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我是相当新的apache spark技术,在尝试分析我从文件中提取的数据时遇到一些问题。比较RDD对象-Apache Spark
我有大量的基因信息,我把这些信息提交给RDD,迄今为止这么好。
JavaRDD<Gene> inputfile = sc.textFile(logFile).map(
new Function<String, Gene>() {
@Override
public Gene call(String line) throws Exception {
String[] values = line.split("\t");
Gene gen = null;
//We are only interested in genes;
if(values.length > 2 && values[2].equalsIgnoreCase("gene") && !line.contains("#")){
String[] infoGene = values[8].split(";");
String geneId = StringUtils.substringBetween(infoGene[0], "\"");
String geneType = StringUtils.substringBetween(infoGene[2], "\"");
String geneName = StringUtils.substringBetween(infoGene[4], "\"");
gen = new Gene(geneName,values[3],values[4]);
return gen;
}
return gen;
}
}
).filter(new Function<Gene, Boolean>() {
@Override
public Boolean call(Gene gene) throws Exception {
if(gene == null)
return false;
else
return true;
}
});
基因类:
public class Gene implements Serializable{
String firstBp;
String lastBp;
String name;
public Gene(String name, String firstBp, String lastBp) {
this.name = name;
this.firstBp = firstBp;
this.lastBp = lastBp;
}
public String getFirstBp() {
return firstBp;
}
public String getLastBp() {
return lastBp;
}
public String getName() {
return name;
}
public String toString(){
return name + " " + firstBp + " " + lastBp;
}}
问题从这里开始,我需要的,如果2个基因叠加分析,并为我做了这个简单的实用功能:
public static Boolean isOverlay(Gene gene1, Gene gene2){
int gene1First = Integer.parseInt(gene1.getFirstBp());
int gene1Last = Integer.parseInt(gene1.getLastBp());
int gene2First = Integer.parseInt(gene2.getFirstBp());
int gene2Last = Integer.parseInt(gene2.getLastBp());
if(gene2First >= gene1First && gene2First <= gene1Last) // FirstBp - Gene2 inside
return true;
else if (gene2Last >= gene1First && gene2Last <= gene1Last) // LastBP - Gene2 inside
return true;
else if (gene1First >= gene2First && gene1First <= gene2Last) // FirstBp - Gene1 inside
return true;
else if (gene1Last >= gene2First && gene1Last <= gene2Last) // LastBP - Gene1 inside
return true;
else
return false;
}
现在我在做什么,我认为是错误的是将RDD对象转变为列表:
List<Gene> genesList = inputfile.collect();
并遍历该列表以检查是否有重叠并将保存到文件的结果花费时间,因为我没有使用spark。
List<OverlayPair> overlayPairList= new ArrayList<OverlayPair>();
List<String> visitedGenes = new ArrayList<String>();
for (Gene gene1 : genesList){
for (Gene gene2 : genesList) {
if (gene1.getName().equalsIgnoreCase(gene2.getName()) || visitedGenes.contains(gene2.getName())) {
continue;
}
if (isOverlay(gene1, gene2))
overlayPairList.add(new OverlayPair(gene1.getName(), gene2.getName()));
}
visitedGenes.add(gene1.getName());
}
JavaRDD<OverlayPair> overlayFile = sc.parallelize(overlayPairList);
//Export the results to the file
String outputDirectory = "/Users/joaoalmeida/Desktop/Dissertacao/sol/data/mitocondrias/feup-pp/project/data/output/overlays";
overlayFile.coalesce(1).saveAsTextFile(outputDirectory);
Overlay对基本上是一个具有2个基因名称的对象。
有没有办法做这第二部分,同时利用火花?因为这些2的时间复杂性对于我目前拥有的数据量来说是很大的。