Starting with a GTF file

Note

These tutorials are still under active development.

Because GAnnotation is able to handle both GTF and GFF, you can replace the GTF file in the tutorials below with the GFF file. Here we show only GTFs as examples.

Get all the genes from a GTF file

GTF_hg38 is the path to the hg38 GTF file for annotation.

from genomkit import GAnnotation

gtf = GAnnotation(file_path=GTF_hg38, file_format="gtf")
genes = gtf.get_regions(element_type="gene")
genes.write(filename="hg38_genes.bed")

Extract exon, intron, and intergenetic regions in BED format from a GTF file

GTF_hg38 is the path to the hg38 GTF file for annotation. Now you want to generate 3 BED files as below:

hg38_exons.bed
hg38_introns.bed
hg38_intergenic_regions.bed

from genomkit import GRegions
from genomkit import GAnnotation

gtf = GAnnotation(file_path=GTF_hg38, file_format="gtf")
genes = gtf.get_regions(element_type="gene")
exons = gtf.get_regions(element_type="exon")
introns = genes.subtract(exons, inplace=False)

chromosomes = GRegions(name="chromosomes")
chromosomes.get_chromosomes(organism="hg38")
intergenic_regions = chromosomes.subtract(genes, inplace=False)
exons.write(filename="hg38_exons.bed")
introns.write(filename="hg38_introns.bed")
intergenic_regions.write(filename="hg38_intergenic_regions.bed")

Get all promoter regions in BED format from a GTF file

GTF_hg38 is the path to the hg38 GTF file for annotation. Now you want to generate 3 BED files as below:

from genomkit import GAnnotation

gtf = GAnnotation(file_path=GTF_hg38, file_format="gtf")
genes = gtf.get_regions(element_type="gene")
promoters = genes.resize(extend_upstream=2000,
                        extend_downstream=0,
                        center="5prime", inplace=False)
promoters.write(filename="hg38_promoters.bed")

Extract the genes by their biotypes from a GTF file

GTF_hg38 is the path to the hg38 GTF file for annotation. Now you want to generate BED files for the biotypes below:

protein_coding
lncRNA
snRNA
miRNA

from genomkit import GAnnotation

gtf = GAnnotation(file_path=GTF_hg38, file_format="gtf")
target_biotypes = ["protein_coding", "lncRNA", "snRNA", "miRNA"]
for biotype in target_biotypes:
    genes = gtf.get_regions(element_type="gene",
                            attribute="gene_type", value=biotype)
    genes.write(filename="hg38_genes_"+biotype+".bed")