per_library_stats.py – Calculate statistics on data in a BIOM-formatted OTU table

Description:

Given an otu table in BIOM format, compute and print the (min, max, median, mean) number of seqs per library.

Usage: per_library_stats.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --otu_table_fp

Path to the input OTU table (i.e., the output from make_otu_table.py)

[OPTIONAL]

-m, --mapping_fp

A mapping file. If included, this script will modify the mapping file to include sequences per sample (library) information, and write the modified mapping file to the path specified by -o. The sequences per sample is presented in a new column entitled “SequenceCount”, and samples present in the mapping file but not the otu table have the value “na” in this column. Note also that the location of comments is not preserved in the new mapping file

-o, --output_mapping_fp

The output filepath where the modified mapping file will be written

--num_otus

Counts are presented as number of observed OTUs per sample, rather than counts of sequences per sample [default: False]

Output:

The resulting statistics are written to stdout. If -m is passed, a new mapping file is written to the path specified by -o, in addition to the statistics written to stdout

Write to standard out:

Calculate statistics on an OTU table

per_library_stats.py -i otu_table.biom

Write to standard out and edit mapping file:

Calculate statistics on an OTU table and add sequence/sample count data to mapping file.

per_library_stats.py -i otu_table.biom -m Fasting_Map.txt -o map.txt