Adding Ixodes info., modif. Anoph, Aedes and Culex info.

misc-scripts/xref_mapping/xref_config.ini

@@ -150,6 +150,19 @@ parser          = VbDirectParser
 release_uri     =
 data_uri        = file:Aedes_aegypti/UCR/UCR_GillMgMT_0.2k_v2.txt
 
+[source Aedes_ManualAnnotation::aedes_aegypti]
+# Used by aedes_aegypti
+name            = Aedes_ManualAnnotation
+download        = Y
+order           = 40
+priority        = 1
+prio_descr      =
+parser          = AedesCAPParser
+release_uri     =
+#data_uri        = file:Aedes_aegypti/Aedes_AaeL1-2_ManualModels.fa
+data_uri        = file:Aedes_aegypti/Aedes_AaeL1-2_ManualModels_ALL_descr.fa
+#data_uri        = file:Aedes_aegypti/Aedes_AaeL1-2_ManualModels_DescrOnly_descr.fa
+
 [source AedesGenBank::aedes_aegypti]
 # Used by aedes_aegypti
 name            = AedesGenBank
@@ -161,6 +174,17 @@ parser          = AedesGenBankParser
 release_uri     =
 data_uri        = file:AedesGenBank/Aedes_proteinID.fa
 
+[source Ixodes_ManualAnnotation::ixodes_scapularis]
+# Used by ixodes_scapularis
+name            = Ixodes_ManualAnnotation
+download        = Y
+order           = 40
+priority        = 1
+prio_descr      =
+parser          = IxodesCAPParser
+release_uri     =
+data_uri        = file:Ixodes_scapularis/ixodes_CAP.fa
+
 [source AgilentCGH::homo_sapiens]
 # Used by homo_sapiens
 name            = AgilentCGH
@@ -227,6 +251,17 @@ parser          = AnophelesSymbolParser
 release_uri     =
 data_uri        = file:Anopheles_symbol/GeneName_translation_UniqID.txt
 
+[source VB_Community_Symbol::anopheles_gambiae]
+# Used by anopheles_gambiae
+name            = VB_Community_Symbol
+download        = Y
+order           = 40
+priority        = 1
+prio_descr      =
+parser          = VBCommunitySymbolParser
+release_uri     =
+data_uri        = file:VB_Community_Symbols/xref_Anopheles_symbol_lookup
+
 [source bdgpinsituexpr::drosophila_melanogaster]
 # Used by drosophila_melanogaster
 name            = bdgpinsituexpr
@@ -280,7 +315,7 @@ priority        = 1
 prio_descr      =
 parser          = CeleraProteinParser
 release_uri     =
-data_uri        = file:Celera_Pep/consensus-proteins_xref.fasta
+data_uri        = file:Celera/consensus-proteins_xref.fasta
 
 [source Celera_Trans::anopheles_gambiae]
 # Used by anopheles_gambiae
@@ -291,7 +326,7 @@ priority        = 1
 prio_descr      =
 parser          = CeleraTranscriptParser
 release_uri     =
-data_uri        = file:Celera_trans/consensus-transcripts_xref.fasta
+data_uri        = file:Celera/consensus-transcripts_xref.fasta
 
 [source Codelink::homo_sapiens]
 # Used by homo_sapiens
@@ -406,7 +441,7 @@ data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/
 #data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz
 
 [source EntrezGene::MULTI]
-# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, gorilla_gorilla, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_pygmaeus,  rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
+# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, gorilla_gorilla, homo_sapiens, ixodes_scappularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_pygmaeus,  rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
 name            = EntrezGene
 download        = Y
 order           = 10
@@ -583,7 +618,7 @@ data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/
 
 
 [source GO::MULTI]
-# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, loxodonta_africana, macaca_mulatta, monodelphis_domestica, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_pygmaeus,saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri
+# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, ixodes_scappularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_pygmaeus,saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri
 name            = GO
 download        = Y
 order           = 80
@@ -962,7 +997,7 @@ release_uri     =
 data_uri        = file:Illumina_V2/Human-6_v2_sequence.csv
 
 [source Interpro::MULTI]
-# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, pan_troglodytes,pongo_pygmaeus, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
+# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, ixodes__scapularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, pan_troglodytes,pongo_pygmaeus, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
 name            = Interpro
 download        = Y
 order           = 70
@@ -1701,6 +1736,18 @@ release_uri     = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG
 data_uri        = ftp://ftp.ncbi.nih.gov/repository/UniGene/Monodelphis_domestica/Mdm.seq.uniq.gz
 data_uri        = ftp://ftp.ncbi.nih.gov/repository/UniGene/Monodelphis_domestica/Mdm.data.gz
 
+[source UniGene::ixodes_scapularis]
+# Used by ixodes_scapularis
+name            = UniGene
+download        = Y
+order           = 30
+priority        = 1
+prio_descr      =
+parser          = UniGeneParser
+release_uri     =
+data_uri        = ftp://ftp.ncbi.nih.gov/repository/UniGene/Ixodes_scapularis/Isc.seq.uniq.gz
+data_uri        = ftp://ftp.ncbi.nih.gov/repository/UniGene/Ixodes_scapularis/Isc.data.gz
+
 [source UniGene::mus_musculus]
 # Used by mus_musculus
 name            = UniGene
@@ -1805,7 +1852,7 @@ parser          = UniProtParser
 release_uri     =
 
 [source Uniprot/SPTREMBL::MULTI]
-# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_pygmaeus, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
+# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, ixodes_scapularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_pygmaeus, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
 name            = Uniprot/SPTREMBL
 download        = Y
 order           = 20
@@ -1869,7 +1916,7 @@ release_uri     = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldat
 data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz
 
 [source Uniprot/Varsplic::MULTI]
-# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_pygmaeus,rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
+# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, ixodes_scapularis, loxodonta_africana, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_pygmaeus,rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
 name            = Uniprot/Varsplic
 download        = Y
 order           = 30
@@ -2118,7 +2165,15 @@ parser          = ncRNA_DBParser
 release_uri     =
 data_uri        = script:host=>genebuild7,port=>3306,dbname=>sw4_ncRNA_Xrefs,
 
-
+[source ncRNA::culex_pipiens]
+name            = ncRNA_Culex
+download        = Y
+order           = 70
+priority        = 1
+prio_descr      = 
+parser          = ncRNAParser
+release_uri     = 
+data_uri        = file:/lustre/work1/ensembl/kmegy/Culex/Xrefs/culex_ncRNAxref_sw4.txt
 
 [source wormpep_id::caenorhabditis_elegans]
 # Used by caenorhabditis_elegans
@@ -2291,9 +2346,10 @@ source          = ARRAY_JHSPH_AG_GAMBER_15k_v1::anopheles_gambiae
 source          = ARRAY_JHSPH_GAM3_0_21k_v1::anopheles_gambiae
 source          = ARRAY_LIV_GAMDETOX_0_25k_v1::anopheles_gambiae
 source          = ARRAY_LIV_GAMDETOX_0_25k_v2::anopheles_gambiae
-source          = Anopheles_symbol::anopheles_gambiae
+#source          = Anopheles_symbol::anopheles_gambiae
 source          = Celera_Pep::anopheles_gambiae
 source          = Celera_Trans::anopheles_gambiae
+source          = VB_Community_Symbol::anopheles_gambiae
 source          = EntrezGene::MULTI
 source          = GO::MULTI
 source          = InterproGO::MULTI
@@ -2401,6 +2457,18 @@ source          = Uniprot/SWISSPROT::MULTI
 source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
+[species culex_pipiens]
+#taxonomy_id     = 7175   c. pipiens
+taxonomy_id     = 7176    c.quinquefasciatus
+aliases         = cpipiens, culex, culexpipiens, culex quinquefasciatus, cquinquefasciatus, culexquinquefasciatus
+source          = EntrezGene::MULTI
+source          = GO::MULTI
+source          = Interpro::MULTI
+source          = Uniprot/SPTREMBL::MULTI
+source          = Uniprot/SWISSPROT::MULTI
+source          = Uniprot/Varsplic::MULTI
+source          = ncRNA::culex_pipiens
+
 [species danio_rerio]
 taxonomy_id     = 7955
 aliases         = danio, daniorerio, drerio, zebrafish
@@ -2591,6 +2659,19 @@ source          = ncRNA::MULTI
 source          = UCSC::homo_sapiens
 source          = HGNC_curated_transcript::homo_sapiens
 
+[species ixodes_scapularis]
+taxonomy_id     = 6945
+aliases         = ixodes, ixodesscapularis
+source          = Ixodes_ManualAnnotation::ixodes_scapularis
+source          = EntrezGene::MULTI
+source          = GO::MULTI
+source          = InterproGO::MULTI
+source          = Interpro::MULTI
+source          = UniGene::ixodes_scapularis
+source          = Uniprot/SPTREMBL::MULTI
+source          = Uniprot/SWISSPROT::MULTI
+source          = Uniprot/Varsplic::MULTI
+
 [species loxodonta_africana]
 taxonomy_id     = 9785
 aliases         = elephant, lafricana, loxodontaafricana