tracts.tract.Tract#

class Tract(start, end, label, bpstart=None, bpend=None)#

Bases: object

Represent a labeled genomic interval.

A tract is the basic object manipulated by Tracts. Higher-level structures are built from collections of tracts. Each tract is defined by an interval and an associated label, typically corresponding to an ancestry.

Parameters:

  • start (float) – Starting position of the tract, in Morgans.

  • end (float) – Ending position of the tract, in Morgans.

  • label (str) – Identifier associated with the tract. In most applications, this corresponds to the ancestry carried by the tract.

  • bpstart (int, optional) – Starting position of the tract, in base pairs. This attribute is optional, since Tracts primarily uses Morgans internally. Default is None.

  • bpend (int, optional) – Ending position of the tract, in base pairs. This attribute is optional, since Tracts primarily uses Morgans internally. Default is None.

__init__(start, end, label, bpstart=None, bpend=None)#

Initialize a Tract instance.

Parameters:

  • start (float) – Starting position of the tract, in Morgans.

  • end (float) – Ending position of the tract, in Morgans.

  • label (str) – Identifier associated with the tract. In most applications, this corresponds to the ancestry carried by the tract.

  • bpstart (int, optional) – Starting position of the tract, in base pairs. This attribute is optional, since Tracts primarily uses Morgans internally. Default is None.

  • bpend (int, optional) – Ending position of the tract, in base pairs. This attribute is optional, since Tracts primarily uses Morgans internally. Default is None.

copy()#

Return a copy of the tract.

Returns:

New Tract instance with the same attributes as the current tract.

Return type:

Tract

get_label()#

Return the label of the tract.

Returns:

Label associated with the tract.

Return type:

str

is_equal(other)#

Check whether two tracts have the same start, end, and label.

Parameters:

other (Tract) – Tract to compare with the current instance.

Returns:

True if both tracts have identical start, end, and label attributes, and False otherwise.

Return type:

bool

len()#

Return the length of the tract in Morgans.

Returns:

Length of the tract, computed as end - start.

Return type:

float