Biowulf High Performance Computing at the NIH
Biom-format on Biowulf

The biom-format python package contains a command line tool to manipulate and convert biom format files. It also includes an API for programatically manipulating biom files. It is therefore installed as both in independent application and as part of the python environments.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session (user input in bold:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load biom-format

[user@cn3144 ~]$ TD=/usr/local/apps/biom-format/TEST_DATA

[user@cn3144 ~]$ biom head -i $TD/phinch_testdata.biom
# Constructed from biom file
#OTU ID 0.IntakeWater.1 0.IntakeWater.3 0.IntakeWater.2 27.WaterCoralpond.2 
228057  3.0     6.0     3.0     1.0     0.0
988537  0.0     0.0     0.0     2.0     0.0
89370   0.0     0.0     0.0     1.0     1.0
2562097 0.0     0.0     0.0     0.0     0.0
256904  8.0     0.0     1.0     32.0    58.0

[user@cn3144 ~]$ biom convert -i $TD/phinch_testdata.biom -o test.biom --to-hdf5

[user@cn3144 ~]$ module load hdf5

[user@cn3144 ~]$ h5ls test.biom
observation              Group
sample                   Group

[user@cn3144 ~]$ h5ls test.biom/sample
group-metadata           Group
ids                      Dataset {95}
matrix                   Group
metadata                 Group

[user@cn3144 ~]$ biom summarize-table -i test.biom
Num samples: 95
Num observations: 67900
Total count: 10223009
Table density (fraction of non-zero values): 0.056

Counts/sample summary:
 Min: 16.0
 Max: 1106184.0
 Median: 65463.000
 Mean: 107610.621
 Std. dev.: 164313.408
 Sample Metadata Categories: description; alkalinity; material; ammonium; nitrite; 
  LinkerPrimerSequence; sulfide; BarcodeName; InternalCode; temp; 
  collection_date; BarcodeSequence; salinity; phosphate; ReverseBarcode; nitrate; 
  ph; ReverseName; ReversePrimerSequence; Hardness; diss_oxygen
 Observation Metadata Categories: taxonomy

Counts/sample detail:
0.WipesKoipondLgWaterfall.1: 16.0
0.WipesKoipondLFilter.1: 18.0

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

When loading one of the python 2.7 modules, the biom command line tool will also become available (though the version may vary over time), as will the API. For example

[user@cn3144 ~]$ module load python

[user@cn3144 ~]$ which biom

[user@cn3144 ~]$ python
Python 2.7.9 |Continuum Analytics, Inc.| (default, Apr 14 2015, 12:54:25)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: and

>>> import biom

>>> table = biom.load_table("test.biom")

>>> table
67900 x 95 <class 'biom.table.Table'> with 360783 nonzero entries (5% dense)