From 1a024facb6b6d8747ecfe48dc510b2b0335d9da7 Mon Sep 17 00:00:00 2001
From: Mart Lubbers <mart@martlubbers.net>
Date: Sun, 1 Feb 2015 22:58:48 +0100
Subject: [PATCH] mart: ex1 done

---
 ex1/mart/sws1-s4109503-s4202015.tar.gz        | Bin 0 -> 1118 bytes
 .../sws1-s4109503-s4202015/exercise2/2a.txt   |   2 +
 .../sws1-s4109503-s4202015/exercise2/Makefile |   2 +
 .../exercise2/gengenome.sh                    |   1 +
 .../exercise2/genome.sh                       |   1 +
 .../exercise2/parsegenome.c                   |  55 ++++++++++++++++++
 6 files changed, 61 insertions(+)
 create mode 100644 ex1/mart/sws1-s4109503-s4202015.tar.gz
 create mode 100644 ex1/mart/sws1-s4109503-s4202015/exercise2/2a.txt
 create mode 100644 ex1/mart/sws1-s4109503-s4202015/exercise2/Makefile
 create mode 100755 ex1/mart/sws1-s4109503-s4202015/exercise2/gengenome.sh
 create mode 100755 ex1/mart/sws1-s4109503-s4202015/exercise2/genome.sh
 create mode 100644 ex1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c

diff --git a/ex1/mart/sws1-s4109503-s4202015.tar.gz b/ex1/mart/sws1-s4109503-s4202015.tar.gz
new file mode 100644
index 0000000000000000000000000000000000000000..02e5755e05247bab9d9e8f20f773ff5e9ef212ba
GIT binary patch
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diff --git a/ex1/mart/sws1-s4109503-s4202015/exercise2/2a.txt b/ex1/mart/sws1-s4109503-s4202015/exercise2/2a.txt
new file mode 100644
index 0000000..30eb450
--- /dev/null
+++ b/ex1/mart/sws1-s4109503-s4202015/exercise2/2a.txt
@@ -0,0 +1,2 @@
+# Answer: 5
+wget -qO- http://cryptojedi.org/peter/teaching/genome.txt | tr -d '\n' | grep -o "GATTACA" | wc -l
diff --git a/ex1/mart/sws1-s4109503-s4202015/exercise2/Makefile b/ex1/mart/sws1-s4109503-s4202015/exercise2/Makefile
new file mode 100644
index 0000000..95d7d4d
--- /dev/null
+++ b/ex1/mart/sws1-s4109503-s4202015/exercise2/Makefile
@@ -0,0 +1,2 @@
+all:
+	gcc -Wall parsegenome.c -o parsegenome
diff --git a/ex1/mart/sws1-s4109503-s4202015/exercise2/gengenome.sh b/ex1/mart/sws1-s4109503-s4202015/exercise2/gengenome.sh
new file mode 100755
index 0000000..4fd66dc
--- /dev/null
+++ b/ex1/mart/sws1-s4109503-s4202015/exercise2/gengenome.sh
@@ -0,0 +1 @@
+tr -cd 'ACGT' < /dev/urandom | fold -w 100 | head -500
diff --git a/ex1/mart/sws1-s4109503-s4202015/exercise2/genome.sh b/ex1/mart/sws1-s4109503-s4202015/exercise2/genome.sh
new file mode 100755
index 0000000..5a771a5
--- /dev/null
+++ b/ex1/mart/sws1-s4109503-s4202015/exercise2/genome.sh
@@ -0,0 +1 @@
+[ "$#" -eq "2" ] && tr -d '\n' < "$1" | grep -o "$2" | wc -l
diff --git a/ex1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c b/ex1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c
new file mode 100644
index 0000000..2572cbe
--- /dev/null
+++ b/ex1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c
@@ -0,0 +1,55 @@
+#include <stdio.h>
+#include <stdlib.h>
+
+int main(int argc, char* argv[])
+{
+	if(argc != 2)
+	{
+		printf("Usage: %s filepath\n", argv[0]);
+		return 2;
+	}
+
+	FILE *f;
+	int c = 0;
+	int charsperline = 0;
+	int numlines = 0;
+	int occs[4] = {0, 0, 0, 0};
+
+	f = fopen(argv[1], "r");
+	if(f == NULL)
+	{
+		printf("Unable to open file...");
+		return 2;
+	}
+
+	while((c = fgetc(f)) != EOF)
+	{
+		if(c == '\n')
+		{
+			if(charsperline != 100)
+				return -1;
+			numlines += 1;
+			charsperline = 0;
+		}
+		else
+		{
+			if(c == 'A')
+				occs[0] += 1;
+			else if(c == 'C')
+				occs[1] += 1;
+			else if(c == 'G')
+				occs[2] += 1;
+			else if(c == 'T')
+				occs[3] += 1;
+			else
+				return -1;
+			charsperline += 1;
+		}
+	}
+	fclose(f);
+	if(numlines != 500)
+		return -1;
+
+	printf("A: %d\nC: %d\nG: %d\nT: %d\n", occs[0], occs[1], occs[2], occs[3]);
+	return 0;
+}
-- 
2.20.1