distance_matrix_from_mapping.py – Calculate the pairwise dissimilarity on one column of a mappping file

Description:

The input for this script is a mapping file and the name of a column, it has to be numeric, from which a distance matrix will be created. The output of this script is a distance matrix containing a dissimilarity value for each pairwise comparison.

As this is a univariate procedure only one metric is supported: d = c-b.

Usage: distance_matrix_from_mapping.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_path

Mapping filepath.

-c, --column

String containing the name of the column in the mapping file, e.g. ‘DOB’. If you pass two colums separated by a comma (e.g. ‘Latitude,Longitud’) the script will calculate the Vincenty formula (WGS-84) for distance between two Latitude/Longitude points.

[OPTIONAL]

-o, --output_fp

Output directory. One will be created if it doesn’t exist. [default=map_distance_matrix.txt]

Output:

The output of distance_matrix_from_mapping.py is a file containing a distance matrix between rows corresponding to a pair of columns in a mapping file.

Pairwise dissimilarity:

To calculate the distance matrix (using euclidean distance) on a column of the mapping file, where the results are output to DOB.txt, use the following command:

distance_matrix_from_mapping.py -i Fasting_Map.txt -c DOB

Pairwise dissimilarity using the Vincenty formula for distance between two Latitude/Longitude points:

To calculate the distance matrix (using Vincenty formula) on a column of the mapping file, where the results are output to lat_long.txt, use the following command:

distance_matrix_from_mapping.py -i lat_long.txt -c Latitute,Longitude -o lat_long_dtx_matrix.txt