Validation

Bioquik includes validation helpers to ensure inputs are correct before processing.

Directory validation

from pathlib import Path
from bioquik.validate import validate_dir

validate_dir(Path("data/fasta"), name="seq_dir")

Ensures the path exists and is a directory.

Pattern validation

from bioquik.validate import validate_patterns

patterns = validate_patterns("ATG,CG*")

Ensures:

  • At least one pattern is provided

  • Patterns are split correctly

  • At least one pattern includes CG

Returns a list of validated patterns.

Common mistakes

Passing a FASTA file instead of a directory

run_count(["ATG"], Path("file.fasta"), ...)

Fix: pass the parent directory containing FASTA files.

Using unsupported keywords

run_count("file.fasta", motifs=["ATG"])

Fix: use the documented signature:

run_count(pattern_list, seq_dir, out_dir, workers)