write_fasta: Write to a FASTA-formatted file

In phylotypr: Classifying DNA Sequences to Taxonomic Groupings

Write to a FASTA-formatted file

Description

Writes a data frame containing id, sequence, and comment columns, write_fasta will write the data frame out to a standard FASTA-formatted file. The header will have a tab character between the sequence id and any comments. There won't be a tab if there's no comment for the sequence. All sequence data will be on a single line

Usage

write_fasta(data_frame, file = NULL)

Arguments

data_frame

A data frame object with three columns. The id column will contain the non-space characters following the > in the header line of each sequence; the sequence column will contain the sequence; and the comment column will contain any text found after the first whitespace character on the header line. The comment column is optional.

file

Either a path to a file, a connection, or literal data (either a single string or a raw vector) to write to a standard FASTA formatted file. There are no checks to determine whether the data are DNA or amino acid sequences. Files ending in .gz, .bz2, .xz, or .zip will be automatically compressed. Files starting with ⁠http://⁠, ⁠https://⁠, ⁠ftp://⁠, or ⁠ftps://⁠ will be automatically downloaded. Remote gz files can also be autom downloaded and decompressed. If the value of file is NULL (default), the string will be written out to the screen

Value

Sequence data is either written out to the screen (file = NULL) or to a file.

Examples

df_d <- data.frame(
  id = c("seqA", "seqB", "seqC"),
  sequence = c("ATGCATGC", "ATGCATGA", "ATGCATGT"),
  comment = c("comment 1", "", "comment 3")
)

string_d <- write_fasta(df_d)

phylotypr documentation built on April 3, 2025, 5:51 p.m.