config.txt

# SET UP 

[configuration]
# external programs
prokka = helpers/programs/prokka-1.12/bin/prokka
blastn = helpers/programs/ncbi-blast-2.6.0+/bin/blastn
blastp = helpers/programs/ncbi-blast-2.6.0+/bin/blastp
makeblastdb = helpers/programs/ncbi-blast-2.6.0+/bin/makeblastdb
mash = helpers/programs/mash-Linux64-v1.1.1/mash

# support databases
attr_db = helpers/support_data/attr_database/update_attR_database
orfX = helpers/support_data/orfx.fasta
pbp2a = helpers/support_data/pbp2a.fasta
ccr = helpers/support_data/ccr.fasta
core_db = helpers/support_data/core_database/core_db
base_network = helpers/support_data/network_k32_s100000_267_SCCmec.eda
chunk = helpers/support_data/sketch_mash_268.msh
threshold = 0.9860

# core analysis
core_proteins_sccmec = helpers/support_data/core_proteins/info.txt
core_dir = helpers/support_data/core_proteins/

# dir with sequence(s) to analize
input_dir = INPUT/
# outputs
output =OUTPUT/
prefix_output = output

# kNN data
features = helpers/support_data/output_mash_distance_columns.txt
labels = helpers/support_data/sccmec_specific_type_labels.txt