coalispr.resources.share.convert_gff3

Script for converting gff to gtf files.

Functions

convert_gff(infile[, delim, outname])

Get gtf2 from gff3, which has different annotation, lacking 'gene_id':

main(args)

Module Contents

coalispr.resources.share.convert_gff3.convert_gff(infile, delim=None, outname='miRNAs.gtf')

Get gtf2 from gff3, which has different annotation, lacking ‘gene_id’:

chr1      .       miRNA   primary_transcript      12425986        12426106        .       +       .       ID=MI0021869;Alias=MI0021869;Name=mmu-mir-6341

replace ID= section with gene_id ".

Parameters:

  • infile (str) – Name of gff3 file in current directory (where this script resides; has been copied to) to be converted to gff2/gtf

  • delim (str) – Substring that forms a unique split point sothat given ID forms start of second fragment created.

  • outname (str) – Name of gtf file created in current directory.

coalispr.resources.share.convert_gff3.main(args)