Jasentool

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

Full documentation: jasentool.readthedocs.io.

Installation

pip install jasentool

A conda environment.yml is also provided for development installs.

Usage

jasentool <subcommand> [options]

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

Subcommands

Post-run analysis

Subcommand	Description
find	Query samples from MongoDB
identify-missing	Identify samples absent from JASEN results directory
validate-pipelines	Compare pipeline outputs against MongoDB records

Pipeline processes

Subcommand	Description
annotate-delly	Annotate Delly structural-variant VCFs with gene symbols and locus tags
concatenate-files	Concatenate multiple YAML files (e.g. versions.yml)
count-reads	Count reads in FASTQ file(s)
create-blacklist	Aggregate minority base frequencies across BAMs to produce a blacklist TSV
create-yaml	Create YAML input file for Bonsai upload
minority-report	Compute minority base frequency distribution from a samtools mpileup file
post-align-qc	Compute post-alignment QC from BAM

Site-specific hooks

Subcommand	Description
reformat-csv	Reformat BJORN CSV/SH files for JASEN

Setup & reference data

Subcommand	Description
converge-catalogues	Merge WHO, TBdb, and FoHM TB mutation catalogues
download-bigsdb	Download cgMLST scheme alleles from PubMLST or BIGSdb
download-ncbi	Download genome FASTA and GFF from NCBI
transform-file-format	Convert cgMLST target TSV to BED format

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

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.