A 'Find k-mer' solution in RScript (Running under shell/terminal)

find_k_mer.R

#! /usr/bin/Rscript
# Lytze Nov 4 2014
# An example of visit stdin (the real stdin, not the console) using RScript
# NO details about seting opts and args

# Usage:
## $ chmod u+x find_k_mer.R
## $ ./find_k_mer.R
# OR
## $ ./find_k_mer.R < inputfile

# Note:
## The 'Find k-mer' problem is a model problem in bioinfomatics. The promblem is
## about taking a DNA sequence and a short motif as input (strings), and find the 
## number of the motif in the sequense. This is really simple and served as one of
## the rudimentals in bioinfomatics.

stdin <- file('stdin'); # Note that the default 'stdin' is not actually the standard input stream
open(stdin);
sequence <- readLines(stdin, 1);
tofind <- readLines(stdin, 1);
close(stdin);

sequence <- strsplit(sequence, '')[[1]];
tofind <- strsplit(tofind, '')[[1]];
## R treat char and string all as 'character', these lines will separete the string

if (length(sequence) > 70) {
	cat('Input Seq (heading):', paste(head(sequence, 20), collapse = ''));
	cat(' ...', paste(tail(sequence, 20), collapse = ''), '\n');
} else {
	cat('Input Seq (heading):', paste(head(sequence, 50), collapse = ''), '\n');
}
cat('Input Mer (heading):', paste(head(tofind), collapse = ''), '\n\n');
## Echo back the inputs
## May I should add optings to earase these echos? :)

count <- 0;
for (i in 1:(length(sequence) - length(tofind) + 1)) {
	if (sequence[i] == tofind[1]) {
	    # start matching when the heading bases are the same
		j <- 1;
		while (j < length(tofind)) {
			if (sequence[i + j] != tofind[1 + j]) break;
			    # go on matching if current base is the same
			j <- j + 1;
		}
		if (j == length(tofind)) count <- count + 1;
	}
}
cat('#mer =', count, '\n');