get_all_vfdb.sh generates the gene databases for ALL genera found in CP_VFs.ffn.
Usage:
bash /srst2/database_clustering/get_all_vfdb.sh ${VFDB_ffn_file} ${OutputDir}
Example usage:
bash /srst2/database_clustering/get_all_vfdb.sh ./CP_VFs.ffn ./VFDB_geneDB
get_genus_vfdb.sh generates the gene database for a single specified genus found in CP_VFs.ffn.
Usage:
bash /srst2/database_clustering/get_genus_vfdb.sh ${VFDB_ffn_file} ${Genus} ${OutputDir}
Example usage:
bash /srst2/database_clustering/get_genus_vfdb.sh ./CP_VFs.ffn Bacillus ./Bacillus_VF_geneDB
These two scripts need to live in the same folder as all the other python scripts in /srst2/database_clustering/
These scripts also require that cd-hit is installed to $PATH somewhere
I added two bash scripts that automate the generation of the VFDB gene databases following the instructions from here: https://github.com/katholt/srst2#using-the-vfbd-virulence-factor-database-with-srst2
get_all_vfdb.sh generates the gene databases for ALL genera found in CP_VFs.ffn. Usage: bash /srst2/database_clustering/get_all_vfdb.sh ${VFDB_ffn_file} ${OutputDir} Example usage: bash /srst2/database_clustering/get_all_vfdb.sh ./CP_VFs.ffn ./VFDB_geneDB
get_genus_vfdb.sh generates the gene database for a single specified genus found in CP_VFs.ffn. Usage: bash /srst2/database_clustering/get_genus_vfdb.sh ${VFDB_ffn_file} ${Genus} ${OutputDir} Example usage: bash /srst2/database_clustering/get_genus_vfdb.sh ./CP_VFs.ffn Bacillus ./Bacillus_VF_geneDB
These two scripts need to live in the same folder as all the other python scripts in /srst2/database_clustering/
These scripts also require that cd-hit is installed to $PATH somewhere