pFad - Phone/Frame/Anonymizer/Declutterfier! Saves Data!


--- a PPN by Garber Painting Akron. With Image Size Reduction included!

URL: http://github.com/biojava/biojava/commit/1bedd9aff008b030bf17555e9e828da33e4ccbfa

ylesheet" href="https://github.githubassets.com/assets/global-d18f184ea1a06a2c.css" /> Merge pull request #701 from valasatava/bug-fix-yana · biojava/biojava@1bedd9a · GitHub
Skip to content

Commit 1bedd9a

Browse files
josemduartejosemduarte
authored
Merge pull request #701 from valasatava/bug-fix-yana
Fixing bug in Chromosome Mapping Tools
2 parents 663c62f + 3e2be54 commit 1bedd9a

2 files changed

Lines changed: 89 additions & 93 deletions

File tree

‎biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java‎

Lines changed: 28 additions & 93 deletions
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,11 @@ public class ChromosomeMappingTools {
2828

2929
public static final String CHROMOSOME = "CHROMOSOME";
3030
public static final String CDS = "CDS";
31-
31+
32+
private static int base = 1;
33+
public static void setCoordinateSystem(int baseInt) {
34+
base = baseInt;
35+
}
3236

3337
/** Pretty print the details of a GeneChromosomePosition to a String
3438
*
@@ -202,25 +206,12 @@ private static String formatExonStructureReverse(GeneChromosomePosition chromPos
202206
*/
203207
public static int getCDSLength(GeneChromosomePosition chromPos) {
204208

205-
logger.debug(chromPos.toString());
206-
207-
logger.debug("chromosomal information: ");
208-
209-
logger.debug("Gene:" + chromPos.getGeneName());
210-
logger.debug(" Transcription (including UTRs): " + chromPos.getTranscriptionStart() + " - " + chromPos.getTranscriptionEnd() + " (length:" + (chromPos.getTranscriptionEnd() - chromPos.getTranscriptionStart()) + ")");
211-
logger.debug(" Orientation: " + chromPos.getOrientation());
212-
logger.debug(" CDS: " + (chromPos.getCdsStart()) + " - " + chromPos.getCdsEnd() + " (length: " + (chromPos.getCdsEnd() - chromPos.getCdsStart()) + ")");
213-
214-
215209
List<Integer> exonStarts = chromPos.getExonStarts();
216210
List<Integer> exonEnds = chromPos.getExonEnds();
217211

218-
logger.debug("Exons:" + exonStarts.size());
219-
220212
int cdsStart = chromPos.getCdsStart();
221213
int cdsEnd = chromPos.getCdsEnd();
222214

223-
224215
int codingLength;
225216
if (chromPos.getOrientation().equals('+'))
226217
codingLength = ChromosomeMappingTools.getCDSLengthForward(exonStarts, exonEnds, cdsStart, cdsEnd);
@@ -504,16 +495,14 @@ public static ChromPos getChromPosForward(int cdsPos, List<Integer> exonStarts,
504495
*/
505496
public static int getCDSLengthReverse(List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd) {
506497

507-
boolean inCoding = false;
508498
int codingLength = 0;
509499

510500
if (cdsEnd < cdsStart) {
511501
int tmp = cdsEnd;
512502
cdsEnd = cdsStart;
513503
cdsStart = tmp;
514504
}
515-
516-
int lengthExons = 0;
505+
cdsStart = cdsStart + base;
517506

518507
// map reverse
519508
for (int i = exonStarts.size() - 1; i >= 0; i--) {
@@ -526,52 +515,19 @@ public static int getCDSLengthReverse(List<Integer> exonStarts, List<Integer> ex
526515
end = start;
527516
start = tmp;
528517
}
529-
lengthExons += end - start;
530-
531-
if (start <= cdsEnd && end >= cdsEnd) {
532-
inCoding = true;
533-
534-
int tmpstart = start;
535-
if (start < cdsStart) {
536-
tmpstart = cdsStart;
537-
}
538-
codingLength += (cdsEnd - tmpstart);
518+
start = start + base;
539519

540-
boolean debug = logger.isDebugEnabled();
541-
542-
if ( debug) {
543-
544-
StringBuffer b = new StringBuffer();
545-
546-
b.append(" UTR :" + (cdsEnd + 1) + " - " + (end) + newline);
547-
if (tmpstart == start)
548-
b.append(" -> ");
549-
else
550-
b.append(" <-> ");
551-
b.append("Exon :" + tmpstart + " - " + cdsEnd + " | " + (cdsEnd - tmpstart) + " | " + codingLength + " | " + (codingLength % 3) + newline);
552-
// single exon with UTR on both ends
553-
if (tmpstart != start)
554-
b.append(" UTR :" + (cdsStart - 1) + " - " + start + newline);
555-
logger.debug(b.toString());
520+
if ((start < cdsStart && end < cdsStart) || (start > cdsEnd && end > cdsEnd))
521+
continue;
556522

557-
}
558-
} else if (start <= cdsStart && end >= cdsStart) {
559-
inCoding = false;
560-
codingLength += (end - cdsStart);
523+
if (start < cdsStart)
524+
start = cdsStart;
561525

562-
logger.debug(" <- Exon : " + (cdsStart+1) + " - " + end + " | " + (end - cdsStart) + " | " + (codingLength-3) + " | " + (codingLength % 3));
563-
logger.debug(" UTR : " + start + " - " + (cdsStart ));
526+
if (end > cdsEnd)
527+
end = cdsEnd;
564528

565-
} else if (inCoding) {
566-
// full exon is coding
567-
codingLength += (end - start);
568-
logger.debug(" Exon : " + start + " - " + end + " | " + (end - start) + " | " + codingLength + " | " + (codingLength % 3));
569-
} else {
570-
// e.g. see UBQLN3
571-
logger.debug(" no translation!");
572-
}
529+
codingLength += (end - start + 1);
573530
}
574-
logger.debug("length exons: " + lengthExons + " codin length: " + (codingLength - 3));
575531
return codingLength - 3;
576532
}
577533

@@ -585,47 +541,26 @@ public static int getCDSLengthReverse(List<Integer> exonStarts, List<Integer> ex
585541
* @return
586542
*/
587543
public static int getCDSLengthForward(List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd) {
588-
boolean inCoding = false;
544+
589545
int codingLength = 0;
590546

591-
int lengthExons = 0;
592-
// map forward
593547
for (int i = 0; i < exonStarts.size(); i++) {
594548

595-
int start = exonStarts.get(i);
549+
int start = exonStarts.get(i)+base;
596550
int end = exonEnds.get(i);
597-
lengthExons += end - start;
598551

599-
logger.debug("forward exon: " + (start+1) + " - " + end + " | " + (end - start));
552+
if ( (start < cdsStart+base && end < cdsStart) || (start > cdsEnd && end > cdsEnd) )
553+
continue;
600554

601-
if (start+1 <= cdsStart +1 && end >= cdsStart+1) {
555+
if (start < cdsStart+base)
556+
start = cdsStart+base;
602557

603-
inCoding = true;
604-
codingLength += (end - cdsStart);
605-
606-
logger.debug(" UTR : " + start + " - " + (cdsStart ));
607-
logger.debug(" -> Exon : " + (cdsStart+1) + " - " + end + " | " + (end - cdsStart+1) + " | " + codingLength + " | " + (codingLength % 3));
608-
609-
} else if (start+1 <= cdsEnd && end >= cdsEnd) {
610-
611-
inCoding = false;
612-
codingLength += (cdsEnd - start);
613-
614-
logger.debug(" <- Exon : " + (start +1)+ " - " + cdsEnd + " | " + (cdsEnd - start+1) + " | " + codingLength + " | " + (codingLength % 3));
615-
logger.debug(" UTR : " + cdsEnd + 1 + " - " + end);
558+
if (end > cdsEnd)
559+
end = cdsEnd;
616560

617-
} else if (inCoding) {
618-
// full exon is coding
619-
codingLength += (end - start);
620-
621-
logger.debug(" Exon :" + (start+1) + " - " + end + " | " + (end - start+1) + " | " + codingLength + " | " + (codingLength % 3));
622-
}
561+
codingLength += (end - start + 1);
623562
}
624-
625-
logger.debug("length exons: " + Integer.toString(lengthExons));
626-
logger.debug("CDS length:" + Integer.toString((codingLength-3)));
627-
628-
return codingLength-3 ;
563+
return codingLength - 3;
629564
}
630565

631566
/** Extracts the exon boundaries in CDS coordinates. (needs to be divided by 3 to get AA positions)
@@ -868,7 +803,7 @@ public static int getCDSPosForward(int chromPos, List<Integer> exonStarts, List<
868803
int cdsStart, int cdsEnd) {
869804

870805
// the genetic coordinate is not in a coding region
871-
if ( (chromPos < (cdsStart+1) ) || ( chromPos > (cdsEnd+1) ) ) {
806+
if ( (chromPos < (cdsStart+base) ) || ( chromPos > (cdsEnd+base) ) ) {
872807
logger.debug("The "+format(chromPos)+" position is not in a coding region");
873808
return -1;
874809
}
@@ -887,7 +822,7 @@ public static int getCDSPosForward(int chromPos, List<Integer> exonStarts, List<
887822

888823
lengthExon = end - start;
889824

890-
if (start+1 <= chromPos && end >= chromPos ) {
825+
if (start+base <= chromPos && end >= chromPos ) {
891826
return codingLength + (chromPos-start);
892827
}
893828
else {
@@ -914,7 +849,7 @@ public static int getCDSPosReverse(int chromPos, List<Integer> exonStarts, List<
914849
int cdsStart, int cdsEnd) {
915850

916851
// the genetic coordinate is not in a coding region
917-
if ( (chromPos < (cdsStart+1)) || ( chromPos > (cdsEnd+1) ) ) {
852+
if ( (chromPos < (cdsStart+base)) || ( chromPos > (cdsEnd+base) ) ) {
918853
logger.debug("The "+format(chromPos)+" position is not in a coding region");
919854
return -1;
920855
}
@@ -933,7 +868,7 @@ public static int getCDSPosReverse(int chromPos, List<Integer> exonStarts, List<
933868

934869
lengthExon = end - start;
935870
// +1 offset to be a base 1
936-
if (start+1 <= chromPos && end >= chromPos ) {
871+
if (start+base <= chromPos && end >= chromPos ) {
937872
return codingLength + (end-chromPos+1);
938873
}
939874
else {

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

Lines changed: 61 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,61 @@
1+
package org.biojava.nbio.genome;
2+
3+
import org.biojava.nbio.genome.util.ChromosomeMappingTools;
4+
import org.junit.Test;
5+
6+
import java.util.ArrayList;
7+
import java.util.Arrays;
8+
import java.util.List;
9+
10+
import static org.junit.Assert.assertEquals;
11+
12+
/**
13+
* Created by Yana Valasatava on 8/14/17.
14+
*/
15+
public class TestChromosomeMappingTools {
16+
17+
@Test
18+
public void testGetCDSLengthForward() {
19+
20+
List<Integer> exonStarts = new ArrayList<>(Arrays.asList(10, 30, 50, 70));
21+
List<Integer> exonEnds = new ArrayList<>(Arrays.asList(20, 40, 60, 80));
22+
int cdsStart = 35;
23+
int cdsEnd = 75;
24+
25+
int cdsDesired = 23 - 3;
26+
ChromosomeMappingTools.setCoordinateSystem(0);
27+
int cdsTest = ChromosomeMappingTools.getCDSLengthForward(exonStarts, exonEnds, cdsStart, cdsEnd);
28+
29+
assertEquals(cdsDesired, cdsTest);
30+
}
31+
32+
@Test
33+
public void testGetCDSLengthReverseAsc() {
34+
35+
List<Integer> exonStarts = new ArrayList<>(Arrays.asList(10, 50, 70));
36+
List<Integer> exonEnds = new ArrayList<>(Arrays.asList(20, 60, 80));
37+
int cdsStart = 55;
38+
int cdsEnd = 75;
39+
40+
int cdsDesired = 12 - 3;
41+
ChromosomeMappingTools.setCoordinateSystem(0);
42+
int cdsTest = ChromosomeMappingTools.getCDSLengthReverse(exonStarts, exonEnds, cdsStart, cdsEnd);
43+
44+
assertEquals(cdsDesired, cdsTest);
45+
}
46+
47+
@Test
48+
public void testGetCDSLengthReverseDesc() {
49+
50+
List<Integer> exonStarts = new ArrayList<>(Arrays.asList(70, 50, 10));
51+
List<Integer> exonEnds = new ArrayList<>(Arrays.asList(80, 60, 20));
52+
int cdsStart = 75;
53+
int cdsEnd = 50;
54+
55+
int cdsDesired = 17 - 3;
56+
ChromosomeMappingTools.setCoordinateSystem(0);
57+
int cdsTest = ChromosomeMappingTools.getCDSLengthReverse(exonStarts, exonEnds, cdsStart, cdsEnd);
58+
59+
assertEquals(cdsDesired, cdsTest);
60+
}
61+
}

0 commit comments

Comments
 (0)
pFad - Phonifier reborn

Pfad - The Proxy pFad © 2024 Your Company Name. All rights reserved.




Check this box to remove all script contents from the fetched content.



Check this box to remove all images from the fetched content.


Check this box to remove all CSS styles from the fetched content.


Check this box to keep images inefficiently compressed and original size.

Note: This service is not intended for secure transactions such as banking, social media, email, or purchasing. Use at your own risk. We assume no liability whatsoever for broken pages.


Alternative Proxies:

Alternative Proxy

pFad Proxy

pFad v3 Proxy

pFad v4 Proxy