Added direct swissprot mappings fro human, mouse and rat

misc-scripts/xref_mapping/xref_config.ini

@@ -728,7 +728,7 @@ priority        = 1
 prio_descr      = ID assigned by FlyBase
 parser          = FlybaseParser
 release_uri     =
-data_uri        = file:/lustre/work1/ensembl/gk4/flybase/dmel_5.13/seqdata/dmel-all-r5.13.gff.gz
+data_uri        = file:/lustre/scratch103/ensembl/ianl/release_57/drosophila_melanogaster/dmel-all-r5.13.gff.gz
 
 [source flybase_gene_id::drosophila_pseudoobscura]
 # Used by drosophila_pseudoobscura
@@ -1016,7 +1016,7 @@ priority        = 1
 prio_descr      = main
 parser          = GOSlimParser
 release_uri     =
-data_uri        = script:host=>ens-staging1,dbname=>ensembl_ontology_57,
+data_uri        = script:host=>ens-livemirror,dbname=>ensembl_ontology_56,
 
 
 [source GO::homo_sapiens]
@@ -2244,12 +2244,33 @@ release_uri     =
 name            = Uniprot/SWISSPROT
 download        = Y
 order           = 20
-priority        = 1
-prio_descr      =
+priority        = 2
+prio_descr      = sequence_mapped
 parser          = UniProtParser
 release_uri     = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldate.txt
 data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz
 
+
+
+#
+# Direct Uniprot mapping for mouse, human and rat.
+# Note these have to be done LAST so that we get all
+# the dependent xrefs that are available from the original.
+# swissprot entry
+
+[source Uniprot/SWISSPROT::DIRECT]
+# Used by homo_sapiens
+name            = Uniprot/SWISSPROT
+download        = Y
+order           = 300
+priority        = 1
+prio_descr      = uniprot_mapped 
+parser          = UniProtDirectParser
+release_uri     =
+data_uri        = ftp://ftp.ebi.ac.uk/pub/contrib/xrefs/ens-sp.map
+
+
+
 [source Uniprot/SWISSPROT::MULTI-predicted]
 # Special source used in UniProtParser.  No species uses this source.
 name            = Uniprot/SWISSPROT_predicted
@@ -3403,8 +3424,9 @@ source          = RefSeq_peptide::homo_sapiens
 source          = UniGene::homo_sapiens
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
+source          = Uniprot/SWISSPROT::DIRECT
 source          = ncRNA::MULTI
-#source          = UCSC::homo_sapiens            ADD WHEN STABLE ID'S ADDED FOR NEW ASEMBLY
+source          = UCSC::homo_sapiens
 source          = HGNC_curated_transcript::homo_sapiens
 source          = goslim_goa::MULTI
 
@@ -3494,6 +3516,7 @@ source          = RefSeq_peptide::mus_musculus
 source          = UniGene::mus_musculus
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
+source          = Uniprot/SWISSPROT::DIRECT
 source          = ncRNA::MULTI
 source          = UCSC::mus_musculus
 source          = Fantom::mus_musculus
@@ -3655,6 +3678,7 @@ source          = RefSeq_peptide::rattus_norvegicus
 source          = UniGene::rattus_norvegicus
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
+source          = Uniprot/SWISSPROT::DIRECT
 source          = ncRNA::MULTI