public static void main(String[] args) throws FileNotFoundException {
String path = args[0];
// This is the default 2 line structure for spark programs in java
// The spark.executor.memory can only take the maximum java heapspace set by -Xmx
SparkConf conf =
new SparkConf()
.setMaster("local[" + NUM_THREADS + "]")
.setAppName(Demo.class.getSimpleName())
.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
JavaSparkContext sc = new JavaSparkContext(conf);
long start = System.nanoTime();
// if you need both the coordinates and the sequences, use this section of code
// read sequence file and map to PdbId.chainId, SimplePolymerChain pairs
List<Tuple2<String, SimplePolymerChain>> chains =
sc.sequenceFile(path, Text.class, ArrayWritable.class, NUM_THREADS * NUM_TASKS_PER_THREAD)
.sample(false, 0.01, 123)
.mapToPair(
new HadoopToSimpleChainMapper()) // convert input to <pdbId.chainId,
// SimplePolymerChain> pairs
.filter(t -> t._2.isProtein())
.collect();
for (Tuple2<String, SimplePolymerChain> t : chains) {
System.out.println(t._1 + ": " + t._2);
}
// if you need just the coordinates, use this section of code
// read sequence file and map to PdbId.chainId, C-alpha coordinate pairs
List<Tuple2<String, Point3d[]>> coordinates =
sc.sequenceFile(path, Text.class, ArrayWritable.class, NUM_THREADS * NUM_TASKS_PER_THREAD)
.sample(false, 0.01, 123)
.mapToPair(
new HadoopToSimpleChainMapper()) // convert input to <pdbId.chainId, protein
// sequence> pairs
.filter(t -> t._2.isProtein())
.mapToPair(t -> new Tuple2<String, Point3d[]>(t._1, t._2.getCoordinates()))
.collect();
for (Tuple2<String, Point3d[]> t : coordinates) {
System.out.println(t._1 + ": " + Arrays.toString(t._2));
}
sc.close();
System.out.println("Time: " + (System.nanoTime() - start) / 1E9 + " sec.");
}
/**
* @param args Path of the hadoop sequence file
* @throws FileNotFoundException
*/
public static void main(String[] args) throws FileNotFoundException {
String path = args[0];
JavaSparkContext sc = getSparkContext();
// sc is an existing JavaSparkContext.
SQLContext sqlContext = new org.apache.spark.sql.SQLContext(sc);
sqlContext.setConf("spark.sql.parquet.compression.codec", "snappy");
sqlContext.setConf("spark.sql.parquet.filterPushdown", "true");
long start = System.nanoTime();
// read sequence file and map
JavaRDD<Row> rowRDD =
sc.sequenceFile(path, Text.class, Text.class)
// .sample(false, 0.01, 123)
.mapToPair(t -> new Tuple2<String, String>(t._1.toString(), t._2.toString()))
.groupByKey()
.map(new HadoopToParqRow())
.cache();
List<StructField> fields =
new ArrayList<StructField>(); // create data fields of features for the DataFrame
fields.add(DataTypes.createStructField("index", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("chainId1", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("chainId2", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("Rnum1", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("Rnum2", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("Ins1", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("Ins2", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("res1", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("res2", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("atom1", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("atom2", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("element1", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("element2", DataTypes.StringType, false));
fields.add(DataTypes.createStructField("distance", DataTypes.IntegerType, false));
fields.add(
DataTypes.createStructField(
"pdbId", DataTypes.createArrayType(DataTypes.StringType), false));
StructType schema = DataTypes.createStructType(fields);
// Apply the schema to the RDD.
DataFrame dataFrame = sqlContext.createDataFrame(rowRDD, schema);
dataFrame
.coalesce(1)
.write()
.mode(SaveMode.Overwrite)
.partitionBy("index")
.parquet("/Users/hina/Data/ExampleFiles/seq.parquet");
sc.close();
System.out.println("Time: " + (System.nanoTime() - start) / 1E9 + " sec.");
}
