cstag.to_sequence 

 1from __future__ import annotations
 2
 3from .split import split
 4from .utils.validator import validate_cs_tag, validate_long_format
 5
 6
 7def to_sequence(cs_tag: str) -> str:
 8    """Reconstruct the reference subsequence in the alignment
 9
10    Args:
11        cs_tag (str): cs tag in the **long** format
12
13    Returns:
14        str: The sequence string derived from the cs tag.
15
16    Example:
17        >>> import cstag
18        >>> cs_tag = "=AC*gt=T-gg=C+tt=A"
19        >>> cstag.to_sequence(cs_tag)
20        'ACTTCTTA'
21    """
22    validate_cs_tag(cs_tag)
23    validate_long_format(cs_tag)
24
25    cs_tag = cs_tag.replace("cs:Z:", "")
26    sequence = []
27    for cs in split(cs_tag):
28        if cs.startswith(("=", "+")):
29            sequence.append(cs[1:].upper())
30        elif cs.startswith("*"):
31            sequence.append(cs[-1].upper())
32
33    return "".join(sequence)
def to_sequence(cs_tag: str) -> str: 
 8def to_sequence(cs_tag: str) -> str:
 9    """Reconstruct the reference subsequence in the alignment
10
11    Args:
12        cs_tag (str): cs tag in the **long** format
13
14    Returns:
15        str: The sequence string derived from the cs tag.
16
17    Example:
18        >>> import cstag
19        >>> cs_tag = "=AC*gt=T-gg=C+tt=A"
20        >>> cstag.to_sequence(cs_tag)
21        'ACTTCTTA'
22    """
23    validate_cs_tag(cs_tag)
24    validate_long_format(cs_tag)
25
26    cs_tag = cs_tag.replace("cs:Z:", "")
27    sequence = []
28    for cs in split(cs_tag):
29        if cs.startswith(("=", "+")):
30            sequence.append(cs[1:].upper())
31        elif cs.startswith("*"):
32            sequence.append(cs[-1].upper())
33
34    return "".join(sequence)

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'