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When performing batch analyses on the OTU table (e.g. rarefaction followed by alpha diversity), the result of alpha_diversity.py comprises many files, which need to be concatenated into a single file for generating rarefaction curves. This script joins those files. Input files are: each file represents one (rarefied) otu table each row in a file represents one sample each column in a file represents one diversity metric
Output files are: each file represents one diversity metric each row in a file represents one (rarefied) otu table each column in a file represents one sample
The input directory should contain only otu tables. The output directory should be empty or nonexistant and the example file is optional.
If you have a set of rarefied OTU tables, make sure the example file contains every sample present in the otu talbes. You should typically choose the file with the fewest sequences per sample, to avoid files with sparse samples omitted.
Usage: collate_alpha.py [options]
This script takes the resulting files from batch alpha diversity and collates them into (one file for each metric used).
This script transforms a series of files, named (e.g. alpha_rarefaction_20_0.txt, alpha_rarefaction_20_1.txt, etc.) into a (usually much smaller) set of files named (e.g. chao1.txt, PD_whole_tree.txt, etc.), where the columns correspond to samples and rows to the rarefaction files inputted, as shown by the following:
|sequences per sample||iteration||PC.354||PC.355|
The user inputs the results from batch alpha diversity (e.g. alpha_div/) and the location where the results should be written (e.g. collated_alpha/), as shown by the following command:
collate_alpha.py -i alpha_div/ -o collated_alpha/