Сommand-line parameters

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

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.

Optional arguments | Data processing

-ufid, --use-filename-as-id: Use filename (wo extension) as track (contig) id instead
of the contig id written in the gff/gb file.
-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.
-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.
-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.)

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>: 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]
-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.

Optional arguments | Additional tracks

-hl, --homology-links: Draw homology link track.
-slt, --scale-line-track: Draw scale line track.

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]

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.