LoVis4u (version 0.0.3):
Home page and documentation: https://github.com/art-egorov/lovis4u
The Atkinson Lab 4U | Artyom Egorov
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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.
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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]
-laf, --loci-annotation-file <file path>
    Path to the loci annotation table.
    (See documentation for details)
-faf, --features-annotation-file <file path>
    Path to the features annotation table.
    (See documentation for details)
-mmseqs-off, --mmseqs-off
   Deactivate mmseqs clustering of proteomes of loci.
-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.
-reorient_loci, --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 | LOCI VISUALISATION]
-sgc-off, --set-group-color-off
    Deactivate auto-setting of feature fill and stroke colors.
    (Pre-set colors specified in feature annotation table will be kept.)
-sgcf, --set-group-color-for <feature_group1 [feature group2 ...]>
    Space-separated list of feature groups for which colors should be set.
    [default: variable, labeled]
-scc, --set-category-color
    Set category color for features and plot category color legend.
-cct, --category-color-table <file path>
    Path to the table with color code for categories.
    Default table can be found in lovis4u_data folder.
-lls, --loci-label-style <id|description|full>
    Locus label style based on input sequence annotation.
-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]
-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]
-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: auto (0.0022 - 0.02, depending on window size)]
-fw, --figure-width <float value>
    Output figure width in cm.
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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 premade 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.
-q, --quiet
    Don't show progress messages.