iLund4u
Home page and documentation: https://art-egorov.github.io/ilund4u/
The Atkinson Lab 4U | AE
-------- PROTEIN MODE ---------
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    COMMAND-LINE PARAMETERS
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[MANDATORY ARGUMENTS]
-fa <path>
    Path to a fasta file with query protein sequence.
-db <path>
    Path to iLund4u database.
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[OPTIONAL ARGUMENTS | DATA PROCESSING]
-hsm, --homology-search-mode <best|all>
    Mode to define homologous families from the database.
    If "best" is selected, results are shown only for the
    protein family which representative sequence is the closest
    to the query. If "all" is selected, results for all families 
    that pass the cutoffs are shown.
    [default: all]
-msqc, --mmseqs-query-cov <float>
    MMseqs search query coverage cutoff [default: 0.65]
-mstc, --mmseqs-target-cov <float>
    MMseqs search query coverage cutoff [default: 0.65]
-msf, --mmseqs-fident <float>
    MMseqs search fident (fraction of identical matches) cutoff
    [default: 0.25]
-mse, --mmseqs-evalue
    MMseqs search evalue cutoff [default: 1e-5]
-rnf, --report-not-flanked
    Report in results hotspots that have flanked conserved genes only on one
    side (located on the end of non-circular sequences) [default: False]
-ql, --query-label <str>
    Label for query protein homologues on LoVis4u visualisation.
    [default: database protein names]
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[OPTIONAL ARGUMENTS | OTHERS]
-o <name>
    Output dir name. This will be created if it does not exist.
	[default: ilund4u_{current_date}; e.g. ilund4u_2022_07_25-20_41]
-c <standard|<file.cfg>
    Path to a configuration file or name of a premade config file
    [default: standard]
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[MISCELLANEOUS ARGUMENTS]
--debug
    Provide a detailed stack trace for debugging purposes.
-q, --quiet
    Don't show progress messages.
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