combine_fasta: Combine fasta files into one

In fishsciences/metabarcode_utils: Meta-barcoding Utilities

Combine fasta files into one

Description

Takes a directory full of fasta files, and combines them into a single one.

Usage

combine_fasta(
  fasta_dir,
  fasta_pattern,
  max_records,
  new_names = paste0("combined_", fasta_pattern, "_"),
  out_dir,
  fasta_files = list.files(fasta_dir, fasta_pattern, full.names = TRUE)
)

Arguments

fasta_dir	directory containing fasta files to combine
fasta_pattern	the pattern to match for fasta files (e.g. "NoHit")
max_records	optional, maximum number of records for each file. The total lines in each file will be twice this number (since records span two lines). If not provided, all files will be written to a single fasta file
new_names	character, the base of the name for the new combined files
out_dir	optional, if not provided combined files will be written into the same directory as input files.
fasta_files	vector of files to combine

Value

file names of new combined files

Author(s)

Matt Espe

fishsciences/metabarcode_utils documentation built on Feb. 25, 2024, 11:31 a.m.