denoiser_postprocess.py – Merge denoiser output with OTU picker output

Description:

Combine mapping files from denoiser and OTU picker, such that we have a combined mapping file that can be used for the subsequent steps of Qiime. Also replace flowgram identifiers with IDs assigned by split_libraries.py.

Usage: denoiser_postprocess.py [options]

Input Arguments:

Note

[REQUIRED]

-p, --otu_picker_map_file

Path to OTU picker mapping file [REQUIRED]

-f, --fasta_fp

Path to fasta input file, output of split_libraries.py [REQUIRED]

-d, --denoised_fasta_fp

Path to denoised fasta file [REQUIRED]

[OPTIONAL]

-o, --output_dir

Path to output directory [default: Denoiser_out_otu_picked/]

-m, --map_file

Path to denoiser mapping file [default: denoiser_mapping.txt]

Output:

The output of denoiser_postprocess.py are two files:

denoised_otu_map.txt: In this mapping the read/flowgram IDs are

replaced by sample_id from the split_libraries.py fasta file. Also, the lists for each OTU are sorted such that the largest cluster from denosing appears first. This will be important for the next step, picking representative sequences.

denoised_all.fasta: A fasta sequence where the header lines are

updated with the sample_ids as assigned by split_libraries.py.

Combine denoiser output with output of QIIME OTU picker, put results into Outdir:

denoiser_postprocess.py -f seqs.fna -d denoised.fasta -m denoiser_mapping.txt -p cdhit_picked_otus/denoised_otus.txt -v -o Outdir