read.fas {haplotypes}

Read sequences from a file in FASTA format

Description

Read DNA sequences from a file in FASTA Format.

Usage

read.fas(file)

Arguments

file

the name of the file, which the sequence in the FASTA format is to be read from. If it does not contain an absolute path, the file name is relative to the current working directory, getwd().

Value

read.fas returns an object of class Dna.

Note

By default, valid characters are "A","C","G","T","a","c","g","t","-","?" for the class Dna. Numeric entries (integers) between 0-5 will be converted to "?","A","C","G","T","-", respectively. Invalid characters will be replaced with "?" with a warning message.

Author(s)

Caner Aktas, [e-mail]

See Also

Dna

Examples

##Reading example file.	
f<-system.file("example.fas",package="haplotypes")
 
# invalid character 'N' was replaced with '?' with a warning message
x<-read.fas(file=f) 

# an object of class 'Dna'
x