Example usage for org.apache.hadoop.mapred FileInputFormat addInputPath

List of usage examples for org.apache.hadoop.mapred FileInputFormat addInputPath

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  6. addInputPath

Introduction

In this page you can find the example usage for org.apache.hadoop.mapred FileInputFormat addInputPath.

Prototype

public static void addInputPath(JobConf conf, Path path)

Source Link

Document

Add a Path to the list of inputs for the map-reduce job.

Usage

From source file:Brush.CutRepeatBoundary.java

License:Apache License

public RunningJob run(String inputPath, String outputPath, long reads, long ctg_sum) throws Exception {
    sLogger.info("Tool name: CutRepeatBoundary");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(CutRepeatBoundary.class);
    conf.setJobName("CutRepeatBoundary " + inputPath + " " + BrushConfig.K);
    //conf.setFloat("Error_Rate", ErrorRate);
    //conf.setFloat("Exp_Cov", Exp_Cov);
    conf.setLong("READS", reads);
    conf.setLong("CTG_SUM", ctg_sum);

    BrushConfig.initializeConfiguration(conf);

    FileInputFormat.addInputPath(conf, new Path(inputPath));
    FileOutputFormat.setOutputPath(conf, new Path(outputPath));

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    conf.setMapOutputKeyClass(Text.class);
    conf.setMapOutputValueClass(Text.class);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);

    conf.setMapperClass(CutRepeatBoundaryMapper.class);
    conf.setReducerClass(CutRepeatBoundaryReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Brush.DefineConsensus.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: DefineConsensus");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(DefineConsensus.class);
    conf.setJobName("DefineConsensus " + inputPath + " " + BrushConfig.K);
    //conf.setFloat("Error_Rate", ErrorRate);
    //conf.setFloat("Exp_Cov", Exp_Cov);

    BrushConfig.initializeConfiguration(conf);

    FileInputFormat.addInputPath(conf, new Path(inputPath));
    FileOutputFormat.setOutputPath(conf, new Path(outputPath));

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    conf.setMapOutputKeyClass(Text.class);
    conf.setMapOutputValueClass(Text.class);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);

    conf.setMapperClass(DefineConsensusMapper.class);
    conf.setReducerClass(DefineConsensusReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Brush.EdgeRemoval.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: EdgeRemoval");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(EdgeRemoval.class);
    conf.setJobName("EdgeRemoval " + inputPath + " " + BrushConfig.K);

    BrushConfig.initializeConfiguration(conf);

    FileInputFormat.addInputPath(conf, new Path(inputPath));
    FileOutputFormat.setOutputPath(conf, new Path(outputPath));

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    conf.setMapOutputKeyClass(Text.class);
    conf.setMapOutputValueClass(Text.class);
    //conf.setBoolean("mapred.output.compress", true);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);

    conf.setMapperClass(EdgeRemovalMapper.class);
    conf.setReducerClass(EdgeRemovalReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Brush.FindBubbles.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: FindBubbles");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(FindBubbles.class);
    conf.setJobName("FindBubbles " + inputPath + " " + BrushConfig.K);

    BrushConfig.initializeConfiguration(conf);

    FileInputFormat.addInputPath(conf, new Path(inputPath));
    FileOutputFormat.setOutputPath(conf, new Path(outputPath));

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    conf.setMapOutputKeyClass(Text.class);
    conf.setMapOutputValueClass(Text.class);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);
    //conf.setBoolean("mapred.output.compress", true);

    conf.setMapperClass(FindBubblesMapper.class);
    conf.setReducerClass(FindBubblesReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Brush.GenNonContainedReads.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: GenNonContainedReads");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(Stats.class);
    conf.setJobName("GenNonContainedReads " + inputPath + " " + BrushConfig.K);

    BrushConfig.initializeConfiguration(conf);

    FileInputFormat.addInputPath(conf, new Path(inputPath));
    FileOutputFormat.setOutputPath(conf, new Path(outputPath));

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    conf.setMapOutputKeyClass(Text.class);
    conf.setMapOutputValueClass(Text.class);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);

    //conf.setBoolean("mapred.output.compress", true);
    //conf.setClass("mapred.output.compression.codec", GzipCodec.class,CompressionCodec.class);

    conf.setMapperClass(GenNonContainedReadsMapper.class);
    conf.setReducerClass(GenNonContainedReadsReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Brush.GenReverseEdge.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: GenReverseEdge");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    //JobConf conf = new JobConf(Stats.class);
    JobConf conf = new JobConf(GenReverseEdge.class);
    conf.setJobName("GenReverseEdge " + inputPath);

    BrushConfig.initializeConfiguration(conf);

    FileInputFormat.addInputPath(conf, new Path(inputPath));
    FileOutputFormat.setOutputPath(conf, new Path(outputPath));

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    conf.setMapOutputKeyClass(Text.class);
    conf.setMapOutputValueClass(Text.class);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);
    //conf.setBoolean("mapred.output.compress", true);

    conf.setMapperClass(GenReverseEdgeMapper.class);
    conf.setReducerClass(GenReverseEdgeReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Brush.Graph2Fasta.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: Graph2Fasta");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(Graph2Fasta.class);
    conf.setJobName("Graph2Fasta " + inputPath);

    FileInputFormat.addInputPath(conf, new Path(inputPath));
    FileOutputFormat.setOutputPath(conf, new Path(outputPath));

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    conf.setMapOutputKeyClass(Text.class);
    conf.setMapOutputValueClass(Text.class);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);

    conf.setMapperClass(Graph2FastaMapper.class);

    BrushConfig.initializeConfiguration(conf);
    conf.setNumReduceTasks(0);/*w  ww .jav  a2s . c om*/

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Brush.Graph2Sfa.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: Graph2Sfa");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(Graph2Sfa.class);
    conf.setJobName("Graph2Sfa " + inputPath);

    FileInputFormat.addInputPath(conf, new Path(inputPath));
    FileOutputFormat.setOutputPath(conf, new Path(outputPath));

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    conf.setMapOutputKeyClass(Text.class);
    conf.setMapOutputValueClass(Text.class);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);

    conf.setMapperClass(Graph2SfaMapper.class);

    BrushConfig.initializeConfiguration(conf);
    conf.setNumReduceTasks(0);//from ww  w.j  a  v  a2s.  co m

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Brush.KmerStatus.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: KmerStatus");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(KmerStatus.class);
    conf.setJobName("KmerStatus " + inputPath + " " + BrushConfig.K);
    // conf.setLong("AllKmer", allkmer);

    BrushConfig.initializeConfiguration(conf);

    FileInputFormat.addInputPath(conf, new Path(inputPath));
    FileOutputFormat.setOutputPath(conf, new Path(outputPath));

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    conf.setMapOutputKeyClass(Text.class);
    conf.setMapOutputValueClass(IntWritable.class);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(IntWritable.class);

    //conf.setBoolean("mapred.output.compress", true);

    conf.setMapperClass(KmerStatusMapper.class);
    conf.setReducerClass(KmerStatusReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Brush.MatchPrefix.java

License:Apache License

public RunningJob run(String inputPath, String outputPath, long allkmer, long diffkmer, long nodes)
        throws Exception {
    sLogger.info("Tool name: MatchPrefix");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(MatchPrefix.class);
    conf.setJobName("MatchPrefix " + inputPath + " " + BrushConfig.K);
    conf.setLong("AllKmer", allkmer);
    conf.setLong("DiffKmer", diffkmer);
    conf.setLong("AllReads", nodes);

    BrushConfig.initializeConfiguration(conf);

    FileInputFormat.addInputPath(conf, new Path(inputPath));
    FileOutputFormat.setOutputPath(conf, new Path(outputPath));

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    conf.setMapOutputKeyClass(Text.class);
    conf.setMapOutputValueClass(Text.class);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);

    conf.setMapperClass(MatchPrefixMapper.class);
    conf.setReducerClass(MatchPrefixReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}