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This script performs like the multiple_rarefactions.py script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.
Usage: parallel_multiple_rarefactions.py [options]
The result of parallel_multiple_rarefactions.py consists of a number of files, which depend on the minimum/maximum number of sequences per samples, steps and iterations. The files have the same otu table format as the input otu_table.biom, and are named in the following way: rarefaction_100_0.txt, where “100” corresponds to the sequences per sample and “0” for the iteration.
OTU tables of different depths:
Build rarefied otu tables containing 10 (-m) to 140 (-x) sequences in steps of 10 (-s) with 2 (-n) repetions per number of sequences, from otu_table.biom (-i). Write the output files to the rarefied_otu_tables directory (-o, will be created if it doesn’t exist). The name of the output files will be of the form rarefaction_<num_seqs>_<reptition_number>.biom. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).
parallel_multiple_rarefactions.py -o $PWD/rarefied_otu_tables/ -m 10 -x 140 -s 10 -n 2 -i $PWD/otu_table.biom
OTU tables of the same depth:
Build 8 rarefied otu tables each containing exactly 100 sequences per sample (even depth rarefaction). ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).
parallel_multiple_rarefactions.py -o $PWD/even_otu_tables/ -m 100 -x 100 -n 8 -i $PWD/otu_table.biom