read_fasta: Load a fasta file.

In castor: Efficient Phylogenetics on Large Trees

Load a fasta file.

Description

Efficiently load headers & sequences from a fasta file.

Usage

read_fasta(file,
		   include_headers		= TRUE,
		   include_sequences	= TRUE,
		   truncate_headers_at	= NULL)

Arguments

file	A character, path to the input fasta file. This file may be gzipped with extension ".gz".
include_headers	Logical, whether to load the headers. If you don't need the headers you can set this to FALSE for efficiency.
include_sequences	Logical, whether to load the sequences. If you don't need the sequences you can set this to FALSE for efficiency.
truncate_headers_at	Optional character, needle at which to truncate headers. Everything at and after the first instance of the needle will be removed from the headers.

Details

This function is a fast and simple fasta loader. Note that all sequences and headers are loaded into memory at once.

Value

A named list with the following elements:

success	Logical, indicating whether the file was loaded successfully. If FALSE, then an error message will be specified by the element error, and all other elements may be undefined.
headers	Character vector, listing the loaded headers in the order encountered. Only included if include_headers was TRUE.
sequences	Character vector, listing the loaded sequences in the order encountered. Only included if include_sequences was TRUE.
Nlines	Integer, number of lines encountered.
Nsequences	Integer, number of sequences encountered.

Author(s)

Stilianos Louca

See Also

read_tree

Examples

## Not run: 
# load a gzipped fasta file
fasta = read_faste(file="myfasta.fasta.gz")

# print the first sequence
cat(fasta$sequences[1])

## End(Not run)

castor documentation built on Aug. 25, 2025, 1:10 a.m.