agglovar.bed.col

Utilities for managing columns.

Classes

CoordCol	Represents coordinate columns to use.
CoordColExpr	Represents coordinate column expressions.

Functions

get_coord_cols(→ CoordCol)	Get columns representing coordinates.
standardize(→ str)	Standardize column names.

Module Contents

class agglovar.bed.col.CoordCol

Bases: collections.abc.Iterable[str], collections.abc.Container[str]

Represents coordinate columns to use.

Variables:

• chrom – Chromosome column name.

• pos – Position column name.

• end – End column name.

__contains__(o: Any | None)

Test whether o is one of the coordinate column names.

__iter__()

Iterate over chrom, pos, and end column names.

__repr__()

Return a string representation.

exprs(alias: Self | str | tuple[str, str, str] | None = None, suffix: str = None) → CoordColExpr

Get column expressions.

Parameters:

• alias – Alias to these columns.

• suffix – Suffix to add to the column names.

Returns:

A tuple of column expressions.

chrom: str

end: str

pos: str

class agglovar.bed.col.CoordColExpr

Bases: collections.abc.Iterable[polars.Expr]

Represents coordinate column expressions.

Variables:

• chrom – Chromosome column expression.

• pos – Position column expression.

• end – End column expression.

__iter__()

Iterate over chrom, pos, and end expressions.

__repr__()

Return a string representation.

col_names()

Get the resulting column name for each column expression.

Returns:

Column names.

chrom: polars.Expr

property chrom_name: str

Output column name of the chromosome expression.

end: polars.Expr

property end_name: str

Output column name of the end expression.

pos: polars.Expr

property pos_name: str

Output column name of the pos expression.

agglovar.bed.col.get_coord_cols(col_names: CoordCol | str | collections.abc.Iterable[str] | None = None) → CoordCol

Get columns representing coordinates.

Columns may have different names, such as “chrom”, “pos”, “end” for references or “qry_id”, “qry_pos”, and “qry_end” for queries. Returns a tuple of three expressions to be used in Polars selects, one for each of these three columns, to select the correct column from the input table and alias them to “chrom”, “pos”, and “end” with a set suffix.

Parameters:

col_names – Column names. Can be an iterable of three strings, or a keyword in “ref” or “qry”. None is equivalent to “ref”.

Returns:

An object with column names.

agglovar.bed.col.standardize(col: str) → str

Standardize column names.

Standard column names are lower-case with alphanumeric, underscore, and dot characters only. Leading and trailing whitespace is stripped, and runs of spaces are replaced with a single underscore. All other characters are removed.

Parameters:

col – Column name.

Returns:

Standard column names.