"""Toolkit functions for working with BLAT."""
from __future__ import annotations
from pathlib import Path
from pxblat.extc import TwoBitToFaOption, faToTwoBit, twoBitToFa
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__all__ = ["fa_to_two_bit", "two_bit_to_fa"]
[docs]
def fa_to_two_bit(
inFiles: list[str],
outFile: str,
*,
noMask: bool = False,
stripVersion: bool = False,
ignoreDups: bool = False,
useLong: bool = False,
):
"""Convert one or more FASTA files to two-bit format.
Args:
inFiles (List[str]): A list of paths to the input FASTA files.
outFile (str): The path to the output two-bit file.
noMask (bool, optional): If True, do not mask the output sequence. Defaults to False.
stripVersion (bool, optional): If True, strip the version number from the sequence IDs. Defaults to False.
ignoreDups (bool, optional): If True, ignore duplicate sequences in the input files. Defaults to False.
useLong (bool, optional): If True, use the long format for the two-bit file. Defaults to False.
Returns:
None
This function converts one or more input FASTA files to two-bit format and saves the result to the specified output file.
The function takes several optional arguments that control the behavior of the conversion process, such as whether to mask
the output sequence or strip the version number from the sequence IDs. The function returns None.
Example:
>>> fa_to_two_bit(["input.fasta"], "output.2bit")
"""
return faToTwoBit(inFiles, outFile, noMask, stripVersion, ignoreDups, useLong)
[docs]
def two_bit_to_fa(
inName: str | Path,
outName: str | Path,
option: TwoBitToFaOption,
):
"""Converts a .2bit file to a .fa file.
This function takes the name of an input .2bit file and an output .fa file, and an option object,
converts the .2bit file to .fa format using the `twoBitToFa` function, and saves the result to the output file.
Args:
inName (Union[str, Path]): The name or Path of the input .2bit file.
outName (Union[str, Path]): The name or Path of the output .fa file.
option (TwoBitToFaOption): The options to use when converting the .2bit file.
Returns:
The return value from the `twoBitToFa` function.
"""
if isinstance(inName, Path):
inName = str(inName)
if isinstance(outName, Path):
outName = str(outName)
return twoBitToFa(inName, outName, option)