NAME
virulencefinder.py - identify virulence genes in total or partial sequenced isolates of bacteria
DESCRIPTION
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]
optional arguments:
- -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
AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.