Feature/scala code/ch02 biman (#8)

.gitignore

@@ -1,5 +1,7 @@
 .DS_Store
+.idea/
+build
+gradle
 .gradle
 .idea
-build
 !gradle-wrapper.jar

code/bonus_chapters/lambda_expressions/README.md

@@ -1,12 +1,12 @@
 # What are [Lambda Functions](./Lambda_Expressions.pdf)?
 
 	Lambda functions = Anonymous functions
-
 A lambda function is a small function containing a single expression. 
 Lambda functions can also act as anonymous functions where they don’t 
 require any name. These are very helpful when we have to perform small 
 tasks with less code.
 
+
 # Python Example
 
 Python programming language supports the creation of anonymous functions 
@@ -63,4 +63,3 @@ You may use lambda expressions or functions in PySpark:
 	# rdd: RDD[(String, Integer)]
 	rdd2 = rdd.filter(filter_function)
 
-

code/chap01/scala/.gitignore

@@ -0,0 +1,4 @@
+.idea
+.idea/
+.gradle/
+build/

code/chap02/scala/.gitignore

@@ -0,0 +1,4 @@
+.idea
+.idea/
+.gradle/
+build/

code/chap02/scala/README.md

@@ -1 +1,42 @@
-Scala Solutions
+# Chapter 2
+
+## DNA-Base-Count Programs using FASTA Input Format
+
+Using FASTA input files, there are 3 versions of DNA-Base-Count
+
+* Version-1:
+    * Uses basic MapReduce programs
+    * Using Spark (`org.data.algorithms.spark.ch02.DNABaseCountVER1`)
+
+* Version-2:
+    * Uses InMapper Combiner design pattern
+    * Using PySpark (`org.data.algorithms.spark.ch02.DNABaseCountVER2`)
+
+* Version-3:
+    * Uses InMapper Combiner design pattern (by using mapPartitions() transformations)
+    * Using PySpark (`org.data.algorithms.spark.ch02.DNABaseCountVER3`)
+
+
+## DNA-Base-Count Programs using FASTQ Input Format
+
+Using FASTQ input files, the following solution is available:
+
+* Uses InMapper Combiner design pattern (by using mapPartitions() transformations)
+* Using PySpark (`org.data.algorithms.spark.ch02.DNABaseCountFastq`)
+
+
+## FASTA Files to Test DNA-Base-Count
+
+* A small sample FASTA file (`data/sample.fasta`) is provided.
+
+* To test DNA-Base-Count programs with large size FASTA files,
+you may download them from here:
+
+
+````
+	ftp://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/dna/
+
+	ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/rs_fasta/
+
+	ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
+````

code/chap02/scala/build.gradle

@@ -0,0 +1,23 @@
+apply plugin: 'scala'
+apply plugin: 'application'
+
+ext.scalaClassifier = '2.13'
+ext.scalaVersion = '2.13.7'
+
+group 'com.spark.algos.data'
+version '1.0-SNAPSHOT'
+
+repositories {
+    mavenLocal()
+    mavenCentral()
+}
+
+dependencies {
+    implementation group: "org.scala-lang", name: "scala-library", version: "2.13.7"
+    implementation group: "org.apache.spark", name: "spark-core_2.13", version: "3.2.0"
+    implementation group: "org.apache.spark", name: "spark-sql_2.13", version: "3.2.0"
+}
+
+application {
+    mainClass = project.hasProperty("mainClass") ? project.getProperty("mainClass") : "NULL"
+}

code/chap02/scala/data/sample.fasta

@@ -0,0 +1,12 @@
+>seq1
+cGTAaccaataaaaaaacaagcttaacctaattc
+>seq2
+agcttagTTTGGatctggccgggg
+>seq3
+gcggatttactcCCCCCAAAAANNaggggagagcccagataaatggagtctgtgcgtccaca
+gaattcgcacca
+AATAAAACCTCACCCAT
+agagcccagaatttactcCCC
+>seq4
+gcggatttactcaggggagagcccagGGataaatggagtctgtgcgtccaca
+gaattcgcacca