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align: create command line to align FastQ. #8
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105 changes: 105 additions & 0 deletions
105
hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/FastqAlignCommandExecutor.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,105 @@ | ||
| /* | ||
| * Copyright 2015 OpenCB | ||
| * | ||
| * 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 | ||
| * | ||
| * http://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. | ||
| */ | ||
|
|
||
| package org.opencb.hpg.bigdata.app.cli; | ||
|
|
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| import org.apache.hadoop.conf.Configuration; | ||
| import org.apache.hadoop.fs.FileSystem; | ||
| import org.apache.hadoop.fs.Path; | ||
| import org.opencb.hpg.bigdata.core.utils.PathUtils; | ||
| import org.opencb.hpg.bigdata.tools.stats.read.mr.ReadKmersMR; | ||
| import org.opencb.hpg.bigdata.tools.stats.read.mr.ReadStatsMR; | ||
|
|
||
| import java.io.IOException; | ||
| import java.util.Date; | ||
|
|
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| /** | ||
| * Created by imedina on 03/02/15. | ||
| */ | ||
| public class FastqAlignCommandExecutor extends CommandExecutor { | ||
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|
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| private CliOptionsParser.FastqAlignCommandOptions fastqAlignCommandOptions; | ||
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| public FastqAlignCommandExecutor(CliOptionsParser.FastqAlignCommandOptions fastqAlignCommandOptions) { | ||
| super(fastqAlignCommandOptions.commonOptions.logLevel, fastqAlignCommandOptions.commonOptions.verbose, | ||
| fastqAlignCommandOptions.commonOptions.conf); | ||
|
|
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| this.fastqAlignCommandOptions = fastqAlignCommandOptions; | ||
| } | ||
|
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| /** | ||
| * Parse specific 'fastq' command options | ||
| */ | ||
| public void execute() { | ||
| logger.info("Executing {} CLI options", "fastq"); | ||
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| // prepare the HDFS output folder | ||
| FileSystem fs = null; | ||
| Configuration conf = new Configuration(); | ||
| try { | ||
| fs = FileSystem.get(conf); | ||
| } catch (IOException e) { | ||
| e.printStackTrace(); | ||
| } | ||
| String outHdfsDirname = new String("" + new Date().getTime()); | ||
|
|
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| // clean paths | ||
| String in = PathUtils.clean(fastqAlignCommandOptions.input); | ||
| String index = PathUtils.clean(fastqAlignCommandOptions.index); | ||
| String out = PathUtils.clean(fastqAlignCommandOptions.output); | ||
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| if (!PathUtils.isHdfs(fastqAlignCommandOptions.input)) { | ||
| logger.error("To align fastq, the input FastQ file '{}' must be stored in the HDFS/Haddop. Use the command 'convert fastq2sa' to import your file.", fastqAlignCommandOptions.input); | ||
| System.exit(-1); | ||
| } | ||
|
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| if (!PathUtils.isHdfs(fastqAlignCommandOptions.index)) { | ||
| logger.error("To align fastq, the index folder '{}' must be stored in the HDFS/Haddop.", fastqAlignCommandOptions.index); | ||
| System.exit(-1); | ||
| } | ||
|
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| if (!PathUtils.isHdfs(fastqAlignCommandOptions.output)) { | ||
| logger.error("To align fastq, the output folder '{}' must be stored in the HDFS/Haddop.", fastqAlignCommandOptions.output); | ||
| System.exit(-1); | ||
| } | ||
|
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| try { | ||
| System.out.println("input = " + in + ", index = " + index + ", out = " + out); | ||
| //AlignMR.run(in, out); | ||
| } catch (Exception e) { | ||
| e.printStackTrace(); | ||
| } | ||
|
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| /* | ||
| // post-processing | ||
| Path outFile = new Path(outHdfsDirname + "/part-r-00000"); | ||
| try { | ||
| if (!fs.exists(outFile)) { | ||
| System.out.println("out file = " + outFile.getName() + " does not exist !!"); | ||
| } else { | ||
| String outRawFileName = fastqCommandOptions.output + "/raw.json"; | ||
| fs.copyToLocalFile(outFile, new Path(outRawFileName)); | ||
| //Utils.parseStatsFile(outRawFileName, out); | ||
| } | ||
| fs.delete(new Path(outHdfsDirname), true); | ||
| } catch (IOException e) { | ||
| e.printStackTrace(); | ||
| } | ||
| */ | ||
| } | ||
| } |