df_to_fasta: Convert Data Frame to FASTA File

In GencoDymo2: Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs

Convert Data Frame to FASTA File

Description

Converts a data frame containing sequence IDs and sequences into a FASTA-formatted file, optionally compressed as gzip.

Usage

df_to_fasta(df, id_col, seq_col, output_file = NULL, gzip = TRUE, verbose = TRUE)

Arguments

df	A data frame with at least two columns: one for sequence IDs and one for sequences.
id_col	A character string specifying the column name containing sequence IDs.
seq_col	A character string specifying the column name containing sequence data.
output_file	A character string specifying the output file path. If NULL, the function will stop with an informative message.
gzip	A logical indicating whether to compress the output as a gzip file. Defaults to TRUE.
verbose	A logical indicating whether to print progress messages. Defaults to TRUE.

Details

This function efficiently writes large sequence datasets to FASTA format, handling compression and progress reporting. It validates input columns and manages memory by processing data in chunks.

Value

No return value. Writes a FASTA file to the specified path.

Examples

temp_dir <- tempdir()
temp_output <- file.path(temp_dir, "output.fa.gz")
seq_data <- data.frame(
  transcript_id = c("ENST0001", "ENST0002"),
  sequence = c("ATGCTAGCTAG", "GCTAGCTAGCT")
)
df_to_fasta(seq_data, "transcript_id", "sequence", temp_output)

GencoDymo2 documentation built on June 8, 2025, 10:29 a.m.