bio gff: convert to GFF

Building a nicer gene model

bio creates more meaningful and nicer GFF visualizations. Get data for chromosome 2L for Drosophila melanogaster (fruit-fly)

bio fetch NT_033779 > chrom2L.gb

Convert it to gff:

bio gff chrom2L.gb > chrom2L.gff

GFF created with bio

Here is a region from the GFF file created with the code above as visualized in IGV:

  • Exons will have transcript_id and gene_id attributes set.
  • CDS features have protein_id and gene_id attributes set.

Get a dataset

Get SARS-COV-2 data:

bio fetch NC_045512 MN996532 > genomes.gb

Convert all features to GFF:

cat genomes.gb | bio gff | head -5

Convert to GFF only the features with type CDS

cat genomes.gb | bio gff --type gene,CDS | head -5

Convert to GFF only the features tagged with gene S

bio gff --gene S  genomes.gb | head -5