virulencefinder.py1
Identify virulence genes in total or partial sequenced isolates of bacteria
Overview
usage: virulencefinder.py [-h] -i INFILE [INFILE ...] [-o OUTDIR]
- [-tmp TMP_DIR] [-mp METHOD_PATH] [-p DB_PATH]
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[-d DATABASES] [-l MIN_COV] [-t THRESHOLD] [-x] [--speciesinfo_json SPECIESINFO_JSON] [-q]
optional arguments:
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-h, --help -
show this help message and exit
-iINFILE [INFILE ...],--infileINFILE [INFILE ...]-
FASTA or FASTQ input files.
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-o OUTDIR, --outputPath OUTDIR -
Path to blast output
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-tmp TMP_DIR, --tmp_dir TMP_DIR -
Temporary directory for storage of the results from the external software.
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-mp METHOD_PATH, --methodPath METHOD_PATH -
Path to method to use (kma or blastn)
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-p DB_PATH, --databasePath DB_PATH -
Path to the databases
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-d DATABASES, --databases DATABASES -
Databases chosen to search in - if non is specified all is used
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-l MIN_COV, --mincov MIN_COV -
Minimum coverage
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-t THRESHOLD, --threshold THRESHOLD -
Minimum hreshold for identity
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-x, --extented_output -
Give extented output with allignment files, template and query hits in fasta and a tab seperated file with gene profile results
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--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