GeneFinder.write_orfs_gff
— Methodwrite_orfs_gff(input::NucleicSeqOrView{DNAAlphabet{N}}, output::Union{IOStream, IOBuffer}, finder::F; kwargs...)
-write_orfs_gff(input::NucleicSeqOrView{DNAAlphabet{N}}, output::String, finder::F; kwargs...)
Write GFF data to a file.
Arguments
input
: The input DNA sequence NucSeq or a view.output
: The otput format, it can be a file (String
) or a buffer (IOStream
or `IOBuffer)finder
: The algorithm used to find ORFs. It can be eitherNaiveFinder()
orNaiveFinderScored()
.
Keywords
code::GeneticCode=BioSequences.standard_genetic_code
: The genetic code by which codons will be translated. SeeBioSequences.ncbi_trans_table
for more info.alternative_start::Bool=false
: If true will pass the extended start codons to search. This will increase 3x the exec. time.minlen::Int64=6
: Length of the allowed ORF. Default value allowaa"M*"
a posible encoding protein from the resulting ORFs.