These functions read a sequence alignment file and return a named list of sequences.
Currently supported formats are `fasta` and `nexus`. Interleaved formats, where sequences are
defined in a repeating blocks, are not supported.
Usage
read_sequences(file, format = NULL)
read_fasta(file)
read_nexus(file)
Arguments
- file
with alignment
- format
requested format
Value
named list of sequences
Details
The function `[read_sequences]` tries to guess the correct format from the file extension.
Alternatively, the correct format can be specified. Currently supported formats are
fasta and nexus.
Functions `[read_fasta]` and `[read_nexus]` are then used to read the sequence alignment file.
Examples
seq1 = c("A" = "AAA", "B" = "BBB", "C" = "CCC")
fasta = tempfile(fileext = ".fasta")
writeLines(paste0(">", names(seq1), "\n", seq1), fasta)
seq2 = read_sequences(fasta)
seq3 = read_fasta(fasta)
identical(seq1, seq2)
#> [1] TRUE
identical(seq1, seq3)
#> [1] TRUE