Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants
Project description
gnomon
Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variations
Provides a library of functions for use within scripts, as well as a CLI tool for linking the functions together to produce output
Usage
usage: gnomon [-h] --vcf_file VCF_FILE --genome_object GENOME_OBJECT [--catalogue_file CATALOGUE_FILE]
[--ignore_vcf_filter] [--progress] [--output_dir OUTPUT_DIR] [--json] [--alt_json] [--fasta FASTA]
options:
-h, --help show this help message and exit
--vcf_file VCF_FILE the path to a single VCF file
--genome_object GENOME_OBJECT
the path to a compressed gumpy Genome object or a genbank file
--catalogue_file CATALOGUE_FILE
the path to the resistance catalogue
--ignore_vcf_filter whether to ignore the FILTER field in the vcf (e.g. necessary for some versions of
Clockwork VCFs)
--progress whether to show progress using tqdm
--output_dir OUTPUT_DIR
Directory to save output files to. Defaults to wherever the script is run from.
--json Flag to create a single JSON output as well as the CSVs
--alt_json Whether to produce the alternate JSON format. Requires the --json flag too
--fasta FASTA Use to output a FASTA file of the resultant genome. Specify either 'fixed' or 'variable'
for fixed length and variable length FASTA respectively.
Helper usage
As the main script can utilise pickled gumpy.Genome objects, there is a supplied helper script. This converts a Genbank file into a pickled gumpy.Genome for significant time saving.
Due to the security implications of the pickle module, DO NOT SEND/RECEIVE PICKLES. This script should be used on a host VM before running nextflow to avoid reinstanciation.
Supports gzip compression to reduce file size significantly (using the --compress flag).
usage: gbkToPkl FILENAME [--compress]
Install
Currently there may be some issues with versions of gumpy/piezo on pypi, so these may need to be installed from git beforehand.
git clone git@github.com:GlobalPathogenAnalysisService/gnomon.git
cd gnomon
pip install .
TODO: PyPi
Docker
A Docker image should be built on releases. To open a shell with Gnomon installed:
docker run -it oxfordmmm/gnomon:latest
User stories
-
As a bioinformatician, I want to be able to run
gnomonon the command line, passing it (i) a GenBank file (or pickledgumpy.Genomeobject), (ii) a resistance catalogue and (iii) a VCF file, and get backpandas.DataFramesof the genetic variants, mutations, effects and predictions/antibiogram. The latter is for all the drugs described in the passed resistance catalogue. -
As a GPAS developer, I want to be able to embed
gnomonin a Docker image/NextFlow pipeline that consumes the outputs of tb-pipeline and emits a structured, well-designedJSONobject describing the genetic variants, mutations, effects and predictions/antibiogram. -
In general, I would also like the option to output fixed- and variable-length FASTA files (the latter takes into account insertions and deletions described in any input VCF file).
Unit testing
For speed, rather than use NC_000962.3 (i.e. H37Rv M. tuberculosis), we shall use SARS-CoV-2 and have created a fictious drug resistance catalogue, along with some vcf files and the expected outputs in tests/.
These can be run with pytest -vv
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