/
TransformFeaturesSuite.scala
50 lines (40 loc) · 1.95 KB
/
TransformFeaturesSuite.scala
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/**
* Licensed to Big Data Genomics (BDG) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The BDG licenses this file
* to you 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.bdgenomics.adam.cli
import java.io._
import org.bdgenomics.adam.util.ADAMFunSuite
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.utils.cli.Args4j
class TransformFeaturesSuite extends ADAMFunSuite {
sparkTest("can convert a simple BED file") {
val loader = Thread.currentThread().getContextClassLoader
val inputPath = loader.getResource("gencode.v7.annotation.trunc10.bed").getPath
val outputFile = File.createTempFile("adam-cli.TransformFeaturesSuite", ".adam")
val outputPath = outputFile.getAbsolutePath
val argLine = "%s %s".format(inputPath, outputPath).split("\\s+")
// We have to do this, since the features2adam won't work if the file already exists,
// but the "createTempFile" method actually creates the file (on some systems?)
assert(outputFile.delete(), "Couldn't delete (empty) temp file")
val args: TransformFeaturesArgs = Args4j.apply[TransformFeaturesArgs](argLine)
val features2Adam = new TransformFeatures(args)
features2Adam.run(sc)
val converted = sc.loadFeatures(outputPath).rdd.collect
assert(converted.size === 10)
assert(converted.find(_.getContigName != "chr1").isEmpty)
}
}