How to obtain cds integrity information from prokka(Similar to prodigal)

Question

[zhangtianyuan]

How to obtain cds integrity information from prokka(Similar to prodigal). prodigal provide the information(partial=00 : complete, partial=01 or partial 10 : partial , partial=11: incomplete)

prokka invokes the prodigal software, but does not display this information,how to get this information? (by tools, perl or python)

Answer 1

[LChart]

By default prokka always filters genes that are off the edge of a contig (you can turn this off using --metagenome); so these annotations will all be partial=00. I don't know if prokka drops this information with the --metagenome flag - but you can always run prodigal a 2nd time and lift the annotation from one gff to the other.