filter_distance_matrix.py – Filter a distance matrix to contain only a specified set of samples.

Description:

Remove samples from a distance matrix based on a mapping file or an otu table or a list of sample ids.

Usage: filter_distance_matrix.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_distance_matrix

The input distance matrix

-o, --output_distance_matrix

Path to store the output distance matrix

[OPTIONAL]

--sample_id_fp

A list of sample identifiers (or tab-delimited lines with a sample identifier in the first field) which should be retained

-t, --otu_table_fp

The otu table filepath

-m, --mapping_fp

Path to the mapping file

-s, --valid_states

String containing valid states, e.g. ‘STUDY_NAME:DOB’

--negate

Discard specified samples (instead of keeping them) [default: False]

Output:

Filter samples ids listed in sample_id_list.txt from dm.txt

filter_distance_matrix.py -i dm.txt -o dm_out_sample_list.txt --sample_id_fp sample_id_list.txt

Filter samples ids in otu_table.biom from dm.txt

filter_distance_matrix.py -i dm.txt -o dm_out_otu_table.txt -t otu_table.biom

Filter samples ids where DOB is 20061218 in Fasting_Map.txt. (Run “filter_samples_from_otu_table.py -h” for additional information on how metadata filtering can be specified.)

filter_distance_matrix.py -i dm.txt -o dm_out_mapping_file.txt -m Fasting_Map.txt -s "DOB:20061218"