read_fasta: Reads fasta file.
In J-Moravec/sighunt: Tool for horizontal transfer detection

Reads fasta file from provided path and returns list of sequences (strings) with sequence names as names of items in list. This include some manipulation with sequence names to remove trailing whitespace and standardization of sequences themselves (uppercase) for future smooth processing. Also, if illegal characters are found in sequence, throws warning.

1	read_fasta(file, skip = 0, nlines = 0, comment.char = "")

`file`	Name of fasta file
`skip`	the number of lines of the input file to skip before beginning to read data values.
`nlines`	if positive, the maximum number of lines of data to be read.
`comment.char`	character: a character vector of length one containing a single character or an empty string. Use `""` to turn off the interpretation of comments altogether (the default).