summary.tax
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 name 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
- 1.40.0 - Allow for () characters in taxonomy definitions. #350