API Reference

cfutils.run.report_mutation

def report_mutation(
    query_ab1_file: str,
    subject_fasta_file: str,
    output_dir: Optional[str] = None,
    file_basename: Optional[str] = None,
    report_all_sites: bool = False,
    report_mut_plot: bool = False,
) -> None:
    """Report mutation within region, optionally generate plot and TSV output."""

• query_ab1_file: Path to the ABI file (Sanger sequencing data)
• subject_fasta_file: Path to the reference FASTA file
• output_dir: Output directory for results (optional)
• file_basename: Output file basename (optional)
• report_all_sites: If True, report all aligned sites; otherwise, only mutation sites
• report_mut_plot: If True, generate a PDF plot of the mutation region

---

cfutils.parser.parse_abi

def parse_abi(path: str) -> SeqRecord:
    """Parse an ABI file and return a SeqRecord object."""

---

cfutils.show.plot_chromatograph

def plot_chromatograph(
    seq: SeqRecord,
    region: Optional[Tuple[int, int]] = None,
    ax: Optional[matplotlib.axes.Axes] = None,
    show_bases: bool = True,
    show_positions: bool = True,
    color_map: Optional[dict] = None,
) -> matplotlib.axes.Axes:
    """Plot a chromatogram for a given sequence region."""

---

For more details, see the source code and docstrings in each module.