/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.feature.genome;
import org.broad.igv.feature.BasicFeature;
import org.broad.igv.util.TestUtils;
import htsjdk.tribble.Feature;
import org.junit.Test;
import java.util.List;
import static junit.framework.Assert.assertEquals;
/**
* Created with IntelliJ IDEA.
* User: jrobinso
* Date: 6/19/12
* Time: 1:13 PM
* To change this template use File | Settings | File Templates.
*/
public class GenbankParserTest {
@Test
public void testReadSequence() throws Exception {
String testFile = TestUtils.DATA_DIR + "gbk/pten_test.gbk";
GenbankParser genbankParser = new GenbankParser(testFile);
genbankParser.readFeatures(true);
String expectedChr = "NT_030059";
assertEquals(expectedChr, genbankParser.getChr());
String[] expectedTypes = {"gene", "mRNA", "CDS", "gene", "variation", "variation"};
int[] expectedStarts = {0, 0, 1032, 82042, -79, 10554};
int[] expectedEnds = {105338, 105338, 102035, 82643, -78, 10555};
List<Feature> features = genbankParser.getFeatures();
for (int i=0; i<expectedTypes.length; i++) {
BasicFeature bf = (BasicFeature) features.get(i);
assertEquals(expectedTypes[i], bf.getType());
assertEquals(expectedStarts[i], bf.getStart());
assertEquals(expectedEnds[i], bf.getEnd());
}
// 61 ttccgaggcg cccgggctcc cggcgcggcg gcggaggggg cgggcaggcc ggcgggcggt
String chr = genbankParser.getChr();
int start = 60;
int end = 70;
String expectedSequence = "ttccgaggcg";
byte[] seqbytes = genbankParser.getSequence(chr, start, end);
String sequence = new String(seqbytes);
assertEquals(expectedSequence, sequence);
// Test end of sequence
expectedSequence = "tcttgtca";
end = 105338;
start = end - expectedSequence.length();
seqbytes = genbankParser.getSequence(chr, start, end);
sequence = new String(seqbytes);
assertEquals(expectedSequence, sequence);
assertEquals(105338, genbankParser.getSequenceLenth());
}
/**
* variation -78
/gene="PTEN"
/replace="a"
/replace="g"
/db_xref="HGMD_null"
variation 10555
*
* gene 1..105338
/gene="PTEN"
/note="Derived by automated computational analysis using
gene prediction method: BestRefseq."
/db_xref="GeneID:5728"
/db_xref="HGNC:9588"
/db_xref="HPRD:03431"
/db_xref="MIM:601728"
mRNA join(1..1111,30588..30672,62076..62120,67609..67652,
69576..69814,88681..88822,94416..94582,97457..97681,
101850..105338)
/gene="PTEN"
/product="phosphatase and tensin homolog"
/exception="unclassified transcription discrepancy"
/note="Derived by automated computational analysis using
gene prediction method: BestRefseq."
/transcript_id="NM_000314.4"
/db_xref="GI:110224474"
/db_xref="GeneID:5728"
/db_xref="HGNC:9588"
/db_xref="HPRD:03431"
/db_xref="MIM:601728"
CDS join(1033..1111,30588..30672,62076..62120,67609..67652,
69576..69814,88681..88822,94416..94582,97457..97681,
101850..102035)
/gene="PTEN"
/note="Derived by automated computational analysis using
gene prediction method: BestRefseq."
/codon_start=1
/product="phosphatidylinositol-3,4,5-trisphosphate
3-phosphatase and dual-specificity protein phosphatase
PTEN"
/protein_id="NP_000305.3"
/db_xref="GI:73765544"
/db_xref="GeneID:5728"
/db_xref="HGNC:9588"
/db_xref="HPRD:03431"
/db_xref="MIM:601728"
gene 82043..82643
/gene="RPL11P3"
/gene_synonym="RPL11_2_1077"
/note="Derived by automated computational analysis using
gene prediction method: Curated Genomic."
/pseudo
/db_xref="GeneID:100271271"
/db_xref="HGNC:36342"
*/
}