compute_core_microbiome.py – Identify the core microbiome.

Description:

Usage: compute_core_microbiome.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fp

The input otu table in BIOM format

-o, --output_dir

Directory to store output data

[OPTIONAL]

--max_fraction_for_core

The max fractions of samples that an OTU must be observed in to be considered part of the core as a number in the range [0,1] [default: 1.0]

--min_fraction_for_core

The min fractions of samples that an OTU must be observed in to be considered part of the core as a number in the range [0,1] [default: 0.5]

--num_fraction_for_core_steps

The number of evenly sizes steps to take between min_fraction_for_core and max_fraction_for_core [default: 11]

--otu_md

The otu metadata category to write to the output file [defualt: taxonomy]

--mapping_fp

Mapping file path (for use with –valid_states) [default: None]

--valid_states

Description of sample ids to retain (for use with –mapping_fp) [default: None]

Output:

Identify the core OTUs in otu_table.biom, defined as the OTUs that are present in at least 50% of the samples. Write the list of core OTUs to a text file, and a new BIOM file containing only the core OTUs.

compute_core_microbiome.py -i otu_table.biom -o otu_table_core

Identify the core OTUs in otu_table.biom, defined as the OTUs that are present in all of the samples in the ‘Fast’ treatment (as specified in the mapping file). Write the list of core OTUs to a text file.

compute_core_microbiome.py -i otu_table.biom -o otu_table_core_fast --mapping_fp map.txt --valid_states "Treatment:Fast"