phyclust (version 0.1-11)

file.write: 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".

Value

• Save a text file.

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.

References

Phylogenetic Clustering Website: http://thirteen-01.stat.iastate.edu/snoweye/phyclust/

See Also

read.fasta, read.phylip.

Examples

# 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")