fa_to_genomic_ranges: Convert FASTA file to GenomicRanges object

In TmCalculator: Genome-Wide Nucleic Acid Melting Temperature Profiling and Multi-Omics Integration

Convert FASTA file to GenomicRanges object

Description

This function reads sequences from a FASTA file and converts them to a GenomicRanges object. If named with format ">chr2:1-10:[+|-]:[seq_name]", the name will be parsed into GRanges components.

Usage

fa_to_genomic_ranges(input_seq)

Arguments

input_seq

Path to the input FASTA file

Value

A GenomicRanges object containing: - GRanges information (seqnames, ranges, strand) - sequence data from FASTA file - Complementary sequences (if provided) - Names from FASTA headers

Examples

# Example with single FASTA file
input_seq <- system.file("extdata", "example1.fasta", package = "TmCalculator")
gr <- fa_to_genomic_ranges(input_seq)

TmCalculator documentation built on Aug. 28, 2026, 5:09 p.m.