protein_from_sequence: Translate protein sequences from a corresponding fasta...

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

Translate protein sequences from a corresponding fasta sequences, given start, end and strand

Description

Translate protein sequences from a corresponding fasta sequences, given start, end and strand. Ideal for getting all protein sequences within a gggenesdf if the fasta sequences from the gff3 file has been extracted.

Usage

protein_from_sequence(fasta_sequence, start, end, strand)

Arguments

fasta_sequence	String of the fasta sequence
start	Integer of the start position of the feature to be translated in the fasta_sequence
end	Integer of the end position of the feature to be translated in the fasta_sequence
strand	Orientation of the feature to be translated ("+", or "-")

Value

Protein sequence

Examples

protein_from_sequence(List of fasta_sequence, start, end, strand)

#Particularly useful if wanting to get all the protein sequences in one/several gff3 files for comparison, e.g. running CDhit:

#E.g. Taking a bunch of gff files in a directory:

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