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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.
 +
 +
===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===
 
===output===
Line 82: Line 87:
 
  "k__Bacteria";"p__Firmicutes";"c__Bacilli";"o__Turicibacterales"; 1 1 0 0
 
  "k__Bacteria";"p__Firmicutes";"c__Bacilli";"o__Turicibacterales"; 1 1 0 0
 
  ...
 
  ...
 +
 +
==Help==
 +
===Common Questions===
 +
Can't find your question? Please feel free to ask questions on our forum, https://forum.mothur.org.
 +
 +
===Common Issues===
 +
 +
# '''Cannot convert error. What do I do?'''  This issue is caused by a matrix_element_type mismatch. The biom file contains a field called 'matrix_element_type'. This field tells mothur what form your observation data is in: int or float. Mothur expects 'int' (an interger value) because the shared file contains interger value abundance counts. If your file contains float values mothur will round down to the nearest integer value. But if your matrix_element_type=int and yet the file contains integer counts in float form, (ie. 31.0 instead of 31) you will get this error. You can resolve this issue by setting matrix_element_type=float in the biom file.
 +
# '''Mothur can't read my biom file. What does this mean?''' This likely caused by failure to set format=hdf5. Mothur allows for 2 formats: classic (http://biom-format.org/documentation/format_versions/biom-1.0.html) and hdf5 (http://biom-format.org/documentation/format_versions/biom-2.0.html). By default mothur assumes your files are in classic form. If your file is in hdf5 format, then set format=hdf5. NOTE: you can only process hdf5 files if you are using our pre-built version or have built your version of mothur with USEHDF5=yes.
 +
 +
===How To===
 +
Not sure how to do what you want? Please feel free to ask questions on our forum, https://forum.mothur.org.
  
 
==Revisions==
 
==Revisions==
* 1.37.0 - First Introduced
+
* 1.37.0 - First Introduced [https://github.com/mothur/mothur/issues/82  #82]
 +
* 1.41.0 - Add sample info to tax.summary in biom.info command.  [https://github.com/mothur/mothur/issues/531  #531]
 +
* 1.41.0 - Updates biom.info to read hdf5 biom files. [https://github.com/mothur/mothur/issues/178  #178]

Latest revision as of 19:12, 31 January 2019

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
...

Help

Common Questions

Can't find your question? Please feel free to ask questions on our forum, https://forum.mothur.org.

Common Issues

  1. Cannot convert error. What do I do? This issue is caused by a matrix_element_type mismatch. The biom file contains a field called 'matrix_element_type'. This field tells mothur what form your observation data is in: int or float. Mothur expects 'int' (an interger value) because the shared file contains interger value abundance counts. If your file contains float values mothur will round down to the nearest integer value. But if your matrix_element_type=int and yet the file contains integer counts in float form, (ie. 31.0 instead of 31) you will get this error. You can resolve this issue by setting matrix_element_type=float in the biom file.
  2. Mothur can't read my biom file. What does this mean? This likely caused by failure to set format=hdf5. Mothur allows for 2 formats: classic (http://biom-format.org/documentation/format_versions/biom-1.0.html) and hdf5 (http://biom-format.org/documentation/format_versions/biom-2.0.html). By default mothur assumes your files are in classic form. If your file is in hdf5 format, then set format=hdf5. NOTE: you can only process hdf5 files if you are using our pre-built version or have built your version of mothur with USEHDF5=yes.

How To

Not sure how to do what you want? Please feel free to ask questions on our forum, https://forum.mothur.org.

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