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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"

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