Installation

Installation

Requirements

• Linux or macOS
• Python 3.10 or later, with ReportLab 4 or later (for the PDF report)
• BBTools 38 or later, for seal.sh, and Java (installed with BBTools by conda)

With conda (recommended)

conda create -n spoligotyper -c conda-forge -c bioconda spoligotyper
conda activate spoligotyper
spoligotyper --version

This installs BBTools and Java too.

With pip

pip install spoligotyper
spoligotyper --version

BBTools is not available from PyPI and must be installed separately, for example with conda install -c bioconda bbmap, or from the BBTools downloads. spoligotyper finds seal.sh in your PATH, or next to the Python interpreter it runs with.

SIT database

SB numbers (Mbovis.org) are included with spoligotyper. Shared international types (SIT) and SITVIT2 families come from the SITVIT2 database, which is not openly licensed and cannot be included. Instead, spoligotyper uses the 9,656 SITVIT2 patterns (3,850 with a SIT) published under GPL-3.0 with SpolLineages (Couvin et al. 2020). Download them once:

spoligotyper-download-sit

The list is downloaded from the SpolLineages repository (a fixed version, checked with its SHA-256 checksum), or from its Zenodo mirror if GitHub cannot be reached, and saved in ~/.cache/spoligotyper/ (or in the folder of the SPOLIGOTYPER_DATA environment variable). spoligotyper then fills the SIT, SITVIT2family and ClosestSIT columns automatically.

• Computers without internet access (e.g. cluster nodes): run spoligotyper-download-sit -o /shared/folder on a computer with access, then spoligotyper --sit-db /shared/folder/sit_database.tsv ..., or set SPOLIGOTYPER_DATA=/shared/folder. Alternatively, copy Spoligo_list.csv and run spoligotyper-download-sit --source Spoligo_list.csv.
• The list dates from 2022: SITs created in SITVIT2 since then are missing (the ClosestSIT column lists the closest known ones).
• Please cite Couvin et al. 2020 (https://doi.org/10.1093/database/baaa108) and Couvin et al. 2019 (https://doi.org/10.1016/j.meegid.2018.12.030) when you report SITs.

From source

git clone https://github.com/duceppemo/spoligotyper
cd spoligotyper
conda env create -f environment.yml
conda activate spoligotyper
pip install --no-deps .
spoligotyper --version

Without installing

From the cloned folder, as long as seal.sh is in your PATH:

python3 -m spoligotyper -h

Updating from 0.3

Version 0.4.0 adds the species check and the lineage, a JSON file and a MultiQC file. The table has 8 new columns after the 12 of version 0.3. Use --no-species for the previous behaviour (one pass over the reads).

Updating from 0.2

Version 0.3.0 needs ReportLab: conda install -c conda-forge reportlab or pip install reportlab (installed automatically with conda or pip). The table has 6 new columns after the original 6, and a PDF report is written next to it (--no-pdf to skip it). See the Changelog.

Updating from 0.1

Version 0.2.0 is an installable package with a spoligotyper command; the spoligotyper.py script is gone. Replace python spoligotyper.py ... by spoligotyper ... (or python -m spoligotyper ... from the cloned folder). The options are the same, except:

• -v now means --verbose; use --version for the version.
• --min-count no longer needs to be set for fasta files: it is 1 for fasta files and 5 for fastq files (0.1 used 4, although its help said 5).

The report has the same name and columns. See the Changelog for all the changes.