write.dna: Write DNA Sequences in a File
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Details Value Note Author(s) References See Also

This function writes in a file a list of DNA sequences in sequential, interleaved, or FASTA format.

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write.dna(x, file, format = "interleaved", append = FALSE,
          nbcol = 6, colsep = " ", colw = 10, indent = NULL,
          blocksep = 1)

`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"').

Three formats are supported in the present function: see the help page of 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.

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 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.

Emmanuel Paradis

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, makeLabel

gjuggler/ape documentation built on May 17, 2019, 6:03 a.m.