add melting_range c code, update python, update makefile

3 files changed, 72 insertions, 17 deletions

diff --git a/Makefile b/Makefile
index 1f8d839..0a9e43f 100644
--- a/Makefile
+++ b/Makefile
@@ -2,10 +2,14 @@ VERSION=\"v0.0.1\"
 CC = gcc
 CFLAGS = -O3 -s -mtune=native -Wall -DVERSION=$(VERSION) -Wextra
 
-all: strstream
+all: strstream melting_range strstreamone
 
 strstream: strstream.c
 	$(CC) strstream.c -o strstream $(CLIBS) $(CFLAGS)
+strstreamone: strstreamone.c
+	$(CC) strstreamone.c -o strstreamone $(CLIBS) $(CFLAGS)
+melting_range: melting_range.c
+	$(CC) melting_range.c -o melting_range $(CLIBS) $(CFLAGS)
 
 clean:
-	rm -vf kmer_total_count kmer_counts_per_sequence libkmer.so libkmer.a libkmer.o
+	rm -vf strstream melting_range 
diff --git a/below_melting_temperature.py b/below_melting_temperature.py
index bc4157e..e2521db 100644
--- a/below_melting_temperature.py
+++ b/below_melting_temperature.py
@@ -1,8 +1,6 @@
 import sys
-from multiprocessing import Pool
 
-def above_melting_temperature(kmer_with_count):
-	kmer = kmer_with_count.split("\t")[0]
+def in_temp_range(kmer):
 
 	A = kmer.count('A')
 	C = kmer.count('C')
@@ -16,18 +14,13 @@ def above_melting_temperature(kmer_with_count):
 	else:
 		melt_temp = 64.9 + 41*(G+C-16.4)/(A+T+G+C)
 
-	if melt_temp < max_melting_temp:
-		return kmer_with_count
-	else:
-		return 0
-
+	return min_melting_temp < melt_temp < max_melting_temp
 
-lines = sys.stdin.readlines()
-max_melting_temp = float(sys.argv[1])
+min_melting_temp = float(sys.argv[1])
+max_melting_temp = float(sys.argv[2])
 
-p = Pool()
-output = p.map(above_melting_temperature, lines)
 
-for line in output:
-	if line != 0:
-		sys.stdout.write(line)
+output = []
+for line in sys.stdin:
+	if in_temp_range(line.split("\t")[0]):
+		sys.stdout.write(line)
\ No newline at end of file
diff --git a/melting_range.c b/melting_range.c
new file mode 100644
index 0000000..2c89195
--- /dev/null
+++ b/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);
+}