diff --git a/fqfa/fastq/fastqread.py b/fqfa/fastq/fastqread.py index e7dd36f..08bd185 100644 --- a/fqfa/fastq/fastqread.py +++ b/fqfa/fastq/fastqread.py @@ -2,12 +2,12 @@ """ -import re from dataclasses import dataclass, field, InitVar from typing import List, Optional, ClassVar, Callable from statistics import mean from fqfa.util.util import reverse_complement - +from fqfa.validator.validator import create_validator +from fqfa.constants.iupac.dna import DNA_BASES @dataclass class FastqRead: @@ -21,7 +21,7 @@ class FastqRead: quality: List[int] = field(init=False) quality_string: InitVar[str] quality_encoding_value: int = 33 - sequence_validator: ClassVar[Callable] = re.compile(r"[ACGTN]+").fullmatch + sequence_validator: ClassVar[Callable] = create_validator(DNA_BASES + ["N"]) def __post_init__(self, quality_string: str) -> None: """