file.write {phyclust} | R Documentation

## Write Data to Files by Formats

### Description

Two major file formats are supported in phyclust, `Format phylip` and `Format fasta`. These functions only write files in basic syntax.

### Usage

    write.fasta(seqdata, filename, classid = NULL, seqname = NULL,
        width.line = 60, lower.case = FALSE, code.type = .code.type[1],
        sep = "")
    write.fasta.format(seqdata, filename, classid = NULL, seqname = NULL,
        width.line = 60, sep = "")

    write.phylip(seqdata, filename, classid = NULL, seqname = NULL,
        width.seqname = 10, width.line = 60, lower.case = FALSE,
        code.type = .code.type[1], sep = "")

    write.phylip.format(seqdata, filename, classid = NULL, seqname = NULL,
        width.seqname = 10, width.line = 60, sep = "")

    write.paml(seqdata, filename, classid = NULL, seqname = NULL,
        width.seqname = 10, width.line = 60, lower.case = FALSE,
        code.type = .code.type[1], sep = "")
    write.paml.format(seqdata, filename, classid = NULL, seqname = NULL,
        width.seqname = 10, width.line = 60, sep = "")

### Arguments

`seqdata` | a matrix contains sequence ids as `X` in `phyclust`.
`filename` | a file name where data is written to.
`classid` | class id of sequences.
`seqname` | sequence names.
`width.seqname` | number of characters of sequence names to be stored.
`width.line` | width of lines for breaking lines.
`lower.case` | use lower case of letters to write
`code.type` | either "NUCLEOTIDE" (default) or "SNP".
`sep` | a character to split sites, "" (default) and "," for "CODON".

### Details

`write.fasta`, `write.phylip`, and `write.paml` are general functions call `write.fasta.format`, `write.phylip.format` and `write.paml.format`.

`write.fasta.format`, `write.phylip.format`, and `wirte.paml.format` will not do any transformation for input sequences, but directly write them into the file as `code.type = NULL` in `write.fasta`, `write.phylip` and `write.paml`.

Note that PAML uses one of PHYLIP format to deal with sequence files, so `write.paml.format` is to write files in a different format of `write.phylip.format`. The main purpose of `write.paml` and `write.paml.format` is to generate files for `pamle.baseml`.

`sep` can specify a character which is used to split sites in file. By default, "" denote no character between sites. Only "CODON" id requires a character to avoid ambiguity.

### Value

Save a text file.

### Author(s)

Wei-Chen Chen wccsnow@gmail.com

### References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

### See Also

`read.fasta`, `read.phylip`.

### Examples

    ## Not run:
    library(phyclust, quiet = TRUE)

    # PHYLIP
    data.path <- paste(.libPaths()[1], "/phyclust/data/crohn.phy", sep = "")
    my.snp <- read.phylip(data.path, code.type = "SNP")
    write.phylip(my.snp$org, "new.crohn.phy", code.type = "SNP")

    # FASTA
    data.path <- paste(.libPaths()[1], "/phyclust/data/pony625.fas", sep = "")
    (my.pony <- read.fasta(data.path))
    write.fasta(my.pony$org, "new.pony.fas")

    # PAML
    write.paml(my.pony$org, "new.pony.pam")

    # Amino acid in PHYLIP
    aa.aid <- nid2aid(my.pony$org)
    aa.acode <- aid2acode(aa.aid)
    write.phylip(aa.aid, "new.pony.aa.phy", code.type = "AMINO_ACID")
    write.phylip.format(aa.aid, "new.pony.aa.aid.phy", sep = ",")
    write.phylip.format(aa.acode, "new.pony.aa.acode.phy")

    # Amino acid in FASTA
    write.fasta(aa.aid, "new.pony.aa.phy", code.type = "AMINO_ACID")
    write.fasta.format(aa.aid, "new.pony.aa.aid.phy", sep = ",")
    write.fasta.format(aa.acode, "new.pony.aa.acode.fas")

    # Amino acid in PAML
    write.paml(aa.aid, "new.pony.aa.pam", code.type = "AMINO_ACID")
    write.paml.format(aa.aid, "new.pony.aa.aid.pam", sep = ",")
    write.paml.format(aa.acode, "new.pony.aa.acode.pam")

    ## End(Not run)

[Package phyclust version 0.1-25 Index]