Jasentool

Multipurpose tool for jobs related to the JASEN pipeline and Bonsai.

Full documentation: jasentool.readthedocs.io.

Installation

pip install jasentool

Older Linux distributions (recommended: conda)

On hosts with glibc < 2.28 (Ubuntu < 18.04, RHEL/CentOS < 8, Debian < 10), pip can't find binary wheels for current pandas and numpy on Python 3.12, so it falls back to source builds that need GCC 9.3 or newer. Use conda instead; conda-forge ships compatible binaries:

git clone https://github.com/SMD-Bioinformatics-Lund/jasentool.git
cd jasentool
conda env create -f environment.yml
conda activate jasentool

environment.yml pulls the heavy dependencies (pandas, numpy, matplotlib, biopython, pysam, cyvcf2, openpyxl) from conda-forge, then installs jasentool itself in editable mode.

compare-distances uses cgmlst-dists (from bioconda) to build its distance matrices, and environment.yml includes it. It isn't a pip dependency, so pip install jasentool won't bring it in; get it through conda or build it yourself. Without it, compare-distances falls back to a slower pure-Python calculation.

Usage

jasentool <subcommand> [options]

Run jasentool --help to list subcommands, or jasentool <subcommand> --help for per-subcommand help.

Subcommands

Post-run analysis

Pipeline processes

Site-specific hooks

Setup & reference data

Quick examples

Query samples from MongoDB

jasentool find \
  --query MySampleID \
  --db-name mydb \
  --db-collection samples \
  --output-file results.json

Identify missing samples

jasentool identify-missing \
  --output-file missing.json \
  --db-name mydb \
  --db-collection samples \
  --analysis-dir /path/to/jasen/results

Validate pipeline outputs

jasentool validate-pipelines \
  --input-dir /path/to/new/results \
  --output-dir /path/to/validation/output \
  --db-name mydb \
  --db-collection samples

Cross-check backup storage

jasentool check-backup \
  --profile staphylococcus_aureus \
  --backup-dir /backup/jasen \
  --db-name bonsai \
  --db-collection samples \
  --address mongodb://bonsai.host:27017/ \
  -o backup_status.csv

Compute post-alignment QC

jasentool post-align-qc \
  --sample-id SAMPLE_ID \
  --bam-file SAMPLE.bam \
  --output-file SAMPLE_qc.json \
  [--bed-file regions.bed] \
  [--cpus 4]

See the Usage docs for full details.