Quickstart

This guide gets you up and running with Bioquik.

Command-line usage

Bioquik operates on a directory of FASTA files.

bioquik count \
  --patterns ATG,CG* \
  --seq-dir data/fasta \
  --out-dir results \
  --workers 4 \
  --plot

Parameters

  • --patterns: Comma-separated motif patterns (wildcards supported)

  • --seq-dir: Directory containing .fasta files

  • --out-dir: Output directory for reports

  • --workers: Number of parallel worker processes

  • --plot: Generate plots

Python usage

from pathlib import Path
from bioquik.processor import run_count

run_count(
    pattern_list=["ATG", "CG*"],
    seq_dir=Path("data/fasta"),
    out_dir=Path("results"),
    workers=4,
)

Notes

  • run_count processes all FASTA files in seq_dir

  • Results are written to out_dir

  • The function returns None

Single-file processing (advanced)

from bioquik.fasta_worker import process_fasta_file
from bioquik.motifs import build_pattern_to_motifs

mapping = build_pattern_to_motifs(["ATG"])

csv_path = process_fasta_file(
    "example.fasta",
    mapping,
    out_dir="results"
)