Configuration file parameters

iLund4u configuration file allows detailed customization of the tool's parameters.

Note:
You can copy the lovis4u_data folder that contains the config files to your wiking directory with ilund4u --data command and safely edit and use them without affecting 'internal' config. If you want to use a copied config file, use -c path_to_config.

Detailed description is under construction...

---

;[Data Loading and processing]
default_transl_table = 11
gff_CDS_name_source = product
min_proteome_size = 15
proteome_uniqueness_cutoff = 0.7
proteome_similarity_cutoff = 0.7
leiden_resolution_parameter_p = 0.5
min_proteome_community_size = 10
circular_genomes = True
variable_protein_cluster_cutoff = 0.25
conserved_protein_cluster_cutoff = 0.75
neighbours_max_distance = 8
neighbours_one_side_max_size = 5
neighbours_min_size = 5
island_neighbours_similarity_cutoff = 0.65
leiden_resolution_parameter_i = 0.55
deduplicate_proteomes_within_hotspot = True
hotspot_presence_cutoff = 0.3
hotspot_signature_presence_cutoff = 0.75
hotspot_similarity_cutoff = 0.65
leiden_resolution_parameter_h = 0.55
protein_search_target_mode = group

;[mmseqs parameters]
mmseqs_cluster_mode = 0
mmseqs_cov_mode = 0
mmseqs_min_seq_id = 0.25
mmseqs_c = 0.8
mmseqs_s = 7
mmseqs_search_qcov = 0.6
mmseqs_search_tcov = 0.6
mmseqs_search_fident = 0.2
mmseqs_search_evalue = 1e-5

;[pyhmmer hmmscan parameters]
hmmscan_query_coverage_cutoff = 0.7
hmmscan_hmm_coverage_cutoff = 0.5

;[visualisation]
show_hmmscan_hits_on_full_proteomes = True
lovis4u_hotspot_vis_figure_width = 8
lovis4u_hotspot_mm_per_nt = 0.0125
lovis4u_proteome_mm_per_nt = 0.005
index_only_for_hypothetical_proteins = auto
island_size_cutoff_to_show_index_only = 7
max_number_of_seqs_to_redefine_order = 300

;[HMM]
hmm_defence= {internal}/HMMs/DefenceFinder_CasFinder
hmm_virulence = {internal}/HMMs/VFDB
hmm_anti_defence = {internal}/HMMs/dbAPIS_Acr
hmm_amr = {internal}/HMMs/AMRFinderPlus
database_names = Defence,Virulence,Anti-defence,AMR

;[Other paths]
mmseqs_binary = {internal}/bin/mmseqs_mac/bin/mmseqs
category_colours = {internal}/category_colours_proteome_groups.tsv

;[Output]
verbose = True
debug = False
output_dir = ilund4u_{current_date}

;[URLs]
hmm_models = https://data-sharing.atkinson-lab.com/iLund4u/HMMs.tar.gz
plasmids_db = https://data-sharing.atkinson-lab.com/iLund4u/iLund4u_DB-plasmids.tar.gz
phages_db = https://data-sharing.atkinson-lab.com/iLund4u/iLund4u_DB-phages.tar.gz