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