DNA Based count in scala

.gitignore

@@ -0,0 +1,5 @@
+/code/chap02/scala/.idea/
+.DS_Store
+.idea
+build
+gradle

code/chap01/scala/.gradle/buildOutputCleanup/cache.properties

@@ -0,0 +1,2 @@
+#Sat Dec 25 20:45:37 IST 2021
+gradle.version=6.8

code/chap02/scala/.gradle/buildOutputCleanup/cache.properties

@@ -0,0 +1,2 @@
+#Mon Dec 27 15:39:02 IST 2021
+gradle.version=6.8

code/chap02/scala/build.gradle

@@ -0,0 +1,21 @@
+apply plugin: 'scala'
+
+sourceCompatibility = JavaVersion.VERSION_1_8
+targetCompatibility = JavaVersion.VERSION_1_8
+
+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"
+}

code/chap02/scala/gradlew

@@ -0,0 +1,185 @@
+#!/usr/bin/env sh
+
+#
+# Copyright 2015 the original author or authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn () {
+    echo "$*"
+}
+
+die () {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+
+    JAVACMD=`cygpath --unix "$JAVACMD"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=`expr $i + 1`
+    done
+    case $i in
+        0) set -- ;;
+        1) set -- "$args0" ;;
+        2) set -- "$args0" "$args1" ;;
+        3) set -- "$args0" "$args1" "$args2" ;;
+        4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Escape application args
+save () {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
+}
+APP_ARGS=`save "$@"`
+
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+
+exec "$JAVACMD" "$@"

code/chap02/scala/gradlew.bat

@@ -0,0 +1,89 @@
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem      https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto execute
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto execute
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

code/chap02/scala/settings.gradle

@@ -0,0 +1 @@
+rootProject.name = 'data-algos-with-spark-ch02'

code/chap02/scala/src/main/resources/input.txt

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

code/chap02/scala/src/main/scala/org/data/algorithms/spark/ch02/DNABaseCountVER1.scala

@@ -0,0 +1,60 @@
+package org.data.algorithms.spark.ch02
+
+import org.apache.spark.sql.SparkSession
+
+import scala.sys.exit
+
+/*
+-----------------------------------------------------
+ Version-1
+ This is a DNA-Base-Count in PySpark.
+ The goal is to show how "DNA-Base-Count" works.
+------------------------------------------------------
+ Input Parameters:
+      argv[1]: String, input path
+  -------------------------------------------------------
+   @author Deepak Kumar
+  -------------------------------------------------------
+*/
+object DNABaseCountVER1 {
+
+  def processFASTARecord(fastaRecord:String) :Map[String,Int] = {
+    var keyValueList = Map[String,Int]()
+    if(fastaRecord.startsWith(">"))
+      keyValueList += ("z" -> 1)
+    else {
+      var chars = fastaRecord.toLowerCase
+      for(c <- chars)
+        keyValueList += c.toString -> 1
+    }
+    return  keyValueList
+  }
+
+  def main(args: Array[String]) = {
+    if(args.length !=2) {
+      println("Usage:" + DNABaseCountVER1 + "  <input-path> "  )
+      exit(-1)
+    }
+    //create an instance of SparkSession object
+    val spark = SparkSession.builder().appName("DNABaseCountVER1").master("local[*]").getOrCreate()
+    println("spark initialised")
+    val inputPath = args(1)
+    println("inputPath :"+ inputPath)
+    val recordsRDD = spark.sparkContext.textFile(inputPath)
+    println("recordsRDD.count() : "+ recordsRDD.count())
+    val recordsAsList = recordsRDD.collect()
+    print("recordsAsList : ", recordsAsList)
+    // if you do not have enough RAM, then do the following
+    // MEMORY_AND_DISK = StorageLevel(True, True, False, False, 1)
+    //recordsRDD.persist(StorageLevel(True, True, False, False, 1))
+    //
+    val pairsRDD = recordsRDD.flatMap(processFASTARecord)
+    pairsRDD.collect.foreach(println)
+
+    val frequenciesRDD = pairsRDD.reduceByKey((x,y)=> (x+y))
+    println("frequenciesRDD : debug")
+    val frequenciesAsList = frequenciesRDD.collect()
+    println("frequenciesAsList : " + frequenciesAsList.foreach(println))
+  }
+
+}