sort_otu_table.py – Script for sorting the sample IDs in an OTU table based on a specified value in a mapping file.

Description:

Usage: sort_otu_table.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_otu_table

Input OTU table filepath in BIOM format.

-o, --output_fp

Output OTU table filepath.

[OPTIONAL]

-m, --mapping_fp

Input metadata mapping filepath. [default: None]

-s, --sort_field

Category to sort OTU table by. [default: None]

-l, --sorted_sample_ids_fp

Sorted sample id filepath [default: None]

Output:

Default:

case insensitive natural sorting i.e. SAMP0, samp1, SAMP2, samp10, samp12

sort_otu_table.py -i otu_table.biom -o sorted_otu_table.biom

sort samples by the age field in the mapping file

sort_otu_table.py -i otu_table.biom -o dob_sorted_otu_table.biom -m Fasting_Map.txt -s DOB

sort samples based on order in a file where each line starts with a sample id

sort_otu_table.py -i otu_table.biom -o sorted_otu_table.biom -l sample_id_list.txt