biotite.sequence.Location

class biotite.sequence.Location(first, last, strand=<Strand.FORWARD: 1>, defect=<Defect.NONE: 0>)[source]

Bases: object

A Location defines at which base(s)/residue(s) a feature is located.

A feature can have multiple Location instances if multiple locations are joined.

Objects of this class are immutable.

Attributes
firstint

Starting base or residue position of the feature.

lastint

Inclusive ending base or residue position of the feature.

strandStrand

The strand direction. Always Strand.FORWARD for peptide features.

defectDefect

A possible defect of the location.

class Defect[source]

Bases: enum.Flag

This enum type describes location defects.

A location has a defect, when the feature itself is not directly located in the range of the first to the last base.

  • NONE - No location defect

  • MISS_LEFT - A part of the feature has been truncated before the first base/residue of the Location (probably by indexing an Annotation object)

  • MISS_RIGHT - A part of the feature has been truncated after the last base/residue of the Location (probably by indexing an Annotation object)

  • BEYOND_LEFT - The feature starts at an unknown position before the first base/residue of the Location

  • BEYOND_RIGHT - The feature ends at an unknown position after the last base/residue of the Location

  • UNK_LOC - The exact position is unknown, but it is at a single base/residue between the first and last residue of the Location, inclusive

  • BETWEEN - The position is between to consecutive bases/residues.

NONE = 0
MISS_LEFT = 1
MISS_RIGHT = 2
BEYOND_LEFT = 4
BEYOND_RIGHT = 8
UNK_LOC = 16
BETWEEN = 32
class Strand[source]

Bases: enum.Enum

This enum type describes the strand of the feature location. This is not relevant for residue peptide features.

FORWARD = 1
REVERSE = 2