fasta_from_gff_list: Get fasta sequence from several single-contig gff3 file

In djw533/micro.gen.extra: Microbial genomics extensions and functions

Get fasta sequence from several single-contig gff3 file

Description

Get fasta sequence from several single-contig gff3 file and return it as a list of strings

Usage

fasta_from_gff_list(
  gff_list,
  gff_names,
  fasta_dir = "temp_fasta_files",
  clean_up = TRUE
)

Arguments

gff_list	a list of the gff_files to be used - with full / relative file path
gff_names	a list of names to be used for each file in gff_list, in the same order
fasta_dir	Directory to put the fasta files in to [Default = "."]
clean_up	TRUE/FALSE - clean up intermediate files. [Default = TRUE]

Value

List of fasta sequences

Examples

fasta_from_gff_list(List of gffs, names of the gff files)

djw533/micro.gen.extra documentation built on Nov. 8, 2024, 5:11 a.m.