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Final dbSNP builder implemented
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@imedina
imedina committed Mar 12, 2024
1 parent 82e57f3 commit bbccffe
Showing 1 changed file with 67 additions and 25 deletions.
92 changes: 67 additions & 25 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/DbSnpBuilder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,7 @@
import java.io.BufferedReader;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.*;

import static org.opencb.cellbase.lib.EtlCommons.DBSNP_NAME;

Expand All @@ -39,8 +37,37 @@
*/
public class DbSnpBuilder extends CellBaseBuilder {

private Path sourceVariationPath;
private DownloadProperties.URLProperties dbSnpUrlProperties;
private final Path sourceVariationPath;
private final DownloadProperties.URLProperties dbSnpUrlProperties;
private static final Map<String, String> CHROMOSOME_MAPPING;

static {
CHROMOSOME_MAPPING = new HashMap<>();
CHROMOSOME_MAPPING.put("NC_000001", "1");
CHROMOSOME_MAPPING.put("NC_000002", "2");
CHROMOSOME_MAPPING.put("NC_000003", "3");
CHROMOSOME_MAPPING.put("NC_000004", "4");
CHROMOSOME_MAPPING.put("NC_000005", "5");
CHROMOSOME_MAPPING.put("NC_000006", "6");
CHROMOSOME_MAPPING.put("NC_000007", "7");
CHROMOSOME_MAPPING.put("NC_000008", "8");
CHROMOSOME_MAPPING.put("NC_000009", "9");
CHROMOSOME_MAPPING.put("NC_000010", "10");
CHROMOSOME_MAPPING.put("NC_000011", "11");
CHROMOSOME_MAPPING.put("NC_000012", "12");
CHROMOSOME_MAPPING.put("NC_000013", "13");
CHROMOSOME_MAPPING.put("NC_000014", "14");
CHROMOSOME_MAPPING.put("NC_000015", "15");
CHROMOSOME_MAPPING.put("NC_000016", "16");
CHROMOSOME_MAPPING.put("NC_000017", "17");
CHROMOSOME_MAPPING.put("NC_000018", "18");
CHROMOSOME_MAPPING.put("NC_000019", "19");
CHROMOSOME_MAPPING.put("NC_000020", "20");
CHROMOSOME_MAPPING.put("NC_000021", "21");
CHROMOSOME_MAPPING.put("NC_000022", "22");
CHROMOSOME_MAPPING.put("NC_000023", "X");
CHROMOSOME_MAPPING.put("NC_000024", "Y");
}

public DbSnpBuilder(Path sourceVariationPath, DownloadProperties.URLProperties dbSnpUrlProperties, CellBaseSerializer serializer) {
super(serializer);
Expand Down Expand Up @@ -80,39 +107,57 @@ public void parse() throws Exception {
String line;
String[] fields;

String currentChromosome = null;
String chromosome = null;
String chromosome;
int position;
String id;
String ref;
String[] alt;
String type;
String version;
String info;
List<String> flags;
Map<String, Object> additionalAttributes;

SnpAnnotation snpAnnotation;

try (BufferedReader bufferedReader = FileUtils.newBufferedReader(dbSnpFilePath)) {
while ((line = bufferedReader.readLine()) != null) {
if (!line.startsWith("#")) {
fields = line.split("\t");

// This only happens the first time, when we start reading the file
if (chromosome == null) {
logger.info("Parsing chr {} ", fields[0]);
currentChromosome = fields[0];
chromosome = fields[0].split("\\.")[0];
}

chromosome = fields[0].split("\\.")[0];
chromosome = CHROMOSOME_MAPPING.get(chromosome);
position = Integer.parseInt(fields[1]);
id = fields[2];
ref = fields[3];
alt = fields[4].split(",");
version = dbSnpUrlProperties.getVersion();
info = fields[7];

String[] infoFields = info.split(";");
// Calculate SNP type
type = "SNV";
if (ref.length() > 1) {
type = "INDEL";
} else {
for (String altAllele : alt) {
if (altAllele.length() > 1) {
type = "INDEL";
break;
}
}
}

snpAnnotation = new SnpAnnotation();
flags = new ArrayList<>();
SnpAnnotation snpAnnotation = new SnpAnnotation();
additionalAttributes = new HashMap<>();

String[] infoFields = info.split(";");
for (String infoField : infoFields) {
String[] infoKeyValue = infoField.split("=");
switch (infoKeyValue[0]) {
case "dbSNPBuildID":
version = infoKeyValue[1];
break;
case "GENEINFO": {
snpAnnotation.setGene(infoKeyValue[1].split(":")[0]);
break;
Expand All @@ -121,6 +166,8 @@ public void parse() throws Exception {
String[] studies = infoKeyValue[1].split("\\|");
List<PopulationFrequency> populationFrequencies = new ArrayList<>();
for (String study : studies) {
// After splitting 'GnomAD:1,1.426e-05,.' we get:
// freqFields: [GnomAD, 1, 1.426e-05, .]
String[] freqFields = study.split("[:,]");
if (freqFields.length == alt.length + 2) {
for (int i = 0; i < alt.length; i++) {
Expand All @@ -129,12 +176,9 @@ public void parse() throws Exception {
alt[i], freqFields[0]);
} else {
PopulationFrequency populationFrequency = new PopulationFrequency();
// Set study
populationFrequency.setStudy(freqFields[0]);
// Set reference
populationFrequency.setRefAllele(ref);
populationFrequency.setRefAlleleFreq(Float.parseFloat(freqFields[1]));
// Set alternate
populationFrequency.setAltAllele(alt[i]);
populationFrequency.setAltAlleleFreq(Float.parseFloat(freqFields[i + 2]));

Expand All @@ -153,18 +197,16 @@ public void parse() throws Exception {
default: {
if (infoKeyValue.length == 1) {
flags.add(infoKeyValue[0]);
} else {
additionalAttributes.put(infoKeyValue[0], infoKeyValue[1]);
}
}
}
}
snpAnnotation.setFlags(flags);
snpAnnotation.setAdditionalAttributes(additionalAttributes);

if (!currentChromosome.equals(fields[0])) {
logger.info("Parsing chr {} ", fields[0]);
}

Snp snp = new Snp(id, chromosome, position, ref, Arrays.asList(alt), "SNV", DBSNP_NAME, dbSnpUrlProperties.getVersion(),
snpAnnotation);
Snp snp = new Snp(id, chromosome, position, ref, Arrays.asList(alt), type, DBSNP_NAME, version, snpAnnotation);
fileSerializer.serialize(snp, DBSNP_NAME);
}
}
Expand Down

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