extract_cds_sequences: Extract Coding Sequences (CDS) from GTF Annotations

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

Extract Coding Sequences (CDS) from GTF Annotations

Description

Extracts CDS regions from a GTF annotation file or data frame using genomic coordinates and retrieves corresponding DNA sequences from a BSgenome reference.

Usage

extract_cds_sequences(input, genome, save_fasta, output_file, verbose)

Arguments

input	A character string (GTF file path) or GRanges object containing CDS annotations.
genome	A BSgenome object for the relevant genome (e.g., BSgenome.Hsapiens.UCSC.hg38).
save_fasta	Logical indicating whether to save sequences to a FASTA file.
output_file	Character string specifying the FASTA output path.
verbose	Logical indicating whether to print progress messages.

Value

A data frame containing CDS annotations with corresponding sequences. If save_fasta = TRUE, also writes a FASTA file.

Examples

## Not run: 
if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly = TRUE)) {
  suppressPackageStartupMessages(library(GenomicRanges))
  genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
  file_v1 <- system.file("extdata", "gencode.v1.example.gtf.gz", package = "GencoDymo2")
  gtf_v1 <- load_file(file_v1) # Should return GRanges
  cds_seqs <- extract_cds_sequences(gtf_v1, genome, save_fasta = FALSE)
}

## End(Not run)

GencoDymo2 documentation built on Aug. 21, 2025, 5:54 p.m.