A software tool for gene discovery using customizable databases. It generates comprehensive, colour-coded reports for easy interpretation and visualization of results.
virtualenv camel_env --python=python3.11
. camel_env/bin/activate
python setup.py install
A config file is required to run the workflow. A sample file is available under camel/config/config.yml.sample.
Be sure to check and modify the values for your system.
cp {PATH_TO_INSTALLATION}/camel/config/config.yml.sample {PATH_TO_INSTALLATION}/camel/config/config.yml
vim {PATH_TO_INSTALLATION}/camel/config/config.yml
- BLAST+ 2.14.0 (for BLAST-based detection)
- CD-HIT 4.6.8 (for constructing databases)
The corresponding executables should be in your PATH to run the workflow. Other versions of these tools may work, but have not been tested.
Note: Absolute paths are recommended for the scripts.
usage: gene_detection [-h] [--sample-name SAMPLE_NAME] --output-dir OUTPUT_DIR --output-html OUTPUT_HTML [--working-dir WORKING_DIR] [--threads THREADS] --fasta FASTA [--fasta-name FASTA_NAME] --database-dir DATABASE_DIR
[--blast-min-percent-identity BLAST_MIN_PERCENT_IDENTITY] [--blast-min-percent-coverage BLAST_MIN_PERCENT_COVERAGE] [--blast-task {blastn,megablast}]
optional arguments:
-h, --help show this help message and exit
--sample-name SAMPLE_NAME
Dataset name (will be determined from the input if not specified)
--output-dir OUTPUT_DIR
Output directory
--output-html OUTPUT_HTML
Output HTML report
--working-dir WORKING_DIR
Working directory for temporary files
--threads THREADS Number of threads to use
--fasta FASTA Input FASTA file
--fasta-name FASTA_NAME
Input FASTA file name
--database-dir DATABASE_DIR
Input database directory
--blast-min-percent-identity BLAST_MIN_PERCENT_IDENTITY
Minimum percent identity
--blast-min-percent-coverage BLAST_MIN_PERCENT_COVERAGE
Minimum percent target coverage
--blast-task {blastn,megablast}
Value of the blast '-task' parameter
--version Print version and exit
A basic usage example is provided below:
gene_detection \
--fasta /path/to/my_contigs.fasta \
--database-dir /path/to/db \
--output-html /path/to/output/report.html
The tool requires a database in the correct format.
The mainmakegenedetectiondb.py script can be used to create databases from FASTA files. Clustering is performed to
limit the output to a single hit for each database cluster (defined by the --identity-cutoff parameter).
usage: gene_detection_create_db [-h] --fasta FASTA [--fasta-name FASTA_NAME] [--identity-cutoff IDENTITY_CUTOFF] --output-html OUTPUT_HTML --output-dir OUTPUT_DIR [--working-dir WORKING_DIR] [--threads THREADS]
optional arguments:
-h, --help show this help message and exit
--fasta FASTA Input FASTA file.
--fasta-name FASTA_NAME
Name of the input FASTA file (for Galaxy input).
--identity-cutoff IDENTITY_CUTOFF
Clustering identity cutoff (%), entries with a higher value are combined into a single cluster.
--output-html OUTPUT_HTML
Output HTML file with database construction information.
--output-dir OUTPUT_DIR
Output directory.
--working-dir WORKING_DIR
Working directory for temporary files.
--threads THREADS Number of threads to use.
A basic usage example is provided below:
mainmakegenedetectiondb.py --fasta /path/to/my_db.fasta --identity-cutoff 90 --output-dir /path/to/db/out
In case of questions, issues or other feedback, you can contact: