Module `cstag.utils.validator`

Expand source code

from __future__ import annotations

import re


def validate_cs_tag(cs_tag: str) -> None:
    pattern = re.compile(
        r"^(=[ACGTN]+|:[0-9]+|\*[acgtn][acgtn]|\+[acgtn]+|\-[acgtn]+|\~[acgtn][acgtn][0-9]+[acgtn][acgtn])*$"
    )

    if not pattern.fullmatch(cs_tag.replace("cs:Z:", "")):
        raise ValueError(f"Invalid cs tag: {cs_tag}")


def validate_short_format(cs_tag: str) -> None:
    if re.search(r"=[ACGTN]+", cs_tag):
        raise ValueError("cs tag must be in short format")


def validate_long_format(cs_tag: str) -> None:
    if re.search(r":[0-9]+", cs_tag):
        raise ValueError("cs tag must be in long format")


def validate_threshold(threshold: int) -> None:
    if not isinstance(threshold, int):
        raise ValueError("threshold must be an integer")

    if not 0 <= threshold <= 40:
        raise ValueError("threshold must be within a range between 0 to 40")


def validate_pos(pos: int) -> None:
    if pos < 1:
        raise ValueError(f"pos must be a positive integer, but got {pos}")

Functions

def validate_cs_tag(cs_tag: str) ‑> None

Expand source code

def validate_cs_tag(cs_tag: str) -> None:
    pattern = re.compile(
        r"^(=[ACGTN]+|:[0-9]+|\*[acgtn][acgtn]|\+[acgtn]+|\-[acgtn]+|\~[acgtn][acgtn][0-9]+[acgtn][acgtn])*$"
    )

    if not pattern.fullmatch(cs_tag.replace("cs:Z:", "")):
        raise ValueError(f"Invalid cs tag: {cs_tag}")

def validate_long_format(cs_tag: str) ‑> None

Expand source code

def validate_long_format(cs_tag: str) -> None:
    if re.search(r":[0-9]+", cs_tag):
        raise ValueError("cs tag must be in long format")

def validate_pos(pos: int) ‑> None

Expand source code

def validate_pos(pos: int) -> None:
    if pos < 1:
        raise ValueError(f"pos must be a positive integer, but got {pos}")

def validate_short_format(cs_tag: str) ‑> None

Expand source code

def validate_short_format(cs_tag: str) -> None:
    if re.search(r"=[ACGTN]+", cs_tag):
        raise ValueError("cs tag must be in short format")

def validate_threshold(threshold: int) ‑> None

Expand source code

def validate_threshold(threshold: int) -> None:
    if not isinstance(threshold, int):
        raise ValueError("threshold must be an integer")

    if not 0 <= threshold <= 40:
        raise ValueError("threshold must be within a range between 0 to 40")