Example 1 with BlastSequenceInput
use of org.nextprot.api.blast.domain.BlastSequenceInput in project nextprot-api by calipho-sib.
the class BlastPRunnerTest method blastpShouldThrowNPException.
@Test(expected = NextProtException.class)
public void blastpShouldThrowNPException() throws Exception {
config = new BlastSequenceInput("/work/devtools/blastw", blastDb);
BlastPRunner runner = new BlastPRunner(config);
runner.run(new BlastPRunner.FastaEntry("subseq 211-239 of NX_P52701", "GTTYVTDKSEEDNEIESEEEVQPKTQGSRR"));
}Example 2 with BlastSequenceInput
use of org.nextprot.api.blast.domain.BlastSequenceInput in project nextprot-api by calipho-sib.
the class BlastPRunnerTest method testDefaultCommandLineBuilding.
@Test
public void testDefaultCommandLineBuilding() throws Exception {
config = new BlastSequenceInput(blastBinPath, blastDb);
BlastPRunner runner = new BlastPRunner(config);
File file = new File("/tmp/input.fasta");
List<String> cl = runner.buildCommandLine(config, file);
Assert.assertNotNull(config.getBinPath());
Assert.assertNotNull(config.getNextprotBlastDbPath());
Assert.assertEquals(7, cl.size());
Assert.assertTrue(cl.get(0).endsWith("blastp"));
Assert.assertEquals("-db", cl.get(1));
Assert.assertTrue(cl.get(2).endsWith("nextprot"));
Assert.assertEquals("-query", cl.get(3));
Assert.assertEquals(file.getAbsolutePath(), cl.get(4));
Assert.assertEquals("-outfmt", cl.get(5));
Assert.assertEquals("15", cl.get(6));
}Example 3 with BlastSequenceInput
use of org.nextprot.api.blast.domain.BlastSequenceInput in project nextprot-api by calipho-sib.
the class BlastPRunnerTest method shouldNotBeAbleToCreateInstance.
@Test(expected = NextProtException.class)
public void shouldNotBeAbleToCreateInstance() throws Exception {
config = new BlastSequenceInput(null, "/tmp/blastdb");
new BlastPRunner(config);
}Example 4 with BlastSequenceInput
use of org.nextprot.api.blast.domain.BlastSequenceInput in project nextprot-api by calipho-sib.
the class BlastPRunnerTest method blastpShouldThrowExceptionWithReason.
@Test(expected = ExceptionWithReason.class)
public void blastpShouldThrowExceptionWithReason() throws Exception {
config = new BlastSequenceInput(blastBinPath, blastDb);
// pam30, gapopen11
config.setBlastSearchParams(BlastSearchParams.valueOf(BlastSearchParams.Matrix.PAM30.toString(), 0.01, 11, 2));
BlastPRunner runner = new BlastPRunner(config);
runner.run(new BlastPRunner.FastaEntry("subseq 211-239 of NX_P52701", "GTTYVTDKSEEDNEIESEEEVQPKTQGSRR"));
}Example 5 with BlastSequenceInput
use of org.nextprot.api.blast.domain.BlastSequenceInput in project nextprot-api by calipho-sib.
the class BlastPRunnerTest method blastpShouldFindResult.
@Test
public void blastpShouldFindResult() throws Exception {
config = new BlastSequenceInput(blastBinPath, blastDb);
BlastPRunner runner = new BlastPRunner(config);
Report blastReport = runner.run(new BlastPRunner.FastaEntry("subseq 211-239 of NX_P52701", "GTTYVTDKSEEDNEIESEEEVQPKTQGSRR"));
Assert.assertNull(config.getBinPath());
Assert.assertNull(config.getNextprotBlastDbPath());
Assert.assertEquals(4, blastReport.getResults().getSearch().getHits().size());
}Aggregations
