text: 
  import gffpandas.gffpandas as gffpd
  
  print(snakemake.input)
  print(snakemake.output)
  
  annotation = gffpd.read_gff3(str(snakemake.input))
  
  #create just one gff with feature replaced as exon purely for htseq counting. Then use the unmodifed gff in the post-htseq-parsing.py
  annotation.df.iloc[:,2] = 'exon'
  
  annotation.to_gff3(str(snakemake.output))