.038\t0.919\t0.043\t0.129\t0.858\t0.012\tvirus\t0.013\t0.983\t0.004\n+1702\tKC985038.1\t873\t2\t0.024\t0.968\t0.008\t0.049\t0.949\t0.002\tvirus\t0.003\t0.995\t0.002\n+1703\tMN955028.1\t795\t0\t0.063\t0.896\t0.041\t0.072\t0.769\t0.159\tvirus\t0.026\t0.966\t0.008\n+1704\tMN955028.1\t795\t1\t0.102\t0.863\t0.035\t0.083\t0.902\t0.016\tvirus\t0.007\t0.985\t0.008\n+1705\tMN955028.1\t795\t2\t0.095\t0.879\t0.027\t0.088\t0.899\t0.013\tvirus\t0.007\t0.982\t0.012\n+1706\tKC466374.1\t1075\t0\t0.227\t0.745\t0.028\t0.164\t0.742\t0.094\tvirus\t0.08\t0.88\t0.04\n+1707\tKC466374.1\t1075\t1\t0.182\t0.809\t0.01\t0.176\t0.819\t0.005\tvirus\t0.027\t0.954\t0.019\n+1708\tKC466374.1\t1075\t2\t0.141\t0.849\t0.01\t0.33\t0.663\t0.007\tvirus\t0.18\t0.792\t0.028\n+1709\tKC466374.1\t1075\t3\t0.129\t0.867\t0.004\t0.216\t0.782\t0.003\tvirus\t0.037\t0.949\t0.015\n+1710\tHM035070.1\t920\t0\t0.221\t0.767\t0.012\t0.463\t0.531\t0.006\tvirus\t0.375\t0.606\t0.018\n+1711\tHM035070.1\t920\t1\t0.092\t0.866\t0.042\t0.109\t0.872\t0.019\tvirus\t0.007\t0.982\t0.012\n+1712\tHM035070.1\t920\t2\t0.125\t0.846\t0.03\t0.273\t0.707\t0.02\tvirus\t0.14\t0.845\t0.015\n+1713\tKF711199.1\t1028\t0\t0.06\t0.916\t0.024\t0.063\t0.925\t0.012\tvirus\t0.005\t0.987\t0.008\n+1714\tKF711199.1\t1028\t1\t0.101\t0.897\t0.003\t0.155\t0.844\t0.001\tvirus\t0.007\t0.985\t0.008\n+1715\tKF711199.1\t1028\t2\t0.283\t0.713\t0.005\t0.634\t0.363\t0.003\tplant\t0.646\t0.29\t0.064\n+1716\tKF711199.1\t1028\t3\t0.179\t0.817\t0.004\t0.454\t0.542\t0.004\tvirus\t0.478\t0.509\t0.013\n+1717\tJF828185.1\t1023\t0\t0.376\t0.525\t0.099\t0.513\t0.422\t0.065\tplant\t0.587\t0.391\t0.022\n+1718\tJF828185.1\t1023\t1\t0.624\t0.212\t0.163\t0.498\t0.337\t0.165\tplant\t0.545\t0.306\t0.149\n+1719\tJF828185.1\t1023\t2\t0.21\t0.441\t0.349\t0.274\t0.624\t0.102\tvirus\t0.193\t0.582\t0.225\n+1720\tJF828185.1\t1023\t3\t0.166\t0.531\t0.303\t0.275\t0.631\t0.094\tvirus\t0.26\t0.515\t0.225\n+1721\tMN901875.1\t1151\t0\t0.127\t0.676\t0.197\t0.152\t0.698\t0.15\tvirus\t0.128\t0.815\t0.057\n+1722\tMN901875.1\t1151\t1\t0.202\t0.775\t0.023\t0.082\t0.894\t0.024\tvirus\t0.024\t0.964\t0.012\n+1723\tMN901875.1\t1151\t2\t0.035\t0.958\t0.007\t0.039\t0.905\t0.056\tvirus\t0.003\t0.995\t0.002\n+1724\tMN901875.1\t1151\t3\t0.025\t0.966\t0.009\t0.042\t0.936\t0.022\tvirus\t0.003\t0.995\t0.002\n+1725\tMN167135.1\t1139\t0\t0.046\t0.855\t0.098\t0.279\t0.38\t0.342\tvirus\t0.172\t0.42\t0.408\n+1726\tMN167135.1\t1139\t1\t0.072\t0.9\t0.028\t0.201\t0.729\t0.07\tvirus\t0.029\t0.949\t0.022\n+1727\tMN167135.1\t1139\t2\t0.061\t0.916\t0.024\t0.215\t0.779\t0.006\tvirus\t0.027\t0.951\t0.022\n+1728\tMN167135.1\t1139\t3\t0.117\t0.877\t0.006\t0.314\t0.684\t0.002\tvirus\t0.082\t0.889\t0.029\n' |
| b |
| diff -r ea2cccb9f73e -r 302332b914ef virhunter.xml --- a/virhunter.xml Thu Jan 05 14:27:54 2023 +0000 +++ b/virhunter.xml Sat Jan 14 21:08:33 2023 +0000 |
| b |
| @@ -18,8 +18,8 @@ --out_path '${predicted_fragments.extra_files_path}' --return_viral True --limit $limit - && cp '${predicted_fragments.extra_files_path}'/predicted_fragments.csv predicted_fragments.csv - && cp '${predicted_fragments.extra_files_path}'/predicted.csv predicted.csv + && cp '${predicted_fragments.extra_files_path}'/predicted_fragments.tsv predicted_fragments.tsv + && cp '${predicted_fragments.extra_files_path}'/predicted.tsv predicted.tsv && cp '${predicted_fragments.extra_files_path}'/viral.fasta viral.fasta ]]></command> @@ -33,16 +33,16 @@ <param argument="--limit" type="integer" min="0" value="750" label="Minimum contig length" help="Do not predict contigs shorter than this value. Default: 750" /> </inputs> <outputs> - <data format="csv" name="predicted_fragments" from_work_dir="predicted_fragments.csv" label="${tool.name} on ${on_string}: predicted fragments"/> - <data format="csv" name="predicted" from_work_dir="predicted.csv" label="${tool.name} on ${on_string}: predicted "/> + <data format="tabular" name="predicted_fragments" from_work_dir="predicted_fragments.tsv" label="${tool.name} on ${on_string}: predicted fragments"/> + <data format="tabular" name="predicted" from_work_dir="predicted.tsv" label="${tool.name} on ${on_string}: predicted "/> <data format="fasta" name="viral" from_work_dir="viral.fasta" label="${tool.name} on ${on_string}: viral FASTA file" /> </outputs> <tests> <test> <param name="fasta_file" value="viruses.fasta"/> <param name="weights" value="test"/> - <output name="predicted_fragments" file="predicted_fragments.csv" ftype="csv" lines_diff="2"/> - <output name="predicted" file="predicted.csv" ftype="csv" lines_diff="2"/> + <output name="predicted_fragments" file="predicted_fragments.tsv" ftype="tabular" lines_diff="2"/> + <output name="predicted" file="predicted.tsv" ftype="tabular" lines_diff="2"/> <output name="viral" file="viral.fasta" ftype="fasta" lines_diff="2"/> </test> </tests> |