fasta_parse() get the current regex
Usage
fasta_parse(fasta_path = NULL, patterns = NULL, as = c("list", "data.frame"))Arguments
- fasta_path
a character string of the path to the fasta formatted file
- patterns
a list, if not provided the default from
regex()will be used. Note: the first element in the regex list will define the list reference name, such that with the list output, each protein can be accessed with that designation. Note: if the patterns list is missing an explicit "sequence" element, no sequence will be returned. This might be beneficial if only a few meta elements are sought.- as
a character designating the output format
Examples
if (FALSE) {
proteins <- fasta_parse("~/Local/data/fasta/ecoli_UniProt.fasta")
# using a custom supplied regex list
proteins <- fasta_parse(fasta_path = "~/Local/data/fasta/ecoli_UniProt.fasta",
pattern = list(
"accession" = "sp\\|[A-Z]",
"gene_name" = "(?<=GN\\=).*?(?=\\s..\\=)"
))
}