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.. _filter_distance_matrix:
.. index:: filter_distance_matrix.py
*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:** :file:`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 <./filter_samples_from_otu_table.html>`_ -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"
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