biocantor.gene.cds_frame

Module Contents

Classes

CDSPhase	It is important not to confuse Phase with Frame. From the GFF3 specification:
CDSFrame	From the GFF3 specification:

class biocantor.gene.cds_frame.CDSPhase

Bases: enum.Enum

It is important not to confuse Phase with Frame. From the GFF3 specification:

The phase is one of the integers 0, 1, or 2, indicating the number of bases forward from the start of the current CDS feature the next codon begins. A phase of “0” indicates that a codon begins on the first nucleotide of the CDS feature (i.e. 0 bases forward), a phase of “1” indicates that the codon begins at the second nucleotide of this CDS feature and a phase of “2” indicates that the codon begins at the third nucleotide of this region.

NONE

ZERO = 0

ONE = 1

TWO = 2

static from_int(value: int) → CDSPhase

to_frame() → CDSFrame

https://github.com/ucscGenomeBrowser/kent/blob/022eb4f62a0af16526ca1bebcd9e68bd456265dc/src/inc/gff3.h#L281-L293

to_gff() → str

In GFF format, Phase is represented with a period for NONE

class biocantor.gene.cds_frame.CDSFrame

Bases: enum.Enum

From the GFF3 specification:

Frame is generally calculated as a value for a given base relative to the start of the complete open reading frame (ORF) or the codon (e.g. modulo 3) while CDS phase describes the start of the next codon relative to a given CDS feature.

Frame is easier to work with computationally because for any given position it can be calculated by the distance from transcription start % 3. Care must be taken for strand – if the CDS is on the minus strand, then this calculation instead becomes distance from transcription stop % 3.

NONE

ZERO = 0

ONE = 1

TWO = 2

static from_int(value: int) → CDSFrame

shift(shift: int) → CDSFrame

to_phase() → CDSPhase

Converts frame to phase