Module `cstag.to_sequence`

Expand source code

from __future__ import annotations

from cstag.split import split
from cstag.utils.validator import validate_cs_tag, validate_long_format


def to_sequence(cs_tag: str) -> str:
    """Reconstruct the reference subsequence in the alignment

    Args:
        cs_tag (str): cs tag in the **long** format

    Returns:
        str: The sequence string derived from the cs tag.

    Example:
        >>> import cstag
        >>> cs_tag = "=AC*gt=T-gg=C+tt=A"
        >>> cstag.to_sequence(cs_tag)
        'ACTTCTTA'
    """
    validate_cs_tag(cs_tag)
    validate_long_format(cs_tag)

    cs_tag = cs_tag.replace("cs:Z:", "")
    sequence = []
    for cs in split(cs_tag):
        if cs.startswith("="):
            sequence.append(cs[1:].upper())
        elif cs.startswith("+"):
            sequence.append(cs[1:].upper())
        elif cs.startswith("*"):
            sequence.append(cs[-1].upper())

    return "".join(sequence)

Functions

def to_sequence(cs_tag: str) ‑> str

Reconstruct the reference subsequence in the alignment

Args

cs_tag : str: cs tag in the long format

Returns

str: The sequence string derived from the cs tag.

Example

>>> import cstag
>>> cs_tag = "=AC*gt=T-gg=C+tt=A"
>>> cstag.to_sequence(cs_tag)
'ACTTCTTA'

Expand source code

def to_sequence(cs_tag: str) -> str:
    """Reconstruct the reference subsequence in the alignment

    Args:
        cs_tag (str): cs tag in the **long** format

    Returns:
        str: The sequence string derived from the cs tag.

    Example:
        >>> import cstag
        >>> cs_tag = "=AC*gt=T-gg=C+tt=A"
        >>> cstag.to_sequence(cs_tag)
        'ACTTCTTA'
    """
    validate_cs_tag(cs_tag)
    validate_long_format(cs_tag)

    cs_tag = cs_tag.replace("cs:Z:", "")
    sequence = []
    for cs in split(cs_tag):
        if cs.startswith("="):
            sequence.append(cs[1:].upper())
        elif cs.startswith("+"):
            sequence.append(cs[1:].upper())
        elif cs.startswith("*"):
            sequence.append(cs[-1].upper())

    return "".join(sequence)