fix file locations. check for motif files temporarily until the better solution is implemented
@@ -102,8 +102,8 @@ public class GeneBuilder extends CellBaseBuilder {
geneDirectoryPath.resolve("idmapping_selected.tab.gz"),
geneDirectoryPath.getParent().resolve("regulation/motif_features.gff.gz"),
geneDirectoryPath.getParent().resolve("regulation/motif_features.gff.gz.tbi"),
- geneDirectoryPath.getParent().getParent().resolve("common/expression/allgenes_updown_in_organism_part.tab.gz"),
- geneDirectoryPath.resolve("geneDrug/dgidb.tsv"),
+ geneDirectoryPath.resolve("allgenes_updown_in_organism_part.tab.gz"),
+ geneDirectoryPath.resolve("dgidb.tsv"),
geneDirectoryPath.resolve("ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt"),
geneDirectoryPath.resolve("all_gene_disease_associations.txt.gz"),
geneDirectoryPath.resolve("gnomad.v2.1.1.lof_metrics.by_transcript.txt.bgz"),
@@ -151,7 +151,7 @@ public class GeneBuilder extends CellBaseBuilder {
Map<String, Fasta> cDnaSequencesMap = getCDnaSequencesMap();
// TODO check all files
- if (Files.exists(tfbsFile) && Files.exists(tabixFile)) {
+ if (!Files.exists(tfbsFile) || !Files.exists(tabixFile)) {
throw new CellbaseException("Tfbs or tabix file not found. Download them and try again.");
}
