compare_alpha_diversity.py – This script compares alpha diversities based on a t_two_sample test

Description:

This script compares the alpha diversity of entries in a rarefaction file after they have been grouped based on some category found in the mapping file based on a t_two_sample test.

Usage: compare_alpha_diversity.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --alpha_diversity_filepath

Path to collated alpha diversity file (as generated by collate_alpha.py) [REQUIRED]

-m, --mapping_filepath

Path to the mapping file [REQUIRED]

-c, --category

Category for comparison [REQUIRED]

-d, --depth

Depth of rarefaction file to use [REQUIRED]

-o, --output_filepath

Output file path [REQUIRED]

Output:

Script generates an output nested dictionary which has as a first

key:value pair the category passed, and a dictionary which gives the t_two_sample score for every possible combination of the values under that category in the mapping file, saved as a text file into the directory specified by the output path.

Explanation:Inputs: mapping file lines (lines of a mapping file which associates to each OTU/sample a number of characteristics, given as file path), rarefaction file lines (lines of a rarefaction file that has scores for each OTU/sample based on a certain rarefaction depth, given as a file path), depth (the depth score of the rarefaction file to use), category (the category to compare OTU/samples on), output file path (a path to the output file).:

compare_alpha_diversity.py -i PD_whole_tree.txt -m map.txt -c Treatment -d 100 -o PD_d100.txt