ConvFas: Convert files to fasta format

In seqRFLP: Simulation and visualization of restriction enzyme cutting pattern from DNA sequences.

Description

This function could be used to convert raw phy,nex, fas files to fasta format. It is also a internal function called by as.fasta() which is more friendly to use.

Usage

ConvFas(fil = NULL, type = c("fas", "nxs", "phy"))

Arguments

fil	file that to be converted.
type	File types that will be converted.

Details

Users may have to use readLines() to import the content when dealing with external datasets. Currently, this function could handling the standard phy, nex, fas files, lines between "[]" must be deleted in nex files.

Value

The "fasta" format data.

Author(s)

Qiong Ding [e-mail]

References

None.

See Also

See Also as.fasta for converting data types.

Examples

data(fil.phy)
ConvFas(fil = fil.phy, type = "phy")
data(fil.nxs)
ConvFas(fil = fil.nxs, type = "nxs")

seqRFLP documentation built on May 2, 2019, 6:02 a.m.