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Summary.tax

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The summary.tax command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information. To run this tutorial please download, Example Data


Default settings

You must provide a taxonomy file.

mothur > summary.tax(taxonomy=stool.trim.unique.good.filter.unique.precluster.pick.rdp.taxonomy)

This command will produce a stool.trim.unique.good.filter.unique.precluster.pick.rdp.tax.summary, which should look like:

0	0	Root	1	3714	
1	0.1	Bacteria	10	3714	
2	0.1.1	"Acidobacteria"	1	5	
3	0.1.1.1	Holophagae	1	5	
4	0.1.1.1.1	Holophagales	1	5	
5	0.1.1.1.1.1	Holophagaceae	1	5	
6	0.1.1.1.1.1.1	Holophaga	0	5	
2	0.1.2	"Actinobacteria"	1	38	
...


name

The name parameter allows you add a names file with your taxonomy file.

mothur > summary.tax(taxonomy=stool.trim.unique.good.filter.unique.precluster.pick.rdp.taxonomy, name=stool.trim.unique.good.filter.unique.precluster.pick.names)
0	0	Root	1	27517	
1	0.1	Bacteria	10	27517	
2	0.1.1	"Acidobacteria"	1	270	
3	0.1.1.1	Holophagae	1	270	
4	0.1.1.1.1	Holophagales	1	270	
5	0.1.1.1.1.1	Holophagaceae	1	270	
6	0.1.1.1.1.1.1	Holophaga	0	270	
2	0.1.2	"Actinobacteria"	1	258	
...


group

The group parameter allows you add a group file to be used to generate group totals in the .summary file.

mothur > summary.tax(taxonomy=stool.trim.unique.good.filter.unique.precluster.pick.rdp.taxonomy, name=stool.trim.unique.good.filter.unique.precluster.pick.names, group=stool.good.pick.groups)
taxlevel	 rankID	 taxon	 daughterlevels	 total	F11Fcsw	F12Fcsw	F13Fcsw	F14Fcsw	F21Fcsw	...	
0	0	Root	1	27517	699	666	925	1301	707	...	
1	0.1	Bacteria	10	27517	699	666	925	1301	707  ...	
2	0.1.1	"Acidobacteria"	1	270	61	52	46	75	2	...	
3	0.1.1.1	Holophagae	1	270	61	52	46	75	2	...	
4	0.1.1.1.1	Holophagales	1	270	61	52	46	75	2	...	
5	0.1.1.1.1.1	Holophagaceae	1	270	61	52	46	75	2	...	
6	0.1.1.1.1.1.1	Holophaga	0	270	61	52	46	75	2	...	
2	0.1.2	"Actinobacteria"	1	258	44	31	55	79	1	...
...	

count

The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information.

mothur > summary.tax(taxonomy=stool.trim.unique.good.filter.unique.precluster.pick.rdp.taxonomy, count=stool.trim.unique.good.filter.unique.precluster.pick.count_table)

relabund

The relabund parameter allows you to indicate you want the summary file values to be relative abundances rather than raw abundances. Default=F.

mothur > summary.tax(taxonomy=stool.trim.unique.good.filter.unique.precluster.pick.rdp.taxonomy, name=stool.trim.unique.good.filter.unique.precluster.pick.names, group=stool.good.pick.groups, relabund=t)

threshold

The threshold parameter allows you to specify a cutoff for the taxonomy file that is being inputted. Once the classification falls below the threshold the mothur will refer to it as unclassified when calculating the summary. This feature is similar to adjusting the cutoff in classify.seqs. Default=0.

output

The output parameter allows you to specify format of your *tax.summary file. Options are simple and detail. The detail format outputs the totals at each level, where as the simple format outputs the highest level. The default is detail.

The detail format looks like:

taxlevel	rankID	taxon	daughterlevels	total	A	B	C
0	0	Root	1	28	14	20	9
1	0.1	"k__Bacteria"	5	28	14	20	9
2	0.1.1	"p__Actinobacteria"	1	3	0	3	0
3	0.1.1.1	"c__Actinobacteria"	1	3	0	3	0
4	0.1.1.1.1	"o__Bifidobacteriales"	1	3	0	3	0
5	0.1.1.1.1.1	"f__Bifidobacteriaceae"	1	3	0	3	0
6	0.1.1.1.1.1.1	"g__Bifidobacterium"	3	3	0	3	0
7	0.1.1.1.1.1.1.1	"s__"	0	1	0	1	0
7	0.1.1.1.1.1.1.2	"s__adolescentis"	0	1	0	1	0
7	0.1.1.1.1.1.1.3	"s__longum"	0	1	0	1	0
2	0.1.2	"p__Bacteroidetes"	1	6	5	3	3
3	0.1.2.1	"c__Bacteroidia"	1	6	5	3	3
4	0.1.2.1.1	"o__Bacteroidales"	2	6	5	3	3
5	0.1.2.1.1.1	"f__Bacteroidaceae"	1	4	4	3	1
6	0.1.2.1.1.1.1	"g__Bacteroides"	4	4	4	3	1
7	0.1.2.1.1.1.1.1	"s__"	0	1	1	1	0
...

The simple format looks like:

taxon	total	A	B	C
"k__Bacteria";"p__Actinobacteria";"c__Actinobacteria";"o__Bifidobacteriales";"f__Bifidobacteriaceae";"g__Bifidobacterium";"s__";	1	0	1	0
"k__Bacteria";"p__Actinobacteria";"c__Actinobacteria";"o__Bifidobacteriales";"f__Bifidobacteriaceae";"g__Bifidobacterium";"s__adolescentis";	1	0	1	0
"k__Bacteria";"p__Actinobacteria";"c__Actinobacteria";"o__Bifidobacteriales";"f__Bifidobacteriaceae";"g__Bifidobacterium";"s__longum";	1	0	1	0
...


printlevel

The printlevel parameter allows you to specify taxlevel of your *tax.summary file to print to. Options are 1 to the maz level in the file. The default is -1, meaning max level. If you select a level greater than the level your sequences classify to, mothur will print to the level your max level.

mothur > biom.info(biom=abrecovery.an.0.03.biom, label=0.03, printlevel=4)

Detail format:

taxlevel	rankID	taxon	daughterlevels	total	A	B	C 
0	0	Root	1	28	14	20	9
1	0.1	"k__Bacteria"	5	28	14	20	9
2	0.1.1	"p__Actinobacteria"	1	3	0	3	0
3	0.1.1.1	"c__Actinobacteria"	1	3	0	3	0
4	0.1.1.1.1	"o__Bifidobacteriales"	1	3	0	3	0
2	0.1.2	"p__Bacteroidetes"	1	6	5	3	3
3	0.1.2.1	"c__Bacteroidia"	1	6	5	3	3
4	0.1.2.1.1	"o__Bacteroidales"	2	6	5	3	3
2	0.1.3	"p__Firmicutes"	2	13	8	10	2
3	0.1.3.1	"c__Bacilli"	1	1	1	0	0
4	0.1.3.1.1	"o__Turicibacterales"	1	1	1	0	0
...

Simple Format:

taxon	total	A	B	C
"k__Bacteria";"p__Actinobacteria";"c__Actinobacteria";"o__Bifidobacteriales";	3	0	3	0
"k__Bacteria";"p__Bacteroidetes";"c__Bacteroidia";"o__Bacteroidales";	6	5	3	3
"k__Bacteria";"p__Firmicutes";"c__Bacilli";"o__Turicibacterales";	1	1	0	0
...

Revisions

  • 1.22.0 First Introduced
  • 1.28.0 Added count parameter
  • 1.37.0 Adds output, printlevel and threshold parameters #204 #158 #31
  • 1.38.0 Removes reftaxonomy parameter
  • 1.38.0 Fixes bug with command not including name file counts in *tax.summary
  • 1.39.0 Taxonomy files can now contain spaces in the taxon names
  • 1.39.2 Fixes summary file printing issue