anospp-analysis

Python package for ANOSPP data analysis

ANOSPP is the multiplexed amplicon sequencing assay for Anopheles mosquito species identification and Plasmodium detection. This repository contains the code for analysis of the sequencing results pre-processed with nf-core ampliseq pipeline.

Installation

For released version

conda install -c bioconda anospp-analysis

For development setup, see instructions below

Usage

Key analysis steps are implemented as standalone scripts:

• anospp-prep takes DADA2 output files and targets primer sequences, demultiplexes the amplicons and yields haplotypes table
• anospp-qc takes haplotypes table, DADA2 stats table and samples manifest and produces QC plots
• anospp-plasm blasts Plasmodium sequences against reference dataset to determine species and infer sample infection status
• anospp-nn compares k-mer profiles of mosquito targets against a reference dataset and provides probabilistic species calls
• anospp-vae provides finer scale species prediction for An. gambiae complex with VAE projection

Development

Setup

Installation is hybrid with conda + poetry:

git clone git@github.com:malariagen/anospp-analysis.git
cd anospp-analysis
mamba env create -f environment.yml
conda activate anospp_analysis_dev
poetry install

Usage & testing

The code in this repository can be accessed via wrapper scripts:

anospp-qc \
    --haplotypes test_data/haplotypes.tsv \
    --samples test_data/samples.csv \
    --stats test_data/stats.tsv \
    --outdir test_data/qc

Besides, individual components are available as a python API:

$ python
>>> from anospp_analysis.util import *
>>> PLASM_TARGETS
['P1', 'P2']

TODO Automated testing & CI

Adding Python deps

Introducing python dependencies should be done via poetry:

poetry add package_name

This should update both pyproject.toml and poetry.lock files

If the package should be used in development environment only, use

poetry add package_name --dev

To update environment after changes made to pyproject.toml and/or poetry.lock

poetry install

Adding non-Python deps

Introducing non-python dependencies should be done via conda: edit environment.yml, then re-create the conda environment and poetry deps:

mamba env create -f environment.yml
conda activate anospp_analysis
poetry install

Changes in conda environment might also introduce changes to the python installation, in which case one should update poetry lock file

poetry lock