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Difference between revisions of "Biom.info"

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===basis===
 
===basis===
 
The basis parameter allows you indicate what you want the summary file to represent, options are otu and sequence. Default is otu.  For example consider the following basis=sequence could give Clostridiales 3 105, where 105 is the total number of sequences whose otu classified to Clostridiales.  Now for basis=otu could give Clostridiales 3 7, where 7 is the number of otus that classified to Clostridiales.
 
The basis parameter allows you indicate what you want the summary file to represent, options are otu and sequence. Default is otu.  For example consider the following basis=sequence could give Clostridiales 3 105, where 105 is the total number of sequences whose otu classified to Clostridiales.  Now for basis=otu could give Clostridiales 3 7, where 7 is the number of otus that classified to Clostridiales.
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===format===
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The format parameter allows you indicate type of biom file you have. Options hdf5 or classic. Default is hdf5.
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mothur > biom.info(biom=hdf5.biom, label=0.03, format=hdf5)
  
 
===output===
 
===output===

Revision as of 16:47, 30 October 2018

The biom.info command reads a biom file creates a Shared_file. If your biom file contains metadata mothur will also create taxonomy or constaxonomy along with tax.summary files.


Default Options

The biom parameter is required. You can run the command as follows:

mothur > biom.info(biom=abrecovery.an.0.03.biom)

Options

label

The label parameter allows you to enter a distance label to be used in the shared file created from your biom file. Default=userLabel.

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

relabund

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

basis

The basis parameter allows you indicate what you want the summary file to represent, options are otu and sequence. Default is otu. For example consider the following basis=sequence could give Clostridiales 3 105, where 105 is the total number of sequences whose otu classified to Clostridiales. Now for basis=otu could give Clostridiales 3 7, where 7 is the number of otus that classified to Clostridiales.

format

The format parameter allows you indicate type of biom file you have. Options hdf5 or classic. Default is hdf5.

mothur > biom.info(biom=hdf5.biom, label=0.03, format=hdf5)

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

  • 1.37.0 - First Introduced #82
  • 1.41.0 - Add sample info to tax.summary in biom.info command. #531
  • 1.41.0 - Updates biom.info to read hdf5 biom files. #178