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Yana Valasatava
committed
Chromosome mapping tool: unit test to check handling multiple UTRs preceding the coding region
1 parent 1c81b01 commit 495e3f1

1 file changed

Lines changed: 49 additions & 50 deletions

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‎biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java‎

Lines changed: 49 additions & 50 deletions
Original file line numberDiff line numberDiff line change
@@ -141,18 +141,34 @@ public void testHBA(){
141141

142142
private void validateExon(int exonNr, int start, int stop, List<Range<Integer>> cdsranges) {
143143

144-
Range exon = cdsranges.get(exonNr);
144+
Range<Integer> exon = cdsranges.get(exonNr);
145145
assertTrue("Exon " + exonNr + " boundary "+ exon.lowerEndpoint() + " does not match " +start , exon.lowerEndpoint().equals(start));
146146
assertTrue("Exon " + exonNr + " boundary " + exon.upperEndpoint() + " does not match " + stop, exon.upperEndpoint().equals(stop));
147147

148148
}
149149

150-
@Test
151-
/** Test to make sure the mapping tool correctly retrieves the mRNA position for a gene
150+
/** Get the position of the nucleotide base corresponding to the position of that base on the mRNA sequence
151+
* for a gene living on the reverse DNA strand.
152+
*
153+
* @author Yana Valasatava
154+
*/
155+
private int getPositionInmRNA(String geneName, String genebankId, int posChrom) {
156+
for (GeneChromosomePosition gcp : gcps) {
157+
if ( gcp.getGeneName().equals(geneName) ) {
158+
if ( gcp.getGenebankId().equals(genebankId) ) {
159+
return ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posChrom, gcp);
160+
}
161+
}
162+
}
163+
return -1;
164+
}
165+
166+
/** Make sure the mapping tool correctly retrieves the mRNA position for a gene
152167
* living on the forward DNA strand for different chromosome positions.
153168
*
154169
* @author Yana Valasatava
155170
*/
171+
@Test
156172
public void testForwardMappingPositions() {
157173

158174
String geneName = "HORMAD2"; // gene on the forward DNA strand
@@ -190,13 +206,13 @@ public void testForwardMappingPositions() {
190206
}
191207
}
192208
}
193-
194-
@Test
195-
/** Test to make sure the mapping tool correctly retrieves the mRNA position for a gene
209+
210+
/** Make sure the mapping tool correctly retrieves the mRNA position for a gene
196211
* living on the reverse DNA strand for different chromosome positions.
197212
*
198213
* @author Yana Valasatava
199214
*/
215+
@Test
200216
public void testReverseMappingPositions() {
201217

202218
String geneName = "BCL11B"; // gene on the reverse DNA strand
@@ -235,12 +251,12 @@ public void testReverseMappingPositions() {
235251
}
236252
}
237253

238-
@Test
239254
/** Test to make sure the mapping tool correctly identify that position falls outside the coding region
240255
* for a gene living on the forward DNA strand.
241256
*
242257
* @author Yana Valasatava
243258
*/
259+
@Test
244260
public void testForwardMappingForExonBoundaries() {
245261

246262
String geneName = "HBA1"; // gene on the reverse DNA strand
@@ -249,68 +265,51 @@ public void testForwardMappingForExonBoundaries() {
249265
int posExonStart = 176717; // starting position of the first base in a coding region (1st exon)
250266
int posExonEnd = 176811; // ending position of the first base in a coding region (1st exon)
251267

252-
for (GeneChromosomePosition gcp : gcps) {
253-
254-
if ( !gcp.getGeneName().equals(geneName) )
255-
continue;
256-
if ( !gcp.getGenebankId().equals(genebankId) )
257-
continue;
258-
259-
int cdsSE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonStart-1, gcp);
260-
assertEquals(cdsSE, -1);
261-
262-
int cdsEE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonEnd+1, gcp);
263-
assertEquals(cdsEE, -1);
268+
int cdsSE = getPositionInmRNA(geneName, genebankId, posExonStart-1);
269+
assertEquals(cdsSE, -1);
264270

265-
break;
266-
}
271+
int cdsEE = getPositionInmRNA(geneName, genebankId, posExonEnd+1);
272+
assertEquals(cdsEE, -1);
267273
}
268-
269-
@Test
274+
270275
/** Test to make sure the mapping tool correctly identify that position falls outside the coding region
271276
* for a gene living on the reverse DNA strand.
272277
*
273278
* @author Yana Valasatava
274279
*/
280+
@Test
275281
public void testReverseMappingForExonBoundaries() {
276282

277283
String geneName = "BCL11B"; // gene on the reverse DNA strand
278284
String genebankId = "NM_138576"; // GeneBank ID for the transcript used for testing (ENST00000357195)
279285

280286
int posExonStart = 99174151; // starting position of the first base in a coding region (1st exon)
281287
int posExonEnd = 99176195; // ending position of the first base in a coding region (1st exon)
282-
283-
for (GeneChromosomePosition gcp : gcps) {
284-
285-
if ( !gcp.getGeneName().equals(geneName) )
286-
continue;
287-
if ( !gcp.getGenebankId().equals(genebankId) )
288-
continue;
289-
290-
int cdsSE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonStart-1, gcp);
291-
assertEquals(cdsSE, -1);
292-
293-
int cdsEE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonEnd+1, gcp);
294-
assertEquals(cdsEE, -1);
295-
296-
break;
297-
}
288+
289+
int cdsSE = getPositionInmRNA(geneName, genebankId, posExonStart-1);
290+
assertEquals(cdsSE, -1);
291+
292+
int cdsEE = getPositionInmRNA(geneName, genebankId, posExonEnd+1);
293+
assertEquals(cdsEE, -1);
298294
}
299295

300-
/** Get the position of the nucleotide base corresponding to the position of that base on the mRNA sequence
301-
* for a gene living on the reverse DNA strand.
296+
/** Test to make sure the mapping tool correctly converts the genetic position to a position on mRNA
297+
* when multiple UTR regions are consecutive.
302298
*
303299
* @author Yana Valasatava
304300
*/
305-
private int getPositionInmRNA(String geneName, String genebankId, int posChrom) {
306-
for (GeneChromosomePosition gcp : gcps) {
307-
if ( !gcp.getGeneName().equals(geneName) )
308-
continue;
309-
if ( !gcp.getGenebankId().equals(genebankId) )
310-
continue;
311-
return ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posChrom, gcp);
312-
}
313-
return -1;
301+
@Test
302+
public void testMappingCromosomePosTomRNAMultiUTRs() {
303+
304+
String geneName = "ILK"; // gene on the reverse DNA strand
305+
String genebankId = "NM_001278442"; // GeneBank ID for the transcript used for testing (ENST00000532063)
306+
307+
int chromPos = 6608760;
308+
int mRNAPos = 16;
309+
310+
int cds = getPositionInmRNA(geneName, genebankId, chromPos);
311+
assertEquals(cds, mRNAPos);
312+
314313
}
315314
}
316315

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