Write DNA Sequences in a File
This function writes in a file a list of DNA sequences in sequential, interleaved, or FASTA format.
write.dna(x, file, format = "interleaved", append = FALSE, nbcol = 6, colsep = " ", colw = 10, indent = NULL, blocksep = 1)
- a list or a matrix of DNA sequences.
- a file name specified by either a variable of mode character, or a double-quoted string.
- a character string specifying the format of the DNA
sequences. Three choices are possible:
"fasta", or any unambiguous abbreviation of these.
- a logical, if
TRUEthe data are appended to the file without erasing the data possibly existing in the file, otherwise the file (if it exists) is overwritten (
- a numeric specifying the number of columns per row (6 by default); may be negative implying that the nucleotides are printed on a single line.
- a character used to separate the columns (a single space by default).
- a numeric specifying the number of nucleotides per column (10 by default).
- a numeric or a character specifying how the blocks of nucleotides are indented (see details).
- a numeric specifying the number of lines between the blocks of nucleotides (this has an effect only if `format = "interleaved"').
Three formats are supported in the present function: see the help page
read.dna and the references below for a description.
If the sequences have no names, then they are given "1", "2", ... as names in the file.
With the interleaved and sequential formats, the sequences must be all of the same length. The names of the sequences are not truncated.
indent specifies how the rows of nucleotides are
indented. In the interleaved and sequential formats, the rows with
the taxon names are never indented; the subsequent rows are indented
with 10 spaces by default (i.e., if
indent = NULL). In the FASTA
format, the rows are not indented by default. This default behaviour
can be modified by specifying a value to
indent: the rows are then
indented with ``indent'' (if it is a character) or `indent' spaces (if
it is a numeric). For example, specifying
indent = "" or
indent = 3 will have the same effect (use
indent = "\t"
for a tabulation).
The different options are intended to give flexibility in formatting the sequences. For instance, if the sequences are very long it may be judicious to remove all the spaces beween columns (colsep = ""), in the margins (indent = 0), and between the blocks (blocksep = 0) to produce a smaller file.
- None (invisible `NULL').
Specifying a negative value for `nbcol' (meaning that the nucleotides are printed on a single line) gives the same result for the interleaved and sequential formats.
The names of the sequences may be truncated with the function
makeLabel. In particular, Clustal is limited to 30
characters, whereas PHYML seems limited to 99 characters.
The FASTA format may be used as input for Clustal.
Anonymous. FASTA format description.
Anonymous. IUPAC ambiguity codes.
Felsenstein, J. (1993) Phylip (Phylogeny Inference Package) version
3.5c. Department of Genetics, University of Washington.