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miniprot-protein-alignments

  • a miniprot alignments to get the alignment ranges for the protein alignments that were done to generate the hints.
  • generate the tabulated table for the length preparation.
  • Run the miniprot as the following. The function below ill map the length so that you can map the aligned length to the plotter.
./miniprot --gff test/DPP3-hs.gen.fa.gz test/DPP3-mm.pep.fa.gz > aln.gff 
miniprotalignment("/home/gaurav/Desktop/aln.gff", splicetype="mRNA")
mRNA = miniprotalignment("/home/gaurav/Desktop/aln.gff", splicetype="mRNA")
length = [i[1]int(i[1][1]) - int(i[1][0]) for i in mRNA]
sns.plot(length)

Gaurav Sablok
University of Potsdam
Potsdam,Germany