use the registry to get the core and vega databses that way we dont have to...

use the registry to get the core and vega databses that way we dont have to remember to update this file for every release and changing the release number. You can still use the old way as well in case you have to, i.e. on different servers

misc-scripts/xref_mapping/xref_config.ini

@@ -1016,7 +1016,7 @@ priority        = 1
 prio_descr      = main
 parser          = GOSlimParser
 release_uri     =
-data_uri        = script:host=>ens-livemirror,dbname=>ensembl_ontology_56,
+data_uri        = script:host=>ens-staging1,dbname=>ensembl_ontology_58,
 
 
 [source GO::homo_sapiens]
@@ -1114,17 +1114,6 @@ parser          = HGNCParser
 release_uri     =
 data_uri        = 
 
-[source HGNC::homo_sapiens#08]
-# used by #02 
-name            = HGNC
-download        = N
-order           = 30
-priority        = 100
-prio_descr      = desc_only
-parser          = HGNCParser
-release_uri     =
-data_uri        = 
-
 [source HGNC::homo_sapiens]
 # Used by homo_sapiens
 name            = HGNC
@@ -1134,8 +1123,8 @@ priority        = 1
 prio_descr      = havana
 parser          = HGNC_ENSTParser
 release_uri     =
-data_uri        = script:host=>ens-staging1,port=>3306,dbname=>homo_sapiens_vega_57_37b,
-
+data_uri        = script:
+#data_uri        = script:vhost=>ens-staging1,vdbname=>homo_sapiens_vega_58_37c,vport=>5306,vuser=>anonymous,chost=>ens-staging1,cport=>3306,cdbname=>homo_sapiens_core_58_37c,
 
 
 [source HGNC::homo_sapiens#02]
@@ -1147,7 +1136,7 @@ priority        = 4
 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=gd_pub_eg_id&col=gd_pub_refseq_ids&col=md_eg_id&col=md_refseq_id&col=gd_pub_ensembl_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_refseq_id&col=gd_pub_ensembl_id&col=md_prot_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 HGNC::homo_sapiens#03]
@@ -1159,7 +1148,18 @@ priority        = 5
 prio_descr      = refseq_manual
 parser          = HGNCParser
 release_uri     =
-data_uri        = file:HGNC/HGNC_TO_ENSG
+data_uri        =
+
+[source HGNC::homo_sapiens#09]
+# used by #02 
+name            = HGNC
+download        = N
+order           = 30
+priority        = 5
+prio_descr      = swissprot_manual
+parser          = HGNCParser
+release_uri     =
+data_uri        = 
 
 [source HGNC::homo_sapiens#04]
 # used by #02 which produces HGNC refseq and entrezgene types
@@ -1170,7 +1170,7 @@ priority        = 6
 prio_descr      = entrezgene_mapped
 parser          = HGNCParser
 release_uri     =
-data_uri        = file:HGNC/HGNC_TO_ENSG
+data_uri        =
 
 [source HGNC::homo_sapiens#05]
 # used by #02 which produces HGNC refseq and entrezgene types
@@ -1181,7 +1181,7 @@ priority        = 7
 prio_descr      = refseq_mapped
 parser          = HGNCParser
 release_uri     =
-data_uri        = file:HGNC/HGNC_TO_ENSG
+data_uri        =
 
 [source HGNC::homo_sapiens#06]
 # used by uniprotParser
@@ -1194,6 +1194,17 @@ parser          = uniprotparser
 release_uri     =
 data_uri        = see_uniprot
 
+[source HGNC::homo_sapiens#08]
+# used by #02 
+name            = HGNC
+download        = N
+order           = 30
+priority        = 100
+prio_descr      = desc_only
+parser          = HGNCParser
+release_uri     =
+data_uri        = 
+
 [source IMGT/GENE_DB::homo_sapiens]
 # Used by homo_sapiens
 name            = IMGT/GENE_DB
@@ -1427,7 +1438,8 @@ priority        = 1
 prio_descr      = vega
 parser          = MGI_Vega_Parser
 release_uri     =
-data_uri        = script:host=>ens-staging2,port=>3306,dbname=>mus_musculus_vega_57_37j,
+data_uri        = script:
+#data_uri        = script:vhost=>ens-staging2,vport=>3306,vdbname=>mus_musculus_vega_58_37k,chost=>ens-staging2,cport=>3306,cdbname=>mus_musculus_core_58_37k,
 
 [source MGI::mus_musculus#03]
 # Used by mus_musculus
@@ -1481,7 +1493,7 @@ priority        = 1
 prio_descr      =
 parser          = OTTTParser
 release_uri     =
-data_uri        = script:host=>ens-staging,port=>5317,dbname=>mus_musculus_vega_56_37i,
+data_uri        =
 
 [source RGD::rattus_norvegicus]
 # Used by rattus_norvegicus
@@ -1599,7 +1611,7 @@ download        = Y
 order           = 20
 priority        = 2
 prio_descr      = refseq
-parser          = RefSeqParser
+parser          = RefSeqGPFFParser
 release_uri     = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
 data_uri        = ftp://ftp.ncbi.nih.gov/genomes/Equus_caballus/RNA/rna.gbk.gz
 
@@ -2353,7 +2365,8 @@ priority        = 1
 prio_descr      =
 parser          = HGNC_curated_transcriptParser
 release_uri     = 
-data_uri        = script:host=>ens-staging1,port=>3306,dbname=>homo_sapiens_vega_57_37b,
+data_uri        = script:
+#data_uri        = script:vhost=>ensembldb.ensembl.org,vport=>5306,vdbname=>homo_sapiens_vega_57_37b,vuser=>anonymous,vprot=>5306,chost=>ens-staging,cport=>3306,cdbname=>homo_sapiens_core_58_37c,
 
 
 [source HGNC_automatic_transcript::homo_sapiens]
@@ -2391,7 +2404,8 @@ priority        = 1
 prio_descr      =
 parser          = MGI_curated_transcriptParser
 release_uri     = 
-data_uri        = script:host=>ens-staging2,port=>3306,dbname=>mus_musculus_vega_57_37j,
+data_uri        = script:
+#data_uri        = script:vhost=>ens-staging2,vport=>3306,vdbname=>mus_musculus_vega_58_37k,chost=>ens-staging2,cport=>3306,cdbname=>mus_musculus_core_58_37k,
 
 [source MGI_curated_gene::mus_musculus]
 name            = MGI_curated_gene