seismicrna.cleanfa package

Submodules

FASTA Cleaner Module

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])

FASTA Cleaning Module

seismicrna.cleanfa.main.run(input_path: tuple[str, ...], *, inplace: bool = False, out_dir: str = './out', force: bool = False, max_procs: int = 16, parallel: bool = True)

Clean the names and sequences in FASTA files.

Parameters:

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

  • out_dir (str) – 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]

  • max_procs (int) – Run up to this many processes simultaneously [keyword-only, default: 16]

  • parallel (bool) – Run tasks in parallel or in series [keyword-only, default: True]