write.dna

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Write DNA Sequences in a File

This function writes in a file a list of DNA sequences in sequential, interleaved, or FASTA format. The names of the vectors of the list are used as taxa names.

Usage
write.dna(x, file, format = "interleaved", append = FALSE,
          nbcol = 6, colsep = " ", colw = 10, indent = NULL,
          blocksep = 1)
Arguments
x
a list or a matrix of DNA sequences.
file
a file name specified by either a variable of mode character, or a double-quoted string.
format
a character string specifying the format of the DNA sequences. Three choices are possible: "interleaved", "sequential", or "fasta", or any unambiguous abbreviation of these.
append
a logical, if TRUE the data are appended to the file without erasing the data possibly existing in the file, otherwise the file (if it exists) is overwritten (FALSE the default).
nbcol
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.
colsep
a character used to separate the columns (a single space by default).
colw
a numeric specifying the number of nucleotides per column (10 by default).
indent
a numeric or a character specifying how the blocks of nucleotides are indented (see details).
blocksep
a numeric specifying the number of lines between the blocks of nucleotides (this has an effect only if `format = "interleaved"').
Details

The same three formats are supported in the present function than in read.dna: see its help page and the references below for a description of these formats.

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; if the taxon names are longer than 10 characters, they are truncated and a warning message is issued.

The argument `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 exactly the same effect (use `indent = ""' for a tabulation). 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 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'). [object Object] Anonymous. FASTA format description. http://www.ncbi.nlm.nih.gov/BLAST/fasta.html

Anonymous. IUPAC ambiguity codes. http://www.ncbi.nlm.nih.gov/SNP/iupac.html

Felsenstein, J. (1993) Phylip (Phylogeny Inference Package) version 3.5c. Department of Genetics, University of Washington. http://evolution.genetics.washington.edu/phylip/phylip.html read.dna, read.GenBank IO

Aliases
  • write.dna
Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)

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