A Python library for plotting single nucleotide polymorhpysm (SNP) data and protein domain information on the exon-intron structure of a gene. it takes as input standard files and formats generated from popular tools, including InterproScan, the General Feature Format v3 (GFF3) and the Variant Call Format (VCF). For more details see:
https://www.biorxiv.org/content/10.1101/2022.11.08.513416v1
https://github.com/gonzalezibeas/geneplot
pip install geneplot
https://geneplot.readthedocs.io/en/latest/#
Plot geneID (from the GFF3 file) and proteinID domains (from IPR file) and SNPs listed on sample_ID from the VCF files directory.
import geneplot as gp
#input data
filegff = '/path-to-data/file.gff3'
iprfile = '/path-to-data/file.ipr'
vcffiles = '/path-to-data/'
# class instantiation (genome object)
genome_1 = gp.genome(filegff, iprfile=iprfile, vcffiles=vcffiles)
# class instantiation (gene object)
gene_1 = genome_1.gene(mRNAid='transcriptID', proteinid='proteinID')
# plot
gene_1.plot('Pfam', sp='sampleID', onlycoding=True)