From 4fb21c71cd8e81d8d5bfa475eba59a42932dcb3c Mon Sep 17 00:00:00 2001
From: Mahmoud Parsian <mparsian@illumina.com>
Date: Sat, 9 Apr 2016 23:58:01 -0700
Subject: [PATCH] added DNA-Base Counting using External Python function

---
 tutorial/dna-basecount/dna-basecount3.md | 52 ++++++------------------
 1 file changed, 13 insertions(+), 39 deletions(-)

diff --git a/tutorial/dna-basecount/dna-basecount3.md b/tutorial/dna-basecount/dna-basecount3.md
index cde5eba..aaeb085 100644
--- a/tutorial/dna-basecount/dna-basecount3.md
+++ b/tutorial/dna-basecount/dna-basecount3.md
@@ -62,44 +62,18 @@ SparkContext available as sc, HiveContext available as sqlContext.
  u'ATCGATCGATAT'
 ]
 
->>> ones = recs.flatMap(lambda x : [(c,1) for c in list(x)])
->>> ones.collect()
-[
- (u'A', 1), 
- (u'T', 1), 
- (u'A', 1), 
- (u'T', 1), 
- (u'C', 1), 
- (u'C', 1), 
- (u'C', 1), 
- (u'C', 1), 
- (u'G', 1), 
- (u'G', 1), 
- (u'G', 1), 
- (u'A', 1), 
- (u'T', 1), 
- (u'A', 1), 
- (u'T', 1), 
- (u'C', 1), 
- (u'G', 1), 
- (u'A', 1), 
- (u'T', 1), 
- (u'C', 1), 
- (u'G', 1), 
- (u'A', 1), 
- (u'T', 1), 
- (u'A', 1), 
- (u'T', 1)
-]
+>>> basemapper = "/Users/mparsian/spark-1.6.1-bin-hadoop2.6/basemapper.py"
+>>> import basemapper
+>>> basemapper
+<module 'basemapper' from 'basemapper.py'>
+>>>
+>>> recs = sc.textFile('file:////Users/mparsian/zmp/github/pyspark-tutorial/tutorial/dna-basecount/dna_seq.txt')
+>>> rdd = recs.flatMap(basemapper.mapper)
+>>> rdd.collect()
+[(u'A', 3), (u'C', 4), (u'T', 3), (u'G', 3), (u'A', 4), (u'C', 2), (u'T', 4), (u'G', 2)]
+
 >>> baseCount = rdd.reduceByKey(lambda x,y : x+y)
 >>> baseCount.collect()
-[
- (u'A', 7), 
- (u'C', 6), 
- (u'G', 5), 
- (u'T', 7)
-]
->>> 
-````
-
-	
+[(u'A', 7), (u'C', 6), (u'G', 5), (u'T', 7)]
+>>>
+````
\ No newline at end of file