addition of RFAM_transcript_name and RFAM_gene_name and the same for miRBASE....

addition of RFAM_transcript_name and RFAM_gene_name and the same for miRBASE. changing of priorities for HGNC and MGI source

misc-scripts/xref_mapping/xref_config.ini

@@ -382,7 +382,7 @@ priority        = 1
 prio_descr      =
 parser          = CCDSParser
 release_uri     =
-data_uri        = script:host=>ens-livemirror,dbname=>ccds_human,tran_name=>ENST,
+data_uri        = script:host=>genebuild7,dbname=>db8_human_cdsonly_22sept2010,tran_name=>ENST,
 
 [source CCDS::mus_musculus]
 # Used by mus_musculus
@@ -393,7 +393,7 @@ priority        = 1
 prio_descr      =
 parser          = CCDSParser
 release_uri     =
-data_uri        = script:host=>ens-livemirror,dbname=>ccds_mouse,tran_name=>ENSMUST,
+data_uri        = script:host=>genebuild7,dbname=>db8_mouse_cdsonly_22sept2010,tran_name=>ENSMUST,
 
 [source Celera_Pep::anopheles_gambiae]
 # Used by anopheles_gambiae
@@ -559,28 +559,6 @@ release_uri     =
 data_uri        = comes via EntrezGene
 
 
-#[source Ens_Ag_gene::drosophila_melanogaster]
-# Used by drosophila_melanogaster
-#name            = Ens_Ag_gene
-#download        = N
-#order           = 50
-#priority        = 1
-#prio_descr      = Ensembl mosquito gene predictions
-#parser          = Flybase_dmel_GFFv3_Parser
-#release_uri     =
-#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz
-
-#[source Ens_Am_gene::drosophila_melanogaster]
-# Used by drosophila_melanogaster
-#name            = Ens_Am_gene
-#download        = N
-#order           = 50
-#priority        = 1
-#prio_descr      = Ensembl bee gene predictions
-#parser          = Flybase_dmel_GFFv3_Parser
-#release_uri     =
-#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz
-
 [source Fantom::mus_musculus]
 # Used by mus_muscullus
 name            = Fantom
@@ -977,7 +955,8 @@ priority        = 1
 prio_descr      = main
 parser          = GOSlimParser
 release_uri     =
-data_uri        = script:host=>ens-staging1,dbname=>ensembl_ontology_61,
+data_uri        = script:
+#data_uri        = script:host=>ens-staging1,dbname=>ensembl_ontology_61,
 
 [source goslim_goa::EG]
 # Used by Ensembl Genomes
@@ -1059,7 +1038,7 @@ priority        = 1
 prio_descr      = Human Protein Atlas (HPA) database
 parser          = HPAParser
 release_uri     = 
-data_uri        = http://www.proteinatlas.org/data/xref.php
+data_uri        = http://www.proteinatlas.org/download/xref.php
 
 #[source IMGT_HLA::homo_sapiens]
 # Used by homo_sapiens
@@ -1072,6 +1051,16 @@ data_uri        = http://www.proteinatlas.org/data/xref.php
 #release_uri     = 
 #data_uri        = http://hla.alleles.org/xrefs/embl.txt
 
+[source LRG_HGNC_notransfer]
+name            = LRG_HGNC_notransfer
+download        = N
+order           = 30
+priority        = 5
+prio_descr      = 
+parser          = HGNCParser
+release_uri     =
+data_uri        =
+
 [source HGNC::homo_sapiens#01]
 # Used by homo_sapiens
 name            = HGNC
@@ -1082,7 +1071,7 @@ priority        = 2
 prio_descr      = ccds
 parser          = HGNC_CCDSParser
 release_uri     =
-data_uri        = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=HGNC+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_status&col=gd_ccds_ids&status=Approved&status_opt=2&level=pri&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag,dbname=>ccds_human,host=>ens-livemirror,
+data_uri        = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=HGNC+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_status&col=gd_ccds_ids&status=Approved&status_opt=2&level=pri&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag,host=>genebuild7,dbname=>db8_human_cdsonly_22sept2010,
 
 
 [source HGNC::homo_sapiens#07]
@@ -1090,7 +1079,7 @@ data_uri        = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.c
 name            = HGNC
 download        = N
 order           = 30
-priority        = 3
+priority        = 1
 prio_descr      = ensembl_manual
 parser          = HGNCParser
 release_uri     =
@@ -1101,12 +1090,12 @@ data_uri        =
 name            = HGNC
 download        = Y
 order           = 30
-priority        = 1
-prio_descr      = havana
+priority        = 3
+prio_descr      = vega
 parser          = HGNC_ENSTParser
 release_uri     =
 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,
+#data_uri        = script:vuser=>ensro,vhost=>ens-research,vdbname=>st3_homo_sapiens_vega_59_20100903,vport=>3306,cuser=>ensro,chost=>ens-staging1,cport=>3306,cdbname=>homo_sapiens_core_61_37f,
 
 
 [source HGNC::homo_sapiens#02]
@@ -1198,8 +1187,8 @@ parser          = IKMCParser
 release_uri     =
 data_uri        = script:
 
-[source IKMC_No_products_available_yet::mus_musculus]
-name            = IKMC_No_products_available_yet
+[source IKMCs_No_products_available_yet::mus_musculus]
+name            = IKMCs_No_products_available_yet
 download        = N
 order           = 40
 priority        = 1
@@ -1208,8 +1197,8 @@ parser          = IKMCParser
 release_uri     =
 data_uri        = 
 
-[source IKMC_Vector_available::mus_musculus]
-name            = IKMC_Vector_available
+[source IKMCs_Vector_available::mus_musculus]
+name            = IKMCs_Vector_available
 download        = N
 order           = 40
 priority        = 1
@@ -1218,8 +1207,8 @@ parser          = IKMCParser
 release_uri     =
 data_uri        = 
 
-[source IKMC_ES_cells_available::mus_musculus]
-name            = IKMC_ES_cells_available
+[source IKMCs_ES_cells_available::mus_musculus]
+name            = IKMCs_ES_cells_available
 download        = N
 order           = 40
 priority        = 1
@@ -1228,8 +1217,8 @@ parser          = IKMCParser
 release_uri     =
 data_uri        = 
 
-[source IKMC_Mice_available::mus_musculus]
-name            = IKMC_Mice_available
+[source IKMCs_Mice_available::mus_musculus]
+name            = IKMCs_Mice_available
 download        = N
 order           = 40
 priority        = 1
@@ -1408,30 +1397,41 @@ parser          = Mim2GeneParser
 release_uri     =
 data_uri        = ftp://ftp.ncbi.nih.gov/gene/DATA/mim2gene
 
-[source MGI::mus_musculus#01]
+[source MGI::mus_musculus#04]
 # Used by mus_musculus
 name            = MGI
 download        = N
 order           = 30
-priority        = 3
+priority        = 4
 prio_descr      = uniprot
 parser          = 
 release_uri     =
 data_uri        = taken from uniprot files
 
+[source MGI::mus_musculus#01]
+# Used by mus_musculus
+name            = MGI
+download        = Y
+order           = 30
+priority        = 1
+prio_descr      = official
+parser          = MGIParser
+release_uri     =
+data_uri        = ftp://ftp.informatics.jax.org/pub/reports/MRK_ENSEMBL.rpt
+
 [source MGI::mus_musculus#02]
 # Used by mus_musculus
 name            = MGI
 download        = Y
 order           = 45
-priority        = 1
+priority        = 2
 prio_descr      = vega
 parser          = MGI_Vega_Parser
 release_uri     =
 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,
+#data_uri        = script:vhost=>ens-research,vport=>3306,vdbname=>st3_mus_musculus_vega_61_20100917,chost=>ens-staging2,cport=>3306,cdbname=>mus_musculus_core_61_37n,
 
-[source MGI::mus_musculus#03]
+[source MGI::mus_musculus#05]
 # Used by mus_musculus
 name            = MGI
 download        = Y
@@ -1443,12 +1443,12 @@ release_uri     =
 data_uri        = ftp://ftp.informatics.jax.org/pub/reports/MRK_List2.sql.rpt
 data_uri        = ftp://ftp.informatics.jax.org/pub/reports/MRK_Synonym.sql.rpt
 
-[source MGI::mus_musculus#04]
+[source MGI::mus_musculus#03]
 # Used by mus_musculus
 name            = MGI
 download        = Y
 order           = 35
-priority        = 2
+priority        = 3
 prio_descr      = ccds
 parser          = MGI_CCDS_Parser
 release_uri     =
@@ -1660,7 +1660,7 @@ priority        = 1
 prio_descr      = ccds
 parser          = RefSeq_CCDSParser
 release_uri     =
-data_uri        = script:host=>ens-livemirror,dbname=>ccds_human,
+data_uri        = script:host=>genebuild7,dbname=>db8_human_cdsonly_22sept2010,
 
 [source RefSeq_dna::homo_sapiens#01]
 # Used by homo_sapiens
@@ -1693,7 +1693,7 @@ priority        = 1
 prio_descr      = ccds
 parser          = RefSeq_CCDSParser
 release_uri     =
-data_uri        = script:host=>ens-livemirror,dbname=>ccds_mouse,
+data_uri        = script:host=>genebuild7,dbname=>db8_mouse_cdsonly_22sept2010,
 
 
 [source RefSeq_dna::pan_troglodytes]
@@ -2428,19 +2428,19 @@ release_uri     =
 
 
 [source HGNC_curated_transcript::homo_sapiens]
-name            = HGNC_curated_transcript
+name            = HGNC_curated_transcript_notransfer
 download        = Y
 order           = 49
 priority        = 1
-prio_descr      =
+prio_descr      = curated with transcript number postfix
 parser          = curated_transcriptParser
 release_uri     = 
 data_uri        = script:
-#data_uri        = script:vhost=>ensembldb.ensembl.org,vport=>5306,vdbname=>homo_sapiens_vega_58_37c,vuser=>anonymous,vprot=>5306,chost=>ens-livemirror,cport=>3306,cdbname=>homo_sapiens_core_58_37c,
+#data_uri        = script:vhost=>ens-research,vdbname=>st3_homo_sapiens_vega_59_20100903,vuser=>ensro,vport=>3306,chost=>ens-staging,cport=>3306,cdbname=>homo_sapiens_core_61_37f,
 
 
-[source HGNC_automatic_transcript::homo_sapiens]
-name            = HGNC_automatic_transcript
+[source HGNC_transcript_name]
+name            = HGNC_transcript_name
 download        = N
 order           = 49
 priority        = 1
@@ -2448,8 +2448,8 @@ prio_descr      =
 parser          = done_in_official_naming
 release_uri     = 
 
-[source HGNC_curated_gene::homo_sapiens]
-name            = HGNC_curated_gene
+[source HGNC_gene_name]
+name            = HGNC_gene_name
 download        = N
 order           = 49
 priority        = 1
@@ -2457,17 +2457,9 @@ prio_descr      =
 parser          = done_in_official_naming
 release_uri     = 
 
-[source HGNC_automatic_gene::homo_sapiens]
-name            = HGNC_automatic_gene
-download        = N
-order           = 49
-priority        = 1
-prio_descr      =
-parser          = done_in_official_naming
-release_uri     = 
 
 [source MGI_curated_transcript::mus_musculus]
-name            = MGI_curated_transcript
+name            = MGI_curated_transcript_notransfer
 download        = Y
 order           = 49
 priority        = 1
@@ -2475,10 +2467,11 @@ prio_descr      =
 parser          = curated_transcriptParser
 release_uri     = 
 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,
+#data_uri        = script:vhost=>ens-research,vport=>3306,vdbname=>st3_mus_musculus_vega_61_20100917,chost=>ens-staging2,cport=>3306,cdbname=>mus_musculus_core_61_37n,
 
-[source MGI_curated_gene::mus_musculus]
-name            = MGI_curated_gene
+
+[source MGI_automatic_transcript::mus_musculus]
+name            = MGI_automatic_transcript_notransfer
 download        = N
 order           = 49
 priority        = 1
@@ -2486,25 +2479,27 @@ prio_descr      =
 parser          = done_in_official_naming
 release_uri     = 
 
-[source MGI_automatic_gene::mus_musculus]
-name            = MGI_automatic_gene
+[source MGI_gene_name]
+# Used homo_sapiens,mus_musculus
+name            = MGI_gene_name
 download        = N
-order           = 49
+order           = 70
 priority        = 1
 prio_descr      =
-parser          = done_in_official_naming
-release_uri     = 
-
+parser          = comes via official naming
+release_uri     =
+data_uri        =
 
-[source MGI_automatic_transcript::mus_musculus]
-name            = MGI_automatic_transcript
+[source MGI_transcript_name]
+# Used homo_sapiens,mus_musculus
+name            = MGI_transcript_name
 download        = N
-order           = 49
+order           = 70
 priority        = 1
 prio_descr      =
-parser          = done_in_official_naming
-release_uri     = 
-
+parser          = comes via official naming
+release_uri     =
+data_uri        =
 
 [source Clone_based_vega_transcript::homo_sapiens]
 name            = Clone_based_vega_transcript
@@ -2557,13 +2552,13 @@ parser          = XenopusJamboreeParser
 release_uri     =
 data_uri        = ftp://ftp.xenbase.org/pub/GenePageReports/GenePageEnsemblModelMapping.txt
 
-[source ZFIN_ID::danio_rerio]
+[source ZFIN_ID::danio_rerio#01]
 # Used by danio_rerio
 name            = ZFIN_ID
 download        = Y
 order           = 30
-priority        = 1
-prio_descr      =
+priority        = 2
+prio_descr      = uniprot/refseq
 parser          = ZFINParser
 release_uri     =
 data_uri        = http://zfin.org/data_transfer/Downloads/refseq.txt
@@ -2571,6 +2566,57 @@ data_uri        = http://zfin.org/data_transfer/Downloads/uniprot.txt
 data_uri        = http://zfin.org/data_transfer/Downloads/aliases.txt
 data_uri        = http://zfin.org/data_transfer/Downloads/gene_seq.txt
 
+[source ZFIN_ID::danio_rerio#02]
+# Used by danio_rerio
+name            = ZFIN_ID
+download        = Y
+order           = 30
+priority        = 1
+prio_descr      = vega
+parser          = ZFIN_DARTParser
+release_uri     = 
+data_uri        = script:vuser=>ensro,vhost=>ens-staging,vdbname=>danio_rerio_vega_61_9a,vport=>3306,
+
+[source ZFIN_ID::danio_rerio#03]
+# Used by danio_rerio
+name            = ZFIN_ID
+download        = Y
+order           = 1
+priority        = 10
+prio_descr      = description_only
+parser          = ZFINDescParser
+release_uri     = 
+data_uri        = http://zfin.org/data_transfer/Downloads/genetic_markers.txt
+
+[source ZFIN_ID_curated_transcript::danio_rerio]
+name            = ZFIN_ID_curated_transcript_notransfer
+download        = Y
+order           = 49
+priority        = 1
+prio_descr      = curated with transcript number postfix
+parser          = curated_transcriptParser
+release_uri     = 
+data_uri        = script:
+
+[source ZFIN_ID_transcript_name]
+name            = ZFIN_ID_transcript_name
+download        = N
+order           = 49
+priority        = 1
+prio_descr      =
+parser          = done_in_official_naming
+release_uri     = 
+
+[source ZFIN_ID_gene_name]
+name            = ZFIN_ID_gene_name
+download        = N
+order           = 49
+priority        = 1
+prio_descr      =
+parser          = done_in_official_naming
+release_uri     = 
+
+
 [source cint_aniseed_jgi_v1::ciona_intestinalis]
 # Used by ciona_intestinalis
 name            = cint_aniseed_jgi_v1
@@ -2638,6 +2684,29 @@ parser          = comes via ncRNAParser
 release_uri     =
 data_uri        =
 
+[source miRBase_gene_name]
+# Used homo_sapiens,mus_musculus
+name            = miRBase_gene_name
+download        = N
+order           = 70
+priority        = 1
+prio_descr      =
+parser          = comes via official naming
+release_uri     =
+data_uri        =
+
+[source miRBase_transcript_name]
+# Used homo_sapiens,mus_musculus
+name            = miRBase_transcript_name
+download        = N
+order           = 70
+priority        = 1
+prio_descr      =
+parser          = comes via official naming
+release_uri     =
+data_uri        =
+
+
 [source ncRNA::MULTI]
 name            = ncRNA
 download        = Y
@@ -2646,7 +2715,7 @@ priority        = 1
 prio_descr      =
 parser          = ncRNA_DBParser
 release_uri     =
-data_uri        = script:host=>genebuild7,port=>3306,dbname=>sw4_ncRNA_Xrefs
+data_uri        = script:host=>genebuild7,port=>3306,dbname=>sw4_ncRNA_Xrefs,
 
 [source ncRNA::culex_pipiens]
 name            = ncRNA_Culex
@@ -2658,6 +2727,29 @@ parser          = ncRNAParser
 release_uri     =
 data_uri        = file:/lustre/work1/ensembl/kmegy/Culex/Xrefs/culex_ncRNAxref_sw4.txt
 
+[source RFAM_gene_name]
+# Used homo_sapiens,mus_musculus
+name            = RFAM_gene_name
+download        = N
+order           = 70
+priority        = 1
+prio_descr      =
+parser          = comes via official naming
+release_uri     =
+data_uri        =
+
+[source RFAM_transcript_name]
+# Used homo_sapiens,mus_musculus
+name            = RFAM_transcript_name
+download        = N
+order           = 70
+priority        = 1
+prio_descr      =
+parser          = comes via official naming
+release_uri     =
+data_uri        =
+
+
 [source RNAMMER::MULTI-asp]
 # Used by aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri
 name            = RNAMMER
@@ -3186,8 +3278,11 @@ source          = RefSeq_peptide::danio_rerio
 source          = UniGene::danio_rerio
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = ZFIN_ID::danio_rerio
+source          = ZFIN_ID::danio_rerio#01
+source          = ZFIN_ID::danio_rerio#02
+source          = ZFIN_ID::danio_rerio#03
 source          = ncRNA::MULTI
+#source          = ZFIN_ID_curated_transcript::danio_rerio
 
 [species dasypus_novemcinctus]
 taxonomy_id     = 9361
@@ -3623,9 +3718,10 @@ source          = InterproGO::MULTI
 source          = IMGT/GENE_DB::mus_musculus
 source          = IKMCs_KOs::mus_musculus
 source          = IPI::mus_musculus
+source          = MGI::mus_musculus#01
 source          = MGI::mus_musculus#02
 source          = MGI::mus_musculus#03
-source          = MGI::mus_musculus#04
+source          = MGI::mus_musculus#05
 source          = MGI_curated_transcript::mus_musculus
 source          = Interpro::MULTI
 source          = RefSeq_dna::mus_musculus
@@ -3639,6 +3735,7 @@ source          = ncRNA::MULTI
 source          = UCSC::mus_musculus
 source          = Fantom::mus_musculus
 
+
 [species myotis_lucifugus]
 taxonomy_id     = 59463
 aliases         = little brown bat, microbat