kcftools getAttributes

The getAttributes command in kcftools is used to extract attribute information from a KCF (K-mer Comparison Format) file. This is useful for summarizing or analyzing the metadata or numerical properties computed during variation or IBS detection.

Usage

$ kcftools getAttributes -i=<kcfFile> -o=<outFile>

Description

KCF files store per-window or per-feature variation or similarity scores along with associated metadata. getAttributes parses this data and outputs attribute summaries or tables in a more accessible format (e.g., TSV or similar) for downstream analysis.

The command takes an input .kcf file and produces one or more output files prefixed with the name you specify. These files may contain:

  • Per-window attribute scores (e.g., variation score, IBS score, k-mer counts)
  • Any other feature-level statistics computed during KCF generation

This can be used to perform statistical analyses, generate custom plots, or inspect data before further processing.

Options

Option Description Required
-i, --input=<kcfFile> Input KCF file from which to extract attributes Yes
-o, --output=<outFile> Output file prefix for saving extracted results Yes
-a, --attributes=<attrList> Comma-separated list of specific attributes to extract (default: all) No

Output

The output will typically include one or more .tsv or .txt files prefixed by the provided output name. The actual file(s) depends on the structure of the input KCF and may contain:

  • Region identifiers (chromosome, start, end)
  • Per-sample or per-region attribute scores
  • Metadata such as sample name, feature type, score thresholds

For example:

$ attributes_output.tsv

Example

$ kcftools getAttributes -i sample.kcf -o sample_attributes

This will extract all available attribute data from sample.kcf and write it to files prefixed with sample_attributes.

Note

  • This command is read-only—it does not modify the original KCF.
  • Useful when preparing data for visualization (e.g., in R or Python plotting tools).
  • You can use this to summarize scores before applying filters with tools like findIBS or kcfToMatrix.

Help

To view help for this command:

$ kcftools getAttributes --help