NAME

       subset_biom - subset a BIOM file, over either the observations or samples

SYNOPSIS

       subset_biom   [options]   {-i/--biom_fp   BIOM_FP   -a/--axis   AXIS   -s/--ids_fp  IDS_FP
       -o/--output_fp OUTPUT_FP}

DESCRIPTION

       [] indicates optional  input  (order  unimportant)  {}  indicates  required  input  (order
       unimportant)

       Subset  a  BIOM  file,  over either the observations or samples, without fully parsing it.
       This script is intended to assist working with very large tables when tight on memory,  or
       as  a light weight way to subset a full table. Currently, it is possible to produce tables
       with rows or columns (observations or samples) that are fully zerod.

       Example usage: Print help message and exit

              subset_biom -h

       Subset the observations in my_data.biom file.

              subset_biom -i my_data.biom -a observations -s file_with_ids

OPTIONS

       --version
              show program's version number and exit

       -h, --help
              show this help message and exit

       -v, --verbose
              Print information during execution -- useful for debugging [default: False]

              REQUIRED options:

              The following options must be provided under all circumstances.

       -i BIOM_FP, --biom_fp=BIOM_FP
              the BIological Observation Matrix filepath [REQUIRED]

       -a AXIS, --axis=AXIS
              The axis to subset over [REQUIRED]

       -s IDS_FP, --ids_fp=IDS_FP
              A file containing a single column of IDs to retain [REQUIRED]

       -o OUTPUT_FP, --output_fp=OUTPUT_FP
              A file to write the result to [REQUIRED]