From 94d04a1e503121a98b403f882c18a4f0799267d7 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Wed, 29 Jan 2014 11:53:30 -0500
Subject: add filtering based on consecutive mer lengths

---
 src/filter_melting_range.c | 58 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 src/filter_melting_range.c

(limited to 'src/filter_melting_range.c')

diff --git a/src/filter_melting_range.c b/src/filter_melting_range.c
new file mode 100644
index 0000000..2c89195
--- /dev/null
+++ b/src/filter_melting_range.c
@@ -0,0 +1,58 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+
+float melting_temperature(char *mer) {
+
+	float a = 0;
+	float c = 0;
+	float g = 0;
+	float t = 0;
+	int i = 0;
+
+	for(i = 0; i < strlen(mer); i++) {
+		switch(mer[i]) {
+			case 'A':
+			a++;
+			break;
+			case 'C':
+			c++;
+			break;
+			case 'G':
+			g++;
+			break;
+			case 'T':
+			t++;
+			break;
+			default:
+			break;
+		}
+	}
+
+	if(strlen(mer) < 13)
+		return  ((a+t) * 2) + ((c+g) * 4);
+	else
+		return 64.9 + 41.0*(g+c-16.4)/(a+t+g+c);
+}
+
+int main(int argc, char **argv){
+
+	if(argc < 3) {
+		printf("please supply the min and max as stdargs");
+		exit(EXIT_FAILURE);
+	}
+	float min = atof(argv[1]);
+	float max = atof(argv[2]);
+	
+	char mer[24] = { 0 };
+	int count = 0;
+
+	while(fscanf(stdin, "%s\t%d\n", &mer, &count) == 2) {
+		float temp = melting_temperature(mer);
+		if( (temp > min) && (temp < max) )
+			printf("%s\t%d\n", mer, count);
+	}
+
+	exit(EXIT_SUCCESS);
+}
-- 
cgit v1.2.3