ORFfold Parameters#

Mandatory#

  • --faa
    FASTA file containing the amino acid sequences to treat.

  • --options
    Indicates which properties are to be calculated.
    H for estimating the fold potential with HCA,
    I for the estimation of the disorder propensity with IUPred,
    and T for the aggregation propensity with Tango.
    Combinations of letters are accepted if the user wants to calculate several properties at the same time.
    Example: --options HIT will estimate all three properties.
    (Default: H).

  • --path_tango Path to tango executable file

  • --path_iupred Path to iupred executable file

Optional#

  • -h, --help
    Shows this help message and exits.

  • --gff
    GFF annotation file. The ID (i.e., annotation) of the sequences given in the input FASTA file must match the ID label in the GFF file (column #3).
    ORFold generates one GFF file per studied property (fold potential, disorder, and/or aggregation propensities). Each GFF file contains, for the sequences in the input FASTA file, the corresponding property values (fold potential, disorder, or aggregation propensities).
    The values are stored in column #9 of the output GFF files, which can subsequently be uploaded into a genome viewer.
    (See here for examples of this option).

  • --keep
    ORFold uses IUPred and Tango for predicting disorder and aggregation propensities.
    By default, ORFold does not save the output files of these methods to save storage.
    However, with the -keep option, the user can save the Tango output files.
    Example: -keep T will save Tango output files in the TANGO directory.

  • --sample, -N
    Working with large genomes can generate very large files.
    To address this, ORFold allows generating a sample of the initial dataset and performing calculations on this specific subset.
    This option enables the user to specify the number of randomly selected sequences to be treated by ORFold.

  • --out
    Output directory (default: '.').