extract_fasta: Title Extract fasta from file in a loop

In DHatziioanou/simpleepi: Simplifying functions to improve the ease and speed of basic epidemiological analysis

Title Extract fasta from file in a loop

Description

Title Extract fasta from file in a loop

Usage

extract_fasta(
  filepath,
  batch = 1000,
  skip = 0,
  returnids = TRUE,
  fastaids = vector(),
  fastafileout = "fastaout.txt",
  idfileout = "fastaindex.txt"
)

Arguments

filepath	fasta file to search
batch	number of rows to read at a time
skip	number of rows to skip from fasta file
returnids	logical, TRUE to return identifiers
fastaids	fasta identifiers to retrieve
fastafileout	file name to save fasta matching ids to
idfileout	file name to save fasta index to

Value

saves identifier matches fasta to file and returns a list of number of ids searched, last row searched, ids foundand their row numbers, fasta ids searched for,the file names for the fasta id matches and the fasta index.

Examples

extract_fasta(filepath="audit.fasta")

DHatziioanou/simpleepi documentation built on Sept. 24, 2024, 5:25 a.m.