parallel_merge_otu_tables.py – Parallel merge BIOM tables

Description:

This script works like the merge_otu_tables.py script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.

Usage: parallel_merge_otu_tables.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fps

The otu tables in biom format (comma-separated)

-o, --output_dir

The output otu table directory path

[OPTIONAL]

-C, --cluster

Submit to a torque cluster

-N, --merge_otus_fp

Full path to scripts/merge_otu_tables.py [default: /Users/caporaso/code/Qiime/scripts/merge_otu_tables.py]

-Y, --python_exe_fp

Full path to python executable [default: python]

-Z, --seconds_to_sleep

Number of seconds to sleep between checks for run completion when polling runs [default: 1]

-X, --job_prefix

Job prefix [default: descriptive prefix + random chars]

Output:

The output consists of many files (i.e. merged_table.biom, merged_table.log and all intermediate merge tables). The .biom file contains the result of merging the individual BIOM tables. The resulting .log file contains a list of parameters passed to this script along with the output location of the resulting .txt file, the dependency hierarchy and runtime information for each individual merge.

Example:

Merge the OTU tables $PWD/t1.biom,$PWD/t2.biom,$PWD/t3.biom,$PWD/t4.biom and write the resulting output table to the $PWD/merged/ directory.

parallel_merge_otu_tables.py -i $PWD/t1.biom,$PWD/t2.biom,$PWD/t3.biom,$PWD/t4.biom -o $PWD/merged/