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"