From 41efea995d15de5cd056885d597c7f2ea787897d Mon Sep 17 00:00:00 2001 From: risserlin Date: Fri, 18 Dec 2015 11:25:47 -0500 Subject: [PATCH] updated gmt translation using synergizer. In the latest build of ensembl in synergizer uniprot ids have been changed to uniprot_swissprot from uniprot_swissprot_accession --- GeneSetTools/src/GeneSetTranslator.java | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/GeneSetTools/src/GeneSetTranslator.java b/GeneSetTools/src/GeneSetTranslator.java index 0475e56..fff7cf0 100644 --- a/GeneSetTools/src/GeneSetTranslator.java +++ b/GeneSetTools/src/GeneSetTranslator.java @@ -113,7 +113,7 @@ public void translate() throws IOException { //depending on the old ID there are different paths that we can take to maximize coverage //if uniprot, convert to entrezgene(id1)and symbol(id2) - // try ensembl uniprot_swissprot_accession to entrezgene + // try ensembl uniprot_swissprot to entrezgene // then ensembl uniprot_sptrembl to entrezgene // then ncbi uniprot to entrezgene // @@ -122,7 +122,7 @@ public void translate() throws IOException { if(oldID.equalsIgnoreCase("entrezgene")){ //for each conversion place in oldID to newID into hashmap id1="UniProt"; - conversions_id1.put(1,new SynergizerParams("ensembl", "entrezgene","uniprot_swissprot_accession")); + conversions_id1.put(1,new SynergizerParams("ensembl", "entrezgene","uniprot_swissprot")); conversions_id1.put(2,new SynergizerParams("ensembl", "entrezgene","uniprot_sptrembl")); conversions_id1.put(3,new SynergizerParams("ncbi", "entrezgene","uniprot")); //ncbi has no symbols so can only use ensembl @@ -131,20 +131,20 @@ public void translate() throws IOException { }else if(oldID.equalsIgnoreCase("uniprot")){ //for each conversion place in oldID to newID into hashmap id1="entrezgene"; - conversions_id1.put(1, new SynergizerParams("ensembl", "uniprot_swissprot_accession","entrezgene" )); + conversions_id1.put(1, new SynergizerParams("ensembl", "uniprot_swissprot","entrezgene" )); conversions_id1.put(2,new SynergizerParams("ensembl", "uniprot_sptrembl","entrezgene" )); conversions_id1.put(3, new SynergizerParams("ncbi", "uniprot","entrezgene" )); //ncbi has no symbols so can only use ensembl id2="symbol"; - conversions_id2.put(1, new SynergizerParams("ensembl", "uniprot_swissprot_accession",symboldb )); + conversions_id2.put(1, new SynergizerParams("ensembl", "uniprot_swissprot",symboldb )); conversions_id2.put(2, new SynergizerParams("ensembl", "uniprot_sptrembl",symboldb )); }else if(oldID.equalsIgnoreCase("symbol")){ id1="entrezgene"; conversions_id1.put(1, new SynergizerParams("ensembl",symboldb, "entrezgene")); id2="UniProt"; - conversions_id2.put(1, new SynergizerParams("ensembl",symboldb,"uniprot_swissprot_accession")); - conversions_id2.put(2, new SynergizerParams("ensembl",symboldb,"uniprot_sptrembl_accession")); + conversions_id2.put(1, new SynergizerParams("ensembl",symboldb,"uniprot_swissprot")); + conversions_id2.put(2, new SynergizerParams("ensembl",symboldb,"uniprot_sptrembl")); } //Mouse go files use mgi ids, we need to convert the mgi to three different dbs , instead of the standard 2 else if(oldID.equalsIgnoreCase("mgi")){ @@ -158,8 +158,8 @@ else if(oldID.equalsIgnoreCase("mgi")){ //add an additional id. String id3="UniProt"; HashMap conversions_id3 = new HashMap(); - conversions_id3.put(1,new SynergizerParams("ensembl", "mgi_id", "uniprot_swissprot_accession") ); - conversions_id3.put(2,new SynergizerParams("ensembl", "mgi_id", "uniprot_sptrembl_accession") ); + conversions_id3.put(1,new SynergizerParams("ensembl", "mgi_id", "uniprot_swissprot") ); + conversions_id3.put(2,new SynergizerParams("ensembl", "mgi_id", "uniprot_sptrembl") ); conversions_id3.put(3,new SynergizerParams("ncbi", "mgi", "uniprot")); conversions.put(id3, conversions_id3); createNewIdTracker(id3,unfoundIds,logs,translated_genesets );