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switch to create_validator for FastqRead sequence validation
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afrubin committed Dec 17, 2019
1 parent 34846d2 commit 671e73b
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions fqfa/fastq/fastqread.py
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand All @@ -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:
"""
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