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Get.otulist

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Revision as of 13:54, 17 November 2009 by Westcott (Talk | contribs) (New page: The get.listcount command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the bin number the second column is a list of sequences i...)

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The get.listcount command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the bin number the second column is a list of sequences in that bin.


 The get.listcount command can only be executed after a successful read.otu command of a listfile or providing a list file using the  list parameter. 
 The get.listcount command parameters are list and label.  No parameters are required.  
 The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.  
 The get.listcount command should be in the following format: get.listcount(list=yourlistFile, label=yourLabels).  
 Example get.listcount(list=amazon.fn.list, label=0.10).  The default value for label is all lines in your inputfile.  


Example output:

1	AY457808
2	AY457844
3	AY457807
4	AY457686
5	AY457721
6	AY457863
7	AY457886
8	AY457843
9	AY457845
10	AY457702
11	AY457758
12	AY457687
13	AY457841
14	AY457739
15	AY457685
16	AY457875
17	AY457733
18	AY457869
19	AY457846
20	AY457723
21	AY457741
22	AY457865
23	AY457693
24	AY457675
25	AY457705
26	AY457724
27	AY457722
28	AY457703
29	AY457720,AY457728,AY457746,AY457742,AY457781
30	AY457713,AY457719
31	AY457712
32	AY457698,AY457855,AY457804,AY457681,AY457819,AY457727
33	AY457710,AY457691,AY457696,AY457699,AY457743,AY457706,AY457680,AY457688,AY457709,AY457684,AY457711,AY457689,AY457730,AY457761
34	AY457775,AY457788,AY457815,AY457893,AY457690,AY457694,AY457749,AY457776,AY457831,AY457851,AY457911,AY457785,AY457847,AY457881,AY457793,AY457818,AY457813,AY457753,AY457755,AY457763,AY457780,AY457809,AY457701,AY457715,AY457838,AY457774,AY457747,AY457859,AY457864,AY457754,AY457871,AY457910
35	AY457744,AY457745
36	AY457677,AY457679,AY457726,AY457714,AY457740,AY457725
37	AY457678,AY457700,AY457718,AY457674,AY457683,AY457735,AY457704,AY457708,AY457717,AY457878
38	AY457757,AY457824,AY457756,AY457773,AY457816,AY457827,AY457877,AY457889,AY457771,AY457777,AY457883,AY457857,AY457896,AY457884,AY457885,AY457903,AY457765,AY457862,AY457909
39	AY457811,AY457873,AY457900,AY457821,AY457805,AY457853,AY457899
40	AY457858,AY457897
41	AY457861,AY457868,AY457892,AY457902,AY457904
42	AY457801,AY457852,AY457834,AY457856,AY457905,AY457870,AY457879,AY457906,AY457850,AY457890
43	AY457876
44	AY457682,AY457729,AY457734,AY457772,AY457791,AY457792
45	AY457759,AY457794
46	AY457770
47	AY457750,AY457802,AY457822,AY457762,AY457840,AY457783,AY457769,AY457786,AY457915,AY457912,AY457848,AY457882,AY457888,AY457914
48	AY457795,AY457842,AY457833
49	AY457814
50	AY457867
51	AY457751,AY457803
52	AY457820,AY457832,AY457872
53	AY457797,AY457835,AY457829,AY457908,AY457839,AY457874,AY457901,AY457913
54	AY457799
55	AY457731
56	AY457707,AY457854,AY457736,AY457825,AY457907,AY457880
57	AY457764,AY457806,AY457891,AY457894,AY457895,AY457817,AY457898,AY457887
58	AY457760,AY457676,AY457692,AY457837,AY457849,AY457748,AY457800,AY457768,AY457823,AY457798,AY457732,AY457860,AY457695,AY457826,AY457767,AY457716,AY457738,AY457866,AY457830,AY457836
59	AY457766,AY457778,AY457782,AY457812,AY457752,AY457789,AY457828
60	AY457790
61	AY457779
62	AY457697,AY457787,AY457737,AY457784,AY457796,AY457810