SequenceSite#

class biopax-explorer.biopax.sequencesite.SequenceSite(*args, **kwargs)[source]#

Bases: SequenceLocation

Class SequenceSite

Definition: Describes a site on a sequence, i.e. the position of a single

nucleotide or amino acid. Usage: A sequence site is always defined based on the reference sequence of the owning entity. For DNARegion and RNARegion it is relative to the region itself not the genome or full RNA molecule.

code generator : rdfobj (author F.Moreews 2023-2024).

Methods

get_comment()	Attribute _comment getter
get_positionStatus()	Attribute _positionStatus getter
get_sequencePosition()	Attribute _sequencePosition getter

attribute_type_by_name
get_uri_string
object_attributes
set_comment
set_positionStatus
set_sequencePosition
set_uri_string
to_json
type_attributes

Methods Summary

attribute_type_by_name()
get_positionStatus()	Attribute _positionStatus getter
get_sequencePosition()	Attribute _sequencePosition getter
get_uri_string()
object_attributes()
set_positionStatus(value)
set_sequencePosition(value)
set_uri_string(uristr)
to_json()
type_attributes()

Methods Documentation

attribute_type_by_name()[source]#

get_positionStatus()[source]#

Attribute _positionStatus getter

The confidence status of the sequence position. This could be: EQUAL: The

SEQUENCE-POSITION is known to be at the SEQUENCE-POSITION. GREATER-THAN: The site is greater than the SEQUENCE-POSITION. LESS-THAN: The site is less than the SEQUENCE-POSITION.

get_sequencePosition()[source]#

Attribute _sequencePosition getter

The integer listed gives the position. The first base or amino acid is position

1. In combination with the numeric value, the property ‘POSITION-STATUS’ allows to express fuzzy positions, e.g. ‘less than 4’.

get_uri_string()[source]#

object_attributes()[source]#

set_positionStatus(value)[source]#

set_sequencePosition(value)[source]#

set_uri_string(uristr)[source]#

to_json()[source]#

type_attributes()[source]#