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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

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.