Quickstart¶

FinaleToolkit works the same way from the command line or from Python. Pick whichever fits your workflow. The features and results are identical.

Command line¶

List the available subcommands:

$ finaletoolkit --help

A few representative runs:

$ finaletoolkit coverage sample.bam intervals.bed -o coverage.bed
$ finaletoolkit wps sample.bam tss.bed --chrom-sizes hg38.chrom.sizes -o wps.bw -t 8
$ finaletoolkit end-motifs sample.bam hg38.2bit -k 4 -o motifs.tsv
$ finaletoolkit delfi sample.bam autosomes.chrom.sizes hg19.2bit bins.bed -g hg19 -o delfi.tsv

Every subcommand has its own --help with a worked example. Flags are consistent across commands, so once you learn them they transfer everywhere:

Flag	Meaning
`-o` / `--output`	Output file path. Use `-` to write to standard output (stdout).
`-r` / `--reference`	Reference FASTA file (required for CRAM input).
`-q` / `--min-mapq`	Minimum mapping quality.
`--min-length` / `--max-length`	Fragment-length bounds, in base pairs.
`-t` / `--threads`	Number of worker processes.
`-v` / `--verbose`	Increase verbosity. Repeat for more detail (`-vv`).
`-k` / `--kmer-length`	k-mer length (motif commands).

Tip

- as an output means “write to standard output” instead of a file, so you can pipe results into another tool, for example finaletoolkit mds motifs.tsv -o - | less.

See the CLI Reference for the complete reference.

Python API¶

Everything is reachable from the top-level finaletoolkit namespace:

import finaletoolkit as ftk

cov = ftk.coverage("sample.bam", "intervals.bed", output_file=None)
motifs = ftk.end_motifs("sample.bam", "hg38.2bit", k=4)
mds = motifs.motif_diversity_score()

The package is also organized into submodules, which remain importable:

Submodule	Contents
`frag`	Fragmentomic feature generation.
`genome`	Utilities for genome tracks and gaps.
`utils`	Helpers that simplify feature generation.
`io`	Reference and alignment or fragment wrappers.
`cli`	Command-line interface.

To load a specific function from its submodule:

>>> from finaletoolkit.frag import delfi