merge_otu_maps.py – Merge OTU mapping files

Description:

This script merges OTU mapping files generated by denoise_wrapper.py and/or pick_otus.py

For example, if otu_map1.txt contains:

0	seq1	seq2	seq5
1	seq3	seq4
2	seq6	seq7	seq8

and otu_map2.txt contains:

110	0	2
221	1

The resulting OTU map will be:

110	seq1	seq2	seq5	seq6	seq7	seq8
221	seq3	seq4

Usage: merge_otu_maps.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --otu_map_fps

The otu map filepaths, comma-separated and ordered as the OTU pickers were run [REQUIRED]

-o, --output_fp

Path to write output OTU map [REQUIRED]

[OPTIONAL]

-f, --failures_fp

Failures filepath, if applicable

Output:

The result of this script is an OTU mapping file.

Expand an OTU map:

If the seq_ids in otu_map2.txt are otu_ids in otu_map1.txt, expand the seq_ids in otu_map2.txt to be the full list of associated seq_ids from otu_map1.txt. Write the resulting otu map to otu_map.txt (-o).

merge_otu_maps.py -i $PWD/otu_map1.txt,$PWD/otu_map2.txt -o $PWD/otu_map_ex1.txt

Expand a failures file:

Some OTU pickers (e.g. uclust_ref) will generate a list of failures for sequences which could not be assigned to OTUs. If this occurs in a chained OTU picking process, the failures file will need to be expanded to include the orignal sequence ids. To do this, pass the failures file via -f, and the otu maps up to, but not including, the step that generated the failures file.

merge_otu_maps.py -i $PWD/otu_map1.txt,$PWD/otu_map2.txt -f $PWD/fail.txt -o $PWD/all_failures.txt