ANOSPP data analysis
Project description
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.
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 tableanospp-qc
takes haplotypes table, DADA2 stats table and samples manifest and produces QC plots
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
poetry install
Activate development environment:
poetry shell
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']
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
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
Release checklist
While in dev branch
- test functionality (TODO CI)
- bump version in
pyproject.toml
Then
- merge into master
- github release
- pypi release
Conda recipe update conda.recipe/meta.yaml
:
- check deps vs
environment.yaml
andpyproject.toml
- bump version
- update sha256
- test conda recipe with
bioconda-utils build --git-range master
vs bioconda-recipes
Project details
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