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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
.TH VIRULENCEFINDER.PY "1" "July 2021" "virulencefinder.py 2.0.4" "User Commands"
.SH NAME
virulencefinder.py \- identify virulence genes in total or partial sequenced isolates of bacteria
.SH DESCRIPTION
usage: virulencefinder.py [\-h] \fB\-i\fR INFILE [INFILE ...] [\-o OUTDIR]
.TP
[\-tmp TMP_DIR] [\-mp METHOD_PATH] [\-p DB_PATH]
[\-d DATABASES] [\-l MIN_COV] [\-t THRESHOLD] [\-x]
[\-\-speciesinfo_json SPECIESINFO_JSON] [\-q]
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-i\fR INFILE [INFILE ...], \fB\-\-infile\fR INFILE [INFILE ...]
FASTA or FASTQ input files.
.TP
\fB\-o\fR OUTDIR, \fB\-\-outputPath\fR OUTDIR
Path to blast output
.TP
\fB\-tmp\fR TMP_DIR, \fB\-\-tmp_dir\fR TMP_DIR
Temporary directory for storage of the results from
the external software.
.TP
\fB\-mp\fR METHOD_PATH, \fB\-\-methodPath\fR METHOD_PATH
Path to method to use (kma or blastn)
.TP
\fB\-p\fR DB_PATH, \fB\-\-databasePath\fR DB_PATH
Path to the databases
.TP
\fB\-d\fR DATABASES, \fB\-\-databases\fR DATABASES
Databases chosen to search in \- if non is specified
all is used
.TP
\fB\-l\fR MIN_COV, \fB\-\-mincov\fR MIN_COV
Minimum coverage
.TP
\fB\-t\fR THRESHOLD, \fB\-\-threshold\fR THRESHOLD
Minimum hreshold for identity
.TP
\fB\-x\fR, \fB\-\-extented_output\fR
Give extented output with allignment files, template
and query hits in fasta and a tab seperated file with
gene profile results
.TP
\fB\-\-speciesinfo_json\fR 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.
.HP
\fB\-q\fR, \fB\-\-quiet\fR
.SH AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.
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