seismicrna.cleanfa package

Submodules

class seismicrna.cleanfa.cleanfa.FastaCleaner(seq_type: type[XNA])

Bases: object

run(ifasta: Path, ofasta: Path, force: bool = False)
seismicrna.cleanfa.cleanfa.clean_fasta(fasta_in: Path, fasta_out: Path, force: bool = False)

Clean a FASTA file.

seismicrna.cleanfa.cleanfa.get_non_seq_regex(seq_type: type[XNA])
seismicrna.cleanfa.main.run(input_path: Iterable[str | Path], *, inplace: bool = False, out_dir: str | Path = './out', force: bool = False, num_cpus: int = 4)

Clean the names and sequences in FASTA files.

Parameters:

  • inplace (bool) – Modify files in-place instead of writing new files (CAUTION: you cannot recover the original files afterwards) [keyword-only, default: False]

  • out_dir (str | pathlib._local.Path) – Write all output files to this directory [keyword-only, default: ‘./out’]

  • force (bool) – Force all tasks to run, overwriting any existing output files [keyword-only, default: False]

  • num_cpus (int) – Use up to this many CPUs simultaneously [keyword-only, default: 4]