coordmath

Methods for coordinate-based math and interval manipulation.¶

Contains the following public methods:

require_same_refname() -- ensures that all provided intervals have the same reference name.
get_locus_string() -- returns a formatted string for an interval (<refname>:<start>-<end>).
get_closed_end() -- gets the closed end of an interval given its start and length.

Functions¶

get_closed_end ¶

get_closed_end(start: int, length: int) -> int

Get the closed end of an interval given its start and length.

Parameters:

Name	Type	Description	Default
`start`	`int`	The start position of the interval.	required
`length`	`int`	The length of the interval.	required

Returns:

Type	Description
`int`	The closed end of the interval.

Example

get_closed_end(start=10, length=5) 14

Source code in prymer/api/coordmath.py

def get_closed_end(start: int, length: int) -> int:
    """
    Get the closed end of an interval given its start and length.

    Args:
        start: The start position of the interval.
        length: The length of the interval.

    Returns:
        The closed end of the interval.

    Example:
        >>> get_closed_end(start=10, length=5)
        14
    """
    return start + length - 1

get_locus_string ¶

get_locus_string(record: Interval) -> str

Get the locus-string for an interval.

The output string will have the format <refname>:<start>-<end> No conversion on coordinates is performed, so the output is 0-based, open-ended.

Parameters:

Name	Type	Description	Default
`record`	`Interval`	The interval to get the locus-string for.	required

Returns:

Type	Description
`str`	A locus-string for the interval.

Source code in prymer/api/coordmath.py

def get_locus_string(record: Interval) -> str:
    """
    Get the locus-string for an interval.

    The output string will have the format `<refname>:<start>-<end>`
    No conversion on coordinates is performed, so the output is 0-based, open-ended.

    Args:
        record: The interval to get the locus-string for.

    Returns:
        A locus-string for the interval.
    """
    return f"{record.refname}:{record.start}-{record.end}"

require_same_refname ¶

require_same_refname(*intervals: Interval) -> None

Require that the input intervals all have the same refname.

Parameters:

Name	Type	Description	Default
`intervals`	`Interval`	one or more intervals	`()`

Raises:

Type	Description
`ValueError`	if the intervals do not all have the same refname.

Source code in prymer/api/coordmath.py

def require_same_refname(*intervals: Interval) -> None:
    """
    Require that the input intervals all have the same refname.

    Args:
        intervals: one or more intervals

    Raises:
        ValueError: if the intervals do not all have the same refname.
    """

    refnames = set(i.refname for i in intervals)
    if len(refnames) != 1:
        raise ValueError(f"`intervals` must have exactly one refname\n Found {sorted(refnames)}")