genomics-assembly

genomics-assembly

When to use

Load this skill for the file-based analysis named in the description. The function library and CLI share the same calculations; no external aligner, assembler, caller or annotation service is started.

Use from a step

from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill("genomics-assembly")
data = read_input("input.fasta", reader=library.read_records)
result = library.analyze(data)
write_output(result, "tables/result.csv")
write_output(library.distribution_figure(result), "figures/distribution.png")

Run examples/example_step.py through the step runner for a small, hand-worked synthetic fixture. It asserts known summary values. The reader materializes the input in memory; use bounded FASTQ reads or pre-filter large genomic files before loading them.

API

read_records(path: str | Path) -> pd.DataFrame

Read records through read_input(path, reader=library.read_records).

:param path: Existing input file in the format documented under Inputs and outputs. :returns: Parsed records as a DataFrame. :raises ValueError: Input values or file structure cannot be parsed.

analyze(data: pd.DataFrame, *, genome_size: int=0) -> pd.DataFrame

Compute assembly summaries and return a new table, leaving data unchanged.

:param data: Records containing contig, sequence. :param genome_size: CLI default 0 omits completeness; otherwise expected genome bases. :returns: Result table with diagnostics and summary in attrs['run_info']. :raises ValueError: Required columns are absent or records are empty or invalid.

run_info(data: pd.DataFrame, *, keep: bool=True) -> dict

Return the analysis diagnostics and summary.

:param data: Result returned by analyze. :param keep: Keep diagnostics by default; the CLI passes False. :returns: Independent diagnostics dictionary. :raises ValueError: analyze has not populated diagnostics.