jmtsuji / qiime2-helpers

Helper scripts to streamline QIIME2 analyses

qiime2-helpers

Repo with helper scripts for QIIME2 analyses

All scripts can be run through the Linux command line.

Contents

generate_combined_feature_table.py

Adds taxonomy and representative sequence information onto a TSV-format FeatureTable

Dependencies:

• python >= 3
• pandas
• biopython

Installation: First, add the script to your PATH. Then, install all dependencies. If using conda:

conda create -n generate_combined_feature_table -c conda-forge \
  python=3 pandas biopython

conda activate generate_combined_feature_table

If interested, run the automated end-to-end test with:

testing/generate_combined_feature_table/test_generate_combined_feature_table.sh \
  testing/generate_combined_feature_table

Example usage (test data in repo):

# Assuming you are in the Github repo directory
input_dir="testing/generate_combined_feature_table/inputs"

generate_combined_feature_table.py \
  -f "${input_dir}/feature_table.tsv" \
  -s "${input_dir}/representative_seqs.fasta" \
  -t "${input_dir}/taxonomy.tsv" \
  -o "test_table.tsv" \
  --parse_taxonomy

run generate_combined_feature_table.py -h for full usage instructions.

Other scripts

Docs coming soon...