read_fasta {castor} | R Documentation |
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 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 |
include_sequences |
Logical, whether to load the sequences. If you don't need the sequences you can set this to |
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:
headers |
Character vector, listing the loaded headers in the order encountered. Only included if |
sequences |
Character vector, listing the loaded sequences in the order encountered. Only included if |
Nlines |
Integer, number of lines encountered. |
Nsequences |
Integer, number of sequences encountered. |
Author(s)
Stilianos Louca
See Also
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)