uorf4u (version 0.8.0):
a bioinformatics tool for conserved upstream ORF annotation.
Home page and documentation:
art-egorov.github.io/uorf4u
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COMMAND-LINE PARAMETERS
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[POST-INSTALL DATA]
--data
    Creates the 'uorf4u_data' folder in the current working directory.
    The folder contains adjustable configuration files used by uorf4u
    (e.g. config, SD-aSD energies table, palettes...).
--linux
    Replaces the tools paths in the pre-made config files from the MacOS'
    version [default] to the Linux'.
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[MANDATORY ARGUMENTS]
-an <accession_number>	
	Protein's RefSeq accession number.
  OR
-hl <accession_number1 [accession_number2, ...]>
	Space separated list of proteins accession numbers which will be used
	as list of homologous.
  OR
-hlf <file.txt>
	Path to a file with list of accession numbers. File format:
	one accession number per line, no header.
  OR
-fa <file.fa>
    Path to a fasta file with upstream sequences.
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[OPTIONAL ARGUMENTS]
-bh <number_of_hits>
    Max number of blastp hits in homologous search.
-bid <identity_cutoff>
    blastp searching cutoff for hit's identity to your query protein.
-mna <number_of_assemblies>
    Max number of assemblies to take into analysis for each protein.
    If there are more sequences in the identical protein database then
    random sampling will be used.
-al <path_to/assemblies_list.tsv>
	Path to an assemblies list file (see documentation for details).
-annot
    Retrieve sequences annotation from the NCBI to be sure that
    annotated uORFs are not overlapped with a known CDS [default: false].
-ul <length>
    Length of upstream sequences.
-dl <length>
    Length of downstream sequences.
-asc
    Include alternative start codons in uORF annotation step.
    List of alternative start codons are taken from the ncbi genetic code.
-nsd
    Deactivate filtering ORFs by SD sequence presence.
    [default is True for 'prokaryotes' config and False for 'eukaryotes' config].
-at <aa|nt>
	Alignment type used by uorf4u for conserved ORFs searching [default: aa]
-pc <presence_cutoff>
    A cutoff of presence (number of ORFs in a list/number of sequences) for an ORFs set
    to be called conserved and returned [default: 0.4, set in config].
-fast
    Fast searching mode with less accuracy (>~300 sequences or >~2000 ORFs).
-c <bacteria|eukaryotes|<file.cfg>
	Path to a configuration file or name of a premade config file
	[default: prokaryotes].
-o <name> 
	Output dir name. It will be created if it's not exist.
	All output dirs will be then created in this folder
	[default: uorf4u_{current_date}; e.g. uorf4u_2022_07_25-20_41].
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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.