split_fasta: Split fasta file into smaller files.

In GenomeNet/deepG: Deep Learning for Genome Sequence Data

Split fasta file into smaller files.

Description

Returns smaller files with same file name and "_x" (where x is an integer). For example, assume we have input file called "abc.fasta" with 100 entries and split_n = 50. Function will create two files called "abc_1.fasta" and "abc_2.fasta" in target_path.

Usage

split_fasta(
  path_input,
  target_folder,
  split_n = 500,
  shuffle_entries = TRUE,
  delete_input = FALSE
)

Arguments

path_input	Fasta file to split into smaller files
target_folder	Directory for output.
split_n	Maximum number of entries to use in smaller file.
shuffle_entries	Whether to shuffle fasta entries before split.
delete_input	Whether to delete the original file.

Value

None. Writes files to output.

Examples

path_input <- tempfile(fileext = '.fasta')
create_dummy_data(file_path = path_input,
                  num_files = 1,
                  write_to_file_path = TRUE,
                  seq_length = 7,
                  num_seq = 25,
                  vocabulary = c("a", "c", "g", "t"))
target_folder <- tempfile()
dir.create(target_folder)

# split 25 entries into 5 files
split_fasta(path_input = path_input,
            target_folder = target_folder,
            split_n = 5)
length(list.files(target_folder)) 

GenomeNet/deepG documentation built on Jan. 25, 2025, 12:05 a.m.