HUGO -> HGNC. Plus refseq and entrez genes only now used. No swissprot now

misc-scripts/xref_mapping/xref_config.ini

@@ -590,60 +590,73 @@ parser          = GOParser
 release_uri     = http://www.ebi.ac.uk/GOA/RAT_release.html
 data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/RAT/gene_association.goa_rat.gz
 
-[source HUGO::homo_sapiens]
+[source HGNC::homo_sapiens]
 # Used by homo_sapiens
-name            = HUGO
+name            = HGNC
+download        = Y
+order           = 30
+priority        = 1
+prio_descr      = havana
+parser          = HGNC_ENSGParser
+release_uri     =
+data_uri        = file:HGNC/HGNC_TO_ENSG
+
+[source HGNC::homo_sapiens#01]
+# Used by homo_sapiens
+name            = HGNC
 download        = Y
 order           = 51
 priority        = 2
 prio_descr      = ccds
-parser          = HUGO_CCDSParser
+parser          = HGNC_CCDSParser
 release_uri     =
-data_uri        = file:HUGO/CCDS_TO_HUGO
+data_uri        = file:HGNC/CCDS_TO_HGNC
+
 
-[source HUGO::homo_sapiens#01]
+[source HGNC::homo_sapiens#02]
 # Used by homo_sapiens
-name            = HUGO
+name            = HGNC
 download        = Y
 order           = 29
 priority        = 3
-prio_descr      = refseq
-parser          = HUGOParser
+prio_descr      = entrezgene_manual
+parser          = HGNCParser
 release_uri     =
-data_uri        = http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=md_prot_id&col=gd_pub_refseq_ids&col=md_eg_id&status=Approved&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr
+data_uri        = http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_refseq_ids&col=md_eg_id&col=md_eg_id&col=md_refseq_id&status=Approved&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr
 
-[source HUGO::homo_sapiens#02]
-# Used by homo_sapiens
-name            = HUGO
-download        = Y
+
+[source HGNC::homo_sapiens#03]
+# Used by #01
+name            = HGNC
+download        = N
 order           = 30
-priority        = 1
-prio_descr      = havana
-parser          = HUGO_ENSGParser
+priority        = 4
+prio_descr      = refseq_manual
+parser          = HGNC_ENSGParser
 release_uri     =
-data_uri        = file:HUGO/HUGO_TO_ENSG
+data_uri        = file:HGNC/HGNC_TO_ENSG
 
-[source HUGO::homo_sapiens#03]
-# used by #01 which produces HUGO refseq,uniprot and entrezgene types
-name            = HUGO
+[source HGNC::homo_sapiens#04]
+# used by #01 which produces HGNC refseq and entrezgene types
+name            = HGNC
 download        = N
 order           = 30
-priority        = 1
-prio_descr      = uniprot
-parser          = HUGO_ENSGParser
+priority        = 5
+prio_descr      = entrezgene_mapped
+parser          = HGNC_ENSGParser
 release_uri     =
-data_uri        = file:HUGO/HUGO_TO_ENSG
+data_uri        = file:HGNC/HGNC_TO_ENSG
 
-[source HUGO::homo_sapiens#04]
-# Used by #01
-name            = HUGO
+[source HGNC::homo_sapiens#05]
+# used by #01 which produces HGNC refseq and entrezgene types
+name            = HGNC
 download        = N
 order           = 30
-priority        = 1
-prio_descr      = entrezgene
-parser          = HUGO_ENSGParser
+priority        = 6
+prio_descr      = refseq_mapped
+parser          = HGNC_ENSGParser
 release_uri     =
-data_uri        = file:HUGO/HUGO_TO_ENSG
+data_uri        = file:HGNC/HGNC_TO_ENSG
 
 [source IMGT/GENE_DB::homo_sapiens]
 # Used by homo_sapiens
@@ -2361,9 +2374,9 @@ source          = Codelink::homo_sapiens
 source          = EntrezGene::MULTI
 source          = GO::homo_sapiens
 source          = InterproGO::MULTI
-source          = HUGO::homo_sapiens
-source          = HUGO::homo_sapiens#01
-source          = HUGO::homo_sapiens#02
+source          = HGNC::homo_sapiens
+source          = HGNC::homo_sapiens#01
+source          = HGNC::homo_sapiens#02
 source          = IMGT/GENE_DB::homo_sapiens
 source          = IPI::homo_sapiens
 source          = Illumina_V1::homo_sapiens