annotale-tools

A wrapper for running AnnoTALE commands and parsing output.

Dependencies

The following packages/tools are needed for installation

• uv (for installation)
• python>=3.10
• openjdk>=17.0.10
• polars>=1.31.0
• typer>=0.16.0

This tool comes packaged with:

• AnnoTALEcli-1.5.jar

Installation

Building from source:

git clone https://github.com/dagsdags212/annotale-tools.git
cd annotale-tools.git
make

Usage

Show available commands:

annotale --help

TALE gene annotation

Predict TALE sequences from an input Xanthomonas genome:

annotale predict <FASTA>

Enable senitive mode and specify strain:

annotale predict --sensitive --strain PXO99A <FASTA>

TALE gene classification

Extract the components (C-terminus, CVR, N-terminus) of prediced TALE genes:

annotale analyze <FASTA>

Download the class builder file for assigning TALE groups:

annotale load-and-view --outdir <XML>

Classify TALE sequences:

annotale assign <FASTA> \    # FASTA file with predicted TALE components 
    --strain <strain> \      # Specify strain
    --accession <acc>        # Label with accession

Target site prediction

Scan for TALE target sites from a list of query sequences:

annotale targets \
    <query> \                # FASTA file containing query sequences (e.g. promoter list)
    --tales <tales> \        # FASTA file containing TALE sequences
    --outdir <outdir>        # Path to directory for storing output

Use all TALE genes from the class builder rather than specifying your TALE sequences:

annotale targets <query> --use-cb

Running pipelines

The package also allows for running entire workflows using a single command.

Recommended way of running the TALE annotation pipeline:

annotale annotate <FASTA> --strain <strain> --accession <accession> --outdir <outdir>

# Equivalent comand
annotale annotate <FASTA> -s <strain> -a <accession> -O <outdir>

Summarizing results

List all predicted TALE genes:

annotale tabulate \
    <outdir>      \   # Directory containing output from running the `annotate` subcommand
    --csv             # print in CSV format

Query a TALE gene for related classes and display strain information:

# <tale> must match the pattern: Tal[A-Z]{2}[0-9]{1,2}.*
annotale neighbors <tale>

TODO

• add support for annotating multiple FASTA files from a list of filepaths
• add support for annotating Xoo assemblies from NCBI/ENA accessions
• implement the remaining commands
  • rename
  • targets
  • presence
  • repdiff
  • preditale
  • dertale