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Difference between revisions of "Merge.groups"

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==Default settings==
 
==Default settings==
To run the [[merge.groups]] command you need a shared file or group file and a design file.
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To run the [[merge.groups]] command you need a shared file or group file and a [[Design_File]].
  
 
With a shared file:
 
With a shared file:

Revision as of 18:52, 31 July 2015

The merge.groups command reads a shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file. The files that we discuss in this tutorial can be obtained by downloading the AmazonData.zip file and decompressing it, as well as AmazonDesign.zip


Default settings

To run the merge.groups command you need a shared file or group file and a Design_File.

With a shared file:

mothur > merge.groups(shared=98_lt_phylip_amazon.fn.shared, design=98_lt_phylip_amazon.design)

98_lt_phylip_amazon.fn.shared looks like:

unique	forest	96	1	1	1	1	1	1	1	1	1	1 ...
unique	pasture	96	0	0	0	0	0	0	0	0	0	0 ...
0.00	forest	95	1	1	1	1	1	1	1	1	1	1 ...	
0.00	pasture	95	0	0	0	0	0	0	0	0	0	0 ...	
0.01	forest	93	1	1	1	1	1	1	1	1	1	1 ...
0.01	pasture	93	0	0	0	0	0	0	0	0	0	0 ...
0.02	forest	89	1	1	1	1	1	1	1	1	1	1 ...
0.02	pasture	89	0	0	0	0	0	0	0	0	0	0 ...
0.03	forest	84	1	1	1	1	1	1	1	1	1	1 ...
0.03	pasture	84	0	0	0	0	0	0	0	0	0	0 ...
0.04	forest	81	1	1	1	1	1	1	1	2	1	1 ...	
0.04	pasture	81	0	0	0	0	0	0	0	0	0	0 ...	
0.05	forest	73	1	1	1	1	1	1	1	2	2	1 ...
0.05	pasture	73	0	0	0	0	0	0	1	0	0	0 ...
0.06	forest	68	1	1	1	1	1	1	1	2	2	1 ...
0.06	pasture	68	0	0	0	0	0	0	1	0	0	3 ...
0.07	forest	66	1	1	1	1	1	1	1	2	2	1 ...
0.07	pasture	66	0	0	0	1	0	0	1	0	0	3 ...
0.08	forest	59	1	1	1	1	1	1	1	3	2	2 ...
0.08	pasture	59	0	0	0	1	0	0	1	0	0	5 ...
0.09	forest	57	1	1	1	1	1	1	3	3	2	2 ...
0.09	pasture	57	0	0	0	1	0	0	1	0	0	5 ...
0.10	forest	55	1	1	1	1	1	1	3	3	2	2 ...
0.10	pasture	55	0	0	0	1	0	0	1	0	0	5 ...

and after running merge.groups, 98_lt_phylip_amazon.fn.merge.shared looks like:

unique	a	96	1	1	1	1	1	1	1	1	1	1 ...
0.00	a	95	1	1	1	1	1	1	1	1	1	1 ...	
0.01	a	93	1	1	1	1	1	1	1	1	1	1 ...
0.02	a	89	1	1	1	1	1	1	1	1	1	1 ...
0.03	a	84	1	1	1	1	1	1	1	1	1	1 ...
0.04	a	81	1	1	1	1	1	1	1	2	1	1 ...	
0.05	a	73	1	1	1	1	1	1	2	2	2	1 ...
0.06	a	68	1	1	1	1	1	1	2	2	2	4 ...
0.07	a	66	1	1	1	2	1	1	2	2	2	4 ...
0.08	a	59	1	1	1	2	1	1	2	3	2	7 ...
0.09	a	57	1	1	1	2	1	1	4	3	2	7 ...
0.10	a	55	1	1	1	2	1	1	4	3	2	7 ...

With a group file:

mothur > merge.groups(group=amazon.groups, design=98_lt_phylip_amazon.design)

Options

groups

The groups parameter allows you to specify which of the groups you would like analyzed. Default=all. You may separate group names with dashes.

label

The label parameter is used to analyze specific labels in your input. default=all. You may separate label names with dashes.

Revisions