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 <group|proteins>
    Mode to define homologous proteins from the database.
    If "group" is selected, a query protein is assigned to the
    same homologous group as that of the best search hit
    protein. In "proteins" mode, all target proteins that
    pass the cutoffs are considered to be homologues.
    [default: group]
-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: 0.2]
-mse, --mmseqs-evalue
    MMseqs search evalue cutoff [default: 1e-5]
-fm, --fast-mmseqs
    MMseqs search only against a database of representative sequences.
    [default: False]
-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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