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/