LoVis4u (version 0.2.0):
Home page and documentation: https://github.com/art-egorov/lovis4u
The Atkinson Lab 4U | AE
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COMMAND-LINE PARAMETERS
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[POST-INSTALL STEPS]
--data
    Creates the 'lovis4u_data' folder in the current working directory.
    The folder contains adjustable configuration files used by lovis4u
    (e.g. config, palettes...)
--linux
    Replaces the mmseqs path in the pre-made config file from the MacOS
    version [default] to the Linux version.
--mac
    Replaces the mmseqs path in the pre-made config file from the Linux
    version [default] to the MacOS version.
-smp, --set-mmseqs-path <path>
    Specify mmseqs path that will be used by LoVis4u. Can be either full path
    to the binary mmseqs, "default_mac", or "default_linux". In case if mmseqs
    is installed in the system and available without specifying its path, you can
    run "-smp mmseqs" and this should work.
--get-hmms
    Download HMMs (hmmscan format) of defence, anti-defence, virulence,
    and AMR proteins from our server [data-sharing.atkinson-lab.com]
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[MANDATORY ARGUMENTS]
-gff <folder>
    Path to a folder containing extended gff files.
    Each gff file should contain corresponding nucleotide sequence.
    (designed to handle pharokka produced annotation files).
 OR
-gb <folder>
    Path to a folder containing genbank files.
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[OPTIONAL ARGUMENTS | DATA PROCESSING]
-w, --windows <locus_id1:start1:end1:strand [locus_id1:start1:end1:strand ...]>
    Specify window of visualisation (coordinates) for a locus or multiple loci
-wp, --window-by-proteins <protein_id1 protein_id2>
    Specify window of visualisation by protein id from any locus. If homologues of these proteins
    are encoded by each locus, then coordinates of visualisation will be defined automatically.
    If you want to start visualisation from a particular protein (to rotate loci), you can specify it
    for start and end ('-wp protein_id1 protein_id1')
-align, --align-loci
    If a conserved protein with homologues present in all loci exists, then LoVis4u
    automatically defines the visualisation window starting from that protein family.
-bg, --bedgraphs <bedGraph_file1 [bedgGaph_file2 ...]>
    Space separated list of paths to bedGraph files to plot coverage profiles.
    (>=1 file) ! Can be applied only for single locus.
-bw, --bigwigs <bigWig_file1 [bigWig_file2 ...]>
    Space separated list of paths to bigWig files to plot coverage profiles.
    (>=1 file) ! Can be applied only for single locus.
-bgl, --bedgraph-labels <bedgraph_label1 [bedgraph_label2 ...]>
    List of labels for bedgraph/bigWig tracks (order the same as order of bedgraph/bigWig files)
    By default basename of files will be used.
-bgc, --bedgraph-colours <bedgraph_colour1 [bedgraph_colour2 ...]>
    List of colours for bedgraph/bigWig tracks (order the same as order of bedGraph/bigWig files)
    Each value can be either HEX code of colour name (e.g. pink, blue, etc (from the palette file))
-gc, --gc-track
    Show GC content track. ! Can be applied only for single locus.
-gc_skew, --gc_skew-track
    Show GC skew track. ! Can be applied only for single locus.
-ufid, --use-filename-as-id
    Use filename (wo extension) as track (contig) id instead
    of the contig id written in the gff/gb file.
-alip, --add-locus-id-prefix
    Add locus id prefix to each feature id.
-laf, --locus-annotation-file <file path>
    Path to the locus annotation table.
    (See documentation for details)
-faf, --feature-annotation-file <file path>
    Path to the feature annotation table.
    (See documentation for details)
-mmseqs-off, --mmseqs-off
    Deactivate mmseqs clustering of proteomes of loci.
-mmsi, --mmseqs-min-seq-id <float>
    MMSeqs2 parameter for minimal sequence identity during clustering.
    [default: 0.4]
-mc, --mmseqs-coverage <float>
    MMSeqs2 parameter for minimal coverage during clustering.
    [default: 0.75]
-hmmscan, --run-hmmscan
    Run hmmscan search for additional functional annotation.
-dm, --defence-models <DefenseFinder|PADLOC|both>
    Choose which defence system database to use for hmmscan search
    [default: both (DefenseFinder and PADLOC)]
-hmm, --add-hmm-models <folder_path [name]>
    Add your own hmm models database for hmmscan search. Folder should
    contain files in HMMER format (one file per model). Usage: -hmm path [name].
    Specifying name is optional, by default it will be taken from them folder name.
    If you want to add multiple hmm databases you can use this argument several
    times: -hmm path1 -hmm path2.
-omh, --only-mine-hmms
    Force to use only models defined by user with -hmm, --add-hmm-models parameter.
-kdn, --keep-default-name
    Keep default names and labels for proteins that have hits with
    hmmscan search. [default: name is replaced with target hmm model name]
-kdc, --keep-default-category
    Keep default category for proteins that have hits with hmmscan
    search. [default: category is replaced with database name]
-salq, --show-all-labels-for-query
    Force to show all labels for proteins that have hits to any database with hmmscan search.
    [default: False]
-cl-owp, --cluster-only-window-proteins
    Cluster only proteins that are overlapped with the visualisation windows, not all.
-fv-off, --find-variable-off
    Deactivate annotation of variable or conserved protein clusters.
-cl-off, --clust_loci-off
    Deactivate defining locus order and using similarity based hierarchical
    clustering of proteomes.
-oc, --one-cluster
    Consider all sequences to be members of one cluster but use clustering
    dendrogram to define the optimal order.
-rol, --reorient_loci
    Auto re-orient loci (set new strands) if they are not matched.
    (Function tries to maximise co-orientation of homologous features.)
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[OPTIONAL ARGUMENTS | LOCUS VISUALISATION]
-sgc-off, --set-group-colour-off
    Deactivate auto-setting of feature fill and stroke colours.
    (Pre-set colours specified in feature annotation table will be kept.)
-sgcf, --set-group-colour-for <feature_group1 [feature group2 ...]>
    Space-separated list of feature groups for which colours should be set.
    [default: variable, labeled]
-scc, --set-category-colour
    Set category colour for features and plot category colour legend.
-cct, --category-colour-table <file path>
    Path to the table with colour code for categories.
    Default table can be found in lovis4u_data folder.
-lls, --locus-label-style <id|description|full>
    Locus label style based on input sequence annotation.
-llp, --locus-label-position <left|bottom|top_left|top_center>
    Locus label position on figure.
-safl, --show-all-feature-labels
    Display all feature labels.
-sflf, --show-feature-label-for  <feature_group1 [feature group2 ...]>
    Space-separated list of feature groups for which label should be shown.
    [default: variable, labeled]
-sfflf, --show-first-feature-label-for <feature_group1 [feature group2 ...]>
    Space-separated list of feature group types for which label will be displayed
    only for the first occurrence of feature homologues group.
    [default: shell/core]
-snl, --show-noncoding-labels
    Show all labels for non-coding features. [default: False]
-sfnl, --show-first-noncoding-label
    Show labels only for the first occurrence for non-coding features.
    [default: False]
-ifl, --ignored-feature-labels <feature_label1 [feature_label2 ...]>
    Space-separated list of feature names for which label won't be shown.
    [default: hypothetical protein, unknown protein]
-sxa, --show-x-axis
    Plot individual x-axis for each locus track.
-hix, --hide-x-axis
    Do not plot individual x-axis for each locus track.
-dml, --draw-middle-line
    Draw middle line for each locus.
-mm-per-nt, --mm-per-nt <float value>
    Scale which defines given space for each nt cell on canvas.
    [default: 0.05]
-fw, --figure-width <float value>
    Output figure width in mm.
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[OPTIONAL ARGUMENTS | ADDITIONAL TRACKS]
-hl, --homology-links
    Draw homology link track.
-slt, --scale-line-track
    Draw scale line track.
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[OPTIONAL ARGUMENTS | OTHERS]
-o <name>
    Output dir name. It will be created if it does not exist.
	[default: lovis4u_{current_date}; e.g. uorf4u_2022_07_25-20_41]
--pdf-name <name>
    Name of the output pdf file (will be saved in the output folder).
    [default: lovis4u.pdf]
-c <standard|<file.cfg>
    Path to a configuration file or name of a pre-made config file
    [default: standard]
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[MISCELLANEOUS ARGUMENTS]
-h, --help
    Show this help message and exit.
-v, --version
    Show program version.
--debug
    Provide detailed stack trace for debugging purposes.
--parsing-debug
    Provide detailed stack trace for debugging purposes
    for failed reading of gff/gb files.
-q, --quiet
    Don't show progress messages.