lib: minor fix in MANE Select builder
@@ -209,10 +209,10 @@ public class GeneBuilder extends CellBaseBuilder {
String transcriptIdWithoutVersion = transcript.getId().split("\\.")[0];
if (gtf.getFeature().equalsIgnoreCase("exon")) {
// Obtaining the exon sequence
- //String exonSequence = getExonSequence(gtf.getSequenceName(), gtf.getStart(), gtf.getEnd());
+ String exonId = gtf.getAttributes().get("exon_id") + "." + gtf.getAttributes().get("exon_version");
String exonSequence = fastaIndex.query(gtf.getSequenceName(), gtf.getStart(), gtf.getEnd());
- exon = new Exon(gtf.getAttributes().get("exon_id"), gtf.getSequenceName().replaceFirst("chr", ""),
+ exon = new Exon(exonId, gtf.getSequenceName().replaceFirst("chr", ""),
gtf.getStart(), gtf.getEnd(), gtf.getStrand(), 0, 0, 0, 0, 0, 0, -1, Integer.parseInt(gtf
.getAttributes().get("exon_number")), exonSequence);
transcript.getExons().add(exon);
@@ -370,7 +370,7 @@ public class GeneBuilder extends CellBaseBuilder {
String maneRefSeq = indexer.getMane(transcriptIdWithVersion, suffix);
if (StringUtils.isNotEmpty(maneRefSeq)) {
transcript.getXrefs().add(new Xref(maneRefSeq, "mane_select_" + suffix,
- "MANE Select RefSeq" + (suffix.contains("_") ? "protein" : "")));
+ "MANE Select RefSeq" + (suffix.contains("_") ? " Protein" : "")));
}
}
