virulencefinder.py - identify virulence genes in total or partial
sequenced isolates of bacteria
usage: virulencefinder.py [-h] -i INFILE [INFILE ...] [-o
OUTDIR]
- [-tmp TMP_DIR] [-mp METHOD_PATH] [-p DB_PATH]
- [-d DATABASES] [-l MIN_COV] [-t THRESHOLD] [-x] [--speciesinfo_json
SPECIESINFO_JSON] [-q]
- -h, --help
- show this help message and exit
- -i INFILE [INFILE ...],
--infile INFILE [INFILE ...]
- FASTA or FASTQ input files.
- -o OUTDIR,
--outputPath OUTDIR
- Path to blast output
- -tmp TMP_DIR,
--tmp_dir TMP_DIR
- Temporary directory for storage of the results from the external
software.
- -mp METHOD_PATH,
--methodPath METHOD_PATH
- Path to method to use (kma or blastn)
- -p DB_PATH,
--databasePath DB_PATH
- Path to the databases
- -d DATABASES,
--databases DATABASES
- Databases chosen to search in - if non is specified all is used
- -l MIN_COV, --mincov
MIN_COV
- Minimum coverage
- -t THRESHOLD,
--threshold THRESHOLD
- Minimum hreshold for identity
- -x,
--extented_output
- Give extented output with allignment files, template and query hits in
fasta and a tab seperated file with gene profile results
- --speciesinfo_json
SPECIESINFO_JSON
- Argument used by the cge pipeline. It takes a list in json format
consisting of taxonomy, from domain -> species. A database is chosen
based on the taxonomy.
-q, --quiet
This manpage was written by Nilesh Patra for the Debian
distribution and
can be used for any other usage of the program.