GTF

CLASS

BASE

CDS, start_codon, stop_codon, UTR5, UTR3, other and other annotation types use this class.

Attributes	data type	info
chr	str	chromosome
start	int	location start
end	int	location end
strand	str	strand ‘+’ or ‘-‘

more info: The attribute value of BASE is readable. That is, after reading from the gtf file for the first time, it cannot be modified.

EXON

Record exon related information.

Attributes	data type	info
chr	str	exon chromosome
start	int	exon location start
end	int	lexon ocation end
strand	str	exon strand ‘+’ or ‘-‘
id	str	exon id

more info: The attribute value of EXON is readable. That is, after reading from the gtf file for the first time, it cannot be modified.

TRANSCRIPT

Record transcript related information.

Attributes	data type	info
id	str	transcript id
name	str	transcript name
chr	str	transcript location chromosome
start	int	transcript location start
end	int	transcript location end
strand	str	transcript strand ‘+’ or ‘-‘
CDS	List[BASE]	transcript CDSs
start_codon	List[BASE]	transcript start_codons
stop_codon	List[BASE]	transcript stop_codons
UTR5	List[BASE]	transcript UTR5s
UTR3	List[BASE]	transcript UTR3s
exons	Dict[EXON.id]=EXON	transcript exons
other	List[BASE]	transcript other annotation types

GENE

Record gene related information.

Attributes	data type	info
id	str	gene id
name	str	gene name
chr	str	gene location chromosome
start	int	gene location start
end	int	gene location end
strand	str	gene strand ‘+’ or ‘-‘
trans	Dict[TRANSCRIPT.id]=TRANSCRIPT	gene transcripts
trans_map	Dict[TRANSCRIPT.name] = TRANSCRIPT.id	map of id and name

GTF

Parse GTF files

Attributes	data type	info
name	str	gtf name
version	str	gtf version
URL	str	download URL of gtf file
genes	Dict[GENE.id]=GENE	gtf genes
genes_map	Dict[GENE.name]=GENE.id	map of id and name
genes_interval	Dict[chromosome]=IntervalTree	genes location projects to IntervalTree
err	List	Lines in gtf file that cannot be correctly recognized
anno_map	Dict[attributes]=description	Commonly used gene structure attributes and their corresponding relationships described in gtf files

annotation type map

annotation type map, the corresponding description relationship between annotation attributes and annotation types description in annotation files.

raw map table

Attributes	description
gene	gene
trans	transcript
exon	exon
CDS	CDS
start_codon	start_codon
stop_codon	stop_codon
UTR5	five_prime_utr
UTR3	three_prime_utr
other	other

more info: other is an additional reserved attribute for reading special cases that do not exist in the table but exist in the gtf file.

map table description content replacement

from annokit import GTF
gtf = GTF()
gtf_file = "./test/test.gtf"
anno_map = "UTR5,UTR5;other,other_anno"
gtf.read(gtf_file, name="test", anno_map=anno_map)
gtf.anno_map
# " {'gene': 'gene', 'trans': 'transcript', 'exon': 'exon', 'CDS': 'CDS', 'start_codon': 'start_codon', 'stop_codon': 'stop_codon', 'UTR5': 'UTR5', 'UTR3': 'three_prime_utr', 'other': 'other_anno'} "

more info: anno_map can modify the gtf description corresponding to multiple attributes at the same time, separated by semicolons, and the attributes and descriptions are separated by commas, like ‘{attributes1},{description1};{attributes2},{description2};...;{attributesN},{descriptionN}‘

API

from annokit import GTF
gtf = GTF()
gtf_file = "./test/test.gtf"
gtf.read(gtf_file, name="test", version="1.0", URL="none")
gtf.name
# 'test'

more info: The three parameters name, version and URL are all optional parameters. The main purpose is to record the relevant information of the gtf file.

interval search

intervaltree: a mutable, self-balancing interval tree for Python 2 and 3. Queries may be by point, by range overlap, or by range envelopment.

from annokit import GTF
gtf = GTF()
gtf_file = "./test/test.gtf"
gtf.read(gtf_file, name="test", version="1.0", URL="none")
loc = "chr1:1000:5000"
genes = gtf.searchs(loc)
genes
# '[geneid1, geneid2, ..., geneidn]'

more info: The location parameter consists of the chromosome, starting position, and ending position, with a colon between them, like ‘{chr}:{start}:{end}‘.

gene inquires

Use the gene ID or name to query the related information of the gene in the gtf file, and output it in the DataFrame format of pandas.

from annokit import GTF
gtf = GTF()
gtf_file = "./test/test.gtf"
gtf.read(gtf_file, name="test", version="1.0", URL="none")
genes_name = "genename1;genename2"
gtf.inquires(genes_name, itype="name", ilevel="gene")
geneids = "geneid1;geneid2;geneid3"
gtf.inquires(geneids, itype="id", ilevel="exon")

ilevel	gene	trans	exon
geneid	✓	✓	✓
genename	✓	✓	✓
chr	✓	✓	✓
start	✓	✓	✓
end	✓	✓	✓
strand	✓	✓	✓
transid	✕	✓	✓
transname	✕	✓	✓
transstart	✕	✓	✓
transend	✕	✓	✓
exonid	✕	✕	✓
exonstart	✕	✕	✓
exonend	✕	✕	✓

If the corresponding information is missing, the replacement rules are as follows:

str: String types are replaced by -, such as id, name, chr, strand and other attributes.
int: The int data type is replaced by 0, such as start, end and other attributes.

name2id or id2name

Convert gene name and id to each other

# n2i
from annokit import GTF
gtf = GTF()
gtf_file = "./test/test.gtf"
genes_name = "genename1;genename2"
gtf.read(gtf_file, name="test", version="1.0", URL="none")
gtf.maps(genes_name, mapType='n2i')
# Warning: not found genename genename2 in gtf
# "{'genename1':'geneid1', 'genename2':'None'}"

# i2n
genes_id = "geneid1,geneid2"
gtf.maps(genes_id, 'i2n')
# "{'geneid1':'genename1', 'geneid2':'genename2'}"

genes_id: geneid1,geneid2,...,geneidN
genes_name: genename1,genename2,...,genenameN

CLI

interval search

1	AnnoGtf -t searchs -g test.gtf -l chr1:1000:5000 -o test -od ./ -am UTR5,UTR5\;other,other_anno

name2id or id2name

# genes
AnnoGtf -t maps -g test.gtf -m i2n -gs geneid1,genid2 -o test -od ./ -am UTR5,UTR5\;other,other_anno
# genes file
AnnoGtf -t maps -g test.gtf -m n2i -gf genename.tsv -o test -od ./ -am UTR5,UTR5\;other,other_anno

more info: genes file consists of gene name or gene id, one for each line.

gene inquires

# genesid
AnnoGtf -t inquires -g test.gtf -it id -il gene -gs geneid1,genid2 -o test -od ./ -am UTR5,UTR5\;other,other_anno
# genesname file
AnnoGtf -t inquires -g test.gtf -it name -il exon -gf genename.tsv -o test -od ./ -am UTR5,UTR5\;other,other_anno

jupyter sample

more usage: https://github.com/iOLIGO/AnnoKit/blob/main/tests/GTF.ipynb.