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PM-select-func
File Type
PM-select-func
PM-select-func

Data

Input(KO.Count)
Example file

Parameters

2
1
2
3
4
F
TRUE
FALSE
References
 
Instructions

Parses and generates abundance tables at various taxonomic or functional levels.

Similar to the PM-select-taxa tool, this program can parse abundance tables for any taxonomic or functional level from an input sample list (taxa.list or func.list), an OTU/KO count table, or a BIOM file. The -L parameter is used to specify the classification level, but only one level can be processed per execution. The program yields two types of output files: *.Count for sequence counts and *.Abd for relative abundances.

Contributor(s)
Yuzhu Chen, Jian Li, Yufeng Zhang, Mingqian Zhang, Zheng Sun, Gongchao Jing, Shi Huang, Xiaoquan Su
suxq@qdu.edu.cn
#Runs
0
Open Result
Sample Drug_resistance:_antimicrobial Metabolism_of_other_amino_acids Environmental_adaptation Cellular_community_-_prokaryotes Transport_and_catabolism Translation Excretory_system Biosynthesis_of_other_secondary_metabolites Endocrine_system Carbohydrate_metabolism Cell_growth_and_death Not_included_in_regular_maps Aging Infectious_disease:_parasitic Cardiovascular_disease Digestive_system Cancer:_overview Endocrine_and_metabolic_disease Drug_resistance:_antineoplastic Substance_dependence Neurodegenerative_disease Unclassified:_metabolism Nervous_system Protein_families:_genetic_information_processing Metabolism_of_terpenoids_and_polyketides Glycan_biosynthesis_and_metabolism Immune_disease Infectious_disease:_viral Xenobiotics_biodegradation_and_metabolism Lipid_metabolism Cell_motility Unclassified:_genetic_information_processing Metabolism_of_cofactors_and_vitamins Transcription Immune_system Replication_and_repair Energy_metabolism Membrane_transport Folding,_sorting_and_degradation Signaling_molecules_and_interaction Protein_families:_metabolism Amino_acid_metabolism Cellular_community_-_eukaryotes Cancer:_specific_types Poorly_characterized Infectious_disease:_bacterial Protein_families:_signaling_and_cellular_processes Unclassified:_signaling_and_cellular_processes Nucleotide_metabolism Signal_transduction Circulatory_system S0437C 85763.7 106790 15171.7 151608 17145.2 199086 1744.53 77744.5 30554 561983 55865.9 1869.24 25290.3 3982.73 12196.9 2753.85 40942.6 14976.1 20511.3 2 19718.6 215392 8365.4 1.24061e+06 60121.1 101653 3224.77 11562 94713 145916 72167.3 66733.2 293080 9367.95 12226.6 193811 297956 239655 94830.4 1 466576 448108 0 10730 238043 52093.8 1.14138e+06 116717 187507 178651 1671.2 S0824C 61658 77396.4 5656.47 145072 8550.96 94205.2 1626.51 50223.2 17250.4 510177 22196 1030.58 12568.5 1564.92 6087.84 1602.18 21472.3 8416.87 9187.24 0 6804.66 198946 7660.59 729441 36559 61182.1 2004.44 1893.25 69084 89020.8 51044.9 66988.4 176436 4588.98 7232.08 100032 190252 253288 53395.9 0.5 305838 292400 0 4921.05 171253 26170.8 887207 84852.2 118831 143609 3 S1207C 187378 186707 21924.5 336779 25989.6 280189 3202.8 140103 46705.4 1.01865e+06 74365.5 3155.9 42193.3 5757.49 18848.6 572.488 76028.4 22432.4 28061.3 13.6667 20674.6 453753 17459.5 2.11339e+06 85875.5 162902 6069.08 8991.09 138152 260947 156982 140067 530815 13228.4 22705.3 310963 546421 519330 162056 0.833333 837656 734240 0 17447.2 454905 114129 2.3795e+06 237542 327826 358222 3 S2313C 77821.4 102173 6893.49 190433 11120.7 112180 2144.95 55262.7 21390.9 589469 26287.5 1377.33 17191.7 2732 7791.91 2389.76 27752.6 11193.2 11839 210 10175.3 255116 10191.2 891906 43515.1 73798.4 2516.14 3231.48 95708.1 108129 67985.8 91201.7 218846 5314.44 6850.2 114143 231628 306063 63933 0 378841 360514 2 7369.15 226528 35934.9 1.13334e+06 98782.5 145893 193392 235 S2531C 92123.1 116166 8052.55 211392 11413.4 166780 2285.49 73463.2 26740.7 736338 35721.1 1822.58 19455.7 2227.79 9713.29 2553.19 33027.3 13888.9 14058.4 0 9933.23 295504 12408.6 1.17929e+06 54466.2 93180.6 2865.18 3136.01 98086.5 131177 77773.2 105735 271818 7992.02 11797.5 161591 286863 354528 87117.3 0 477929 440786 0 7267.61 261313 41547.8 1.31318e+06 125014 185663 212352 17.6 S2704C 85492.8 109984 9665.68 205296 14191.8 141546 2266.39 73704.1 26503.5 675069 33635.2 1576.73 18483.4 2594.19 9702.65 2510.33 31495.8 12278.3 13623.2 3 9908.07 263434 10399 1.05521e+06 52361.9 91272.3 3132.8 2824.45 99318.9 123537 88834.4 88323.2 255254 6709.74 11320.5 141860 266347 336816 77330.8 0 437660 415786 0 7810.81 243008 40299 1.25429e+06 115617 168182 203168 28.4 S3309C 95693.5 124902 14094.6 233822 17913.6 177362 1530.76 95830.4 32921.2 636039 52935.8 2557.29 27527.2 4685.57 15278.6 1667.93 44959 16797.4 20752.2 1772.5 20373.4 258725 17387 1.22052e+06 70577.8 95084.1 3583.83 11839.8 132295 163425 93287.5 76913.6 312740 8642.35 10840.4 174960 318514 341497 94343.7 0.5 479075 529939 3 13714.1 277629 53216.9 1.42966e+06 134339 183940 243610 1960.7 S3422C 57398.9 72942 4649.46 135088 7881.51 78035.3 1644.76 40223.6 14693.1 433915 18139.7 892.476 11941.6 1735.9 5672.29 1718.77 19686.6 7799.65 7920.88 48 6824.17 189890 7285.21 640689 30436.1 55047 1740.7 1888.59 66333.7 78683.5 48574.8 67652.2 159019 3630.74 5756.11 80671.5 170036 218502 46431.1 0 276071 255420 0 5017.02 163810 25633.5 811131 73896 105178 139526 118 S3521C 158743 183016 24805.5 357068 22025.6 234495 3936.2 114842 45958.1 928424 65089.5 2859.69 38507.9 5657.46 20242.3 1756.83 69922.2 20987.6 27369.8 1017 23243.5 390163 21645.7 1.76243e+06 85967.5 131431 5102.64 11005.8 180478 232321 140867 139845 477375 11267.3 18286.2 238548 471916 536470 136717 0 711108 722370 1 19122.9 433805 104071 2.22304e+06 201451 273877 378264 1771 S3907C 103493 118543 10786.2 221992 13794.1 140061 2214.51 73680.7 25004.9 642669 37076.7 1765 23584.7 3548.6 10859.7 1539.9 40101.7 13220.5 15770.5 363 13855.1 286925 11280.6 1.13685e+06 52095.9 89321.2 3298.28 5488.35 108369 144187 93019.2 96603.1 289490 6606.8 10299.8 152746 300897 349306 84336.4 0 471306 437402 0 10773.1 277672 56691.4 1.41924e+06 130900 179471 234876 425.2 S0108H 71963.7 76374.1 13465.7 102166 25784.3 204605 1225.71 101900 31854.1 610073 51354 1296 18360.1 234.25 10509.9 3203.25 26820.4 11931.1 14029.8 0.333334 5624.02 174428 13918.5 1.10824e+06 51292.6 145334 2748 2541.38 42485.3 116439 29346.2 36915 256403 9082.51 16555.3 186345 262770 148291 93146.4 0.166667 399255 411447 0 2947.36 153821 26481.6 754547 103434 171875 102688 63 S0320H 66214.3 77912.1 12710.2 105886 21471.7 195539 1570.03 102434 32243.4 609114 50860.9 1361.67 15221.2 260.811 10128.4 2616.37 28647 12356.6 13090.6 0 4289.14 174142 16369.7 1.07893e+06 51730.9 124618 2714.86 2450.02 38020.9 114478 30471.9 39937.9 244164 8798.89 16091.7 178268 261452 158258 91165.1 0 393461 410364 0 2925.84 151470 25476.3 762505 104625 163652 104090 50.8 S0515H 55839.5 67060.9 11304.9 87620.9 19091.7 186858 1225.2 84091.7 29817.1 506965 48205.5 1174 15135 679.583 8602.16 4016.93 24100.6 11354 12958.2 0 6687.04 148662 11947.7 973441 48726.7 114759 2430.06 3597.48 35844.9 101116 25577.3 36443.6 234492 8408.01 14035.3 164719 232649 123483 78670.3 0 358752 356494 0 3544.72 131051 23604.4 626318 85616.5 148898 85559.1 574 S0614H 47750.1 57512.3 9885.72 79071.5 16080.3 142165 1050.01 76447.2 23539.5 456624 36832.6 1143.08 11706.1 583.95 7191.98 2550.08 20017.1 9105.89 9327.61 0 3690.3 132952 10894.3 775056 38778.7 90846.9 2446.01 1857.6 29463.3 85763.9 24971.3 29928.3 183263 6300.58 11769 127918 191007 116422 65592.6 0 291488 306631 0 2381.37 114544 19504.1 564446 76705.5 115771 81088.3 120.4 S0729H 57292.6 64747.6 10482.7 83802.9 21785.8 159013 1507.19 84601.7 27675.3 524240 41390.8 1106.25 12687.9 340.2 8947.99 2392.86 23978.4 10153.2 10790.1 0 3617.66 152460 13991.9 889885 43121.8 118647 2139.47 2009.77 33383.3 98340.3 18595.7 33490.4 200856 7278.29 13275.9 145717 218221 135254 73841.6 2 327670 339348 1 2347.74 128440 20340.6 644619 86644.4 135120 83025.2 173.4 S0928H 56971.1 66275.3 11666.4 99693 17685.6 183981 1410.98 85909.5 30642 525780 45407.2 1547 14400.5 511.583 9555.59 2506.23 24858.1 11383.2 12342.2 0 4628.12 158198 13155.9 996556 47018.8 109482 2186.42 2680.41 36000.5 101715 44552.5 36944.3 224554 8432.81 15468.3 165854 230989 133042 82146.8 0 355401 367468 0 2746.74 135375 23606.8 686738 96766.3 147448 96094.5 104 S1007H 87567.3 111332 18385.9 145002 33899.8 235235 2158.56 147788 44962.9 898147 68250.6 1387.5 20062.2 1820.75 13156.3 5121.88 37377.1 16668.4 16502.6 0 5941.75 253627 22290.1 1.33085e+06 70066.5 176249 4127.94 3101.87 50802.2 162024 37630.3 51412.7 327903 10113.9 20690.6 222817 345694 187843 113976 0 515603 534790 0 3837.63 214454 35082.4 958826 139439 211268 131852 125 S1117H 58524.3 68601.3 10494.8 86822.2 23836.3 161785 1237.39 91207.3 28895.7 564442 40971.4 993.967 13254 741.45 8462.42 2361.92 22479.6 10543.6 11046.3 0 3992.24 166483 13325.8 898448 45632.8 122812 1842.76 2068.68 34698.6 109280 18383.8 33064.4 211531 7294.67 12731.5 149135 226068 139545 73370.5 0 330929 346355 0 2154.55 138689 21420.5 645990 86976 141886 79646.6 102.4 S1406H 66150.7 76639 11239.6 119756 16015.1 204900 1334.05 102348 31168.7 628804 49108.3 2028.25 14386.1 714.267 10424.3 1746.69 28400.6 12810.2 13009.5 0 4831.57 181877 15994.8 1.13006e+06 56170.7 106212 2252.49 2988.61 46675.2 121938 39556.4 45858 238961 9251.32 16677.6 181567 260548 194909 90771.2 0 402201 417168 0 3173.59 168119 25618.2 848875 115214 166696 110621 110.2 S1520H 78043.8 95340.7 16154.3 123587 39557.3 231702 2224.74 139686 47643.4 801426 66677.4 1595.79 18197.4 1746.62 15091.7 4603.87 34365.1 16844.5 15483.3 0.333334 5627.25 241195 19981.6 1.29251e+06 68233.5 190830 2521.36 2954.5 47924.5 148908 33718.1 45409.4 294841 11084.8 24819.1 214886 316028 167133 106990 0.166667 474454 507605 51 4187.52 198202 30362.6 891721 127614 198452 120189 5