Gff Class

Gff

Gff(
    gff_file: str | Path,
    name: str | None = None,
    target_seqid: str | None = None,
    min_range: int | None = None,
    max_range: int | None = None,
)

GFF Parser Class

PARAMETER	DESCRIPTION
gff_file	GFF file (*.gz, *.bz2, *.zip compressed file can be readable) TYPE: str | Path
name	name (If None, file name is set) TYPE: str | None DEFAULT: None
target_seqid	Target seqid to be extracted. If None, only first seqid record is extracted. TYPE: str | None DEFAULT: None
min_range	Min range to be extracted. If None, appropriate value is taken from GFF records. TYPE: int | None DEFAULT: None
max_range	Max range to be extracted. If None, appropriate value is taken from GFF records. TYPE: int | None DEFAULT: None

name property

name: str

Name

seq_region property

seq_region: tuple[int, int]

GFF sequence-region start & end tuple

If ##sequence-region pragma is not found, seq_region=(0, max_coords_value)

records property

records: list[GffRecord]

GFF records (target seqid only)

all_records property

all_records: list[GffRecord]

All GFF records

records_within_range property

records_within_range: list[GffRecord]

GFF records within min-max range

range_size property

range_size: int

Range size (max_range - min_range)

target_seqid property

target_seqid: str

Target seqid

seqid_list property

seqid_list: list[str]

seqid list

get_seqid2size

get_seqid2size() -> dict[str, int]

Get seqid & complete/contig/scaffold genome size dict

By default, size is defined by ##sequence-region pragma of target seqid. If ##sequence-region is not found, size is defined by max coordinate size in target seqid features. This may differ from actual genome size.

RETURNS	DESCRIPTION
seqid2size	seqid & genome size dict TYPE: dict[str, int]

get_seqid2features

get_seqid2features(
    feature_type: str | None = "CDS",
    target_strand: int | None = None,
    pseudogene: bool | None = False,
) -> dict[str, list[SeqFeature]]

Get seqid & features in target seqid genome dict

PARAMETER	DESCRIPTION
feature_type	Feature type (CDS, gene, mRNA, etc...) If None, extract regardless of feature type. TYPE: str | None DEFAULT: 'CDS'
target_strand	Extract target strand. If None, extract regardless of strand. TYPE: int | None DEFAULT: None
pseudogene	If True, pseudo=, pseudogene= tagged record only extract. If False, pseudo=, pseudogene= not tagged record only extract. If None, extract regardless of pseudogene tag. TYPE: bool | None DEFAULT: False

RETURNS	DESCRIPTION
seqid2features	seqid & features dict TYPE: dict[str, list[SeqFeature]]

extract_features

extract_features(
    feature_type: str | None = "CDS",
    target_strand: int | None = None,
    pseudogene: bool | None = False,
) -> list[SeqFeature]

Extract features within min-max range

PARAMETER	DESCRIPTION
feature_type	Feature type (CDS, gene, mRNA, etc...) If None, extract regardless of feature type. TYPE: str | None DEFAULT: 'CDS'
target_strand	Extract target strand. If None, extract regardless of strand. TYPE: int | None DEFAULT: None
pseudogene	If True, pseudo=, pseudogene= tagged record only extract. If False, pseudo=, pseudogene= not tagged record only extract. If None, extract all regardless of pseudogene tag. TYPE: bool | None DEFAULT: False

RETURNS	DESCRIPTION
features	Feature list TYPE: list[SeqFeature]

extract_exon_features

extract_exon_features(feature_type: str = 'mRNA') -> list[SeqFeature]

Extract exon structure features within min-max range

Extract exons based on parent feature and exon ID-Parent relation

PARAMETER	DESCRIPTION
feature_type	Feature type (e.g. mRNA, ncRNA , etc...) TYPE: str DEFAULT: 'mRNA'

RETURNS	DESCRIPTION
features	Feature list TYPE: list[SeqFeature]