added CADRE, AspGD, GeneDB and misc_EG::EG sources. updated TRNASCAN_SE and...

added CADRE, AspGD, GeneDB and misc_EG::EG sources. updated TRNASCAN_SE and RNAMMER sources; Updated species config for most of all fungi species

misc-scripts/xref_mapping/xref_config.ini

@@ -2827,8 +2827,8 @@ 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
+[source RNAMMER::MULTI]
+# Used by EnsemblGenomes, e.g. aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri
 name            = RNAMMER
 download        = N
 order           = 70
@@ -2838,9 +2838,86 @@ parser          =
 release_uri     =
 data_uri        =
 
-[source TRNASCAN-SE::MULTI-asp]
+[source TRNASCAN_SE::MULTI]
+# Used by EnsemblGenomes, e.g. aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri
+name            = TRNASCAN_SE
+download        = N
+order           = 70
+priority        = 1
+prio_descr      =
+parser          = 
+release_uri     =
+data_uri        =
+
+[source misc_EG::EG]
+# Used by EnsemblGenomes to maintain sources of xrefs which don't have a proper parser yet.
+name            = misc_EG
+download        = Y
+order           = 70
+priority        = 1
+prio_descr      =
+parser          = EG_DBParser
+release_uri     =
+data_uri        = script:host=>mysql-eg-pan-1,port=>4276,dbname=>EG_Xrefs,
+
+[source CADRE::MULTI]
 # Used by aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri
-name            = TRNASCAN-SE
+name            = CADRE
+download        = N
+order           = 70
+priority        = 1
+prio_descr      =
+parser          = 
+release_uri     =
+data_uri        =
+
+[source CADRE_AFum_A1163::MULTI]
+# Used by aspergillus_fumigatusa1163
+name            = CADRE_Afum_A1163
+download        = N
+order           = 70
+priority        = 1
+prio_descr      =
+parser          = 
+release_uri     =
+data_uri        =
+
+[source AspGD::MULTI]
+# Used by aspergillus_nidulans
+name            = AspGD
+download        = N
+order           = 70
+priority        = 1
+prio_descr      =
+parser          = 
+release_uri     =
+data_uri        =
+
+[source GeneDB::MULTI]
+# Used by plasmodium_falciparum, trypanosoma_brucei, leishmania_major, schistosoma_mansoni
+name            = GeneDB
+download        = N
+order           = 70
+priority        = 1
+prio_descr      =
+parser          = 
+release_uri     =
+data_uri        =
+
+[source GeneDB_Spombe::MULTI]
+# Used by schizosaccharomyces_pombe
+name            = GeneDB_Spombe
+download        = N
+order           = 70
+priority        = 1
+prio_descr      =
+parser          = 
+release_uri     =
+data_uri        =
+
+[source BROAD_U_maydis::MULTI]
+# Used by ustilago_maydis
+name            = BROAD_U_maydis
 download        = N
 order           = 70
 priority        = 1
@@ -3123,8 +3200,8 @@ source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 [species aspergillus_flavus]
 taxonomy_id     = 5059
@@ -3140,8 +3217,8 @@ source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 [species aspergillus_fumigatus]
 taxonomy_id     = 330879
@@ -3154,8 +3231,8 @@ source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 [species afumigatusa1163]
 taxonomy_id     = 451804
@@ -3169,8 +3246,8 @@ source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 [species aspergillus_nidulans]
 taxonomy_id     = 162425
@@ -3184,8 +3261,8 @@ source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 [species aspergillus_niger]
 taxonomy_id     = 425011
@@ -3200,8 +3277,8 @@ source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 [species aspergillus_oryzae]
 taxonomy_id     = 5062
@@ -3217,8 +3294,8 @@ source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 [species aspergillus_terreus]
 taxonomy_id     = 33178
@@ -3234,8 +3311,8 @@ source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 [species neosartorya_fischeri]
 taxonomy_id     = 36630
@@ -3251,8 +3328,8 @@ source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 [species puccinia_graministritici]
 taxonomy_id     = 418459
@@ -3268,6 +3345,8 @@ source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = ncRNA::EG
+source          = misc_EG::EG
+source          = PHIbase::MULTI
 
 [species trichoplax_adhaerens]
 taxonomy_id     = 10228
@@ -3282,8 +3361,8 @@ source          = RefSeq_peptide::MULTI-invertebrate
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 [species schistosoma_mansoni]
 taxonomy_id     = 6183
@@ -3298,8 +3377,8 @@ source          = RefSeq_peptide::MULTI-invertebrate
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 [species leishmania_major]
 taxonomy_id     = 5664
@@ -3315,8 +3394,8 @@ source          = RefSeq_peptide::MULTI-protozoa
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 [species pythium_ultimum]
 taxonomy_id     = 65071
@@ -3349,6 +3428,7 @@ source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = PHIbase::MULTI
 source          = ncRNA::EG
+source          = misc_EG::EG
 
 [species hyaloperonospora_arabidopsidis]
 taxonomy_id     = 559515
@@ -3365,8 +3445,8 @@ source          = RefSeq_peptide::MULTI-protozoa
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 source          = PHIbase::MULTI
 
 [species neurospora_crassa]
@@ -3382,13 +3462,12 @@ source          = RefSeq_dna::MULTI-fungi
 source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = ncRNA::EG
+source          = misc_EG::EG
 
 [species ustilago_maydis]
-taxonomy_id     = 5270
 taxonomy_id     = 237631
+taxonomy_id     = 5270
 aliases         = ustilagomaydis, umaydis, Ustilago maydis, Ustilago maydis 521
 source          = EntrezGene::MULTI
 source          = GO::MULTI
@@ -3401,6 +3480,7 @@ source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = PHIbase::MULTI
 source          = ncRNA::EG
+source          = misc_EG::EG
 
 [species puccinia_triticina]
 taxonomy_id     = 208348
@@ -3415,9 +3495,9 @@ source          = RefSeq_dna::MULTI-fungi
 source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = PHIbase::MULTI
+source          = ncRNA::EG
+source          = misc_EG::EG
 
 [species bos_taurus]
 taxonomy_id     = 9913
@@ -3781,8 +3861,8 @@ source          = Interpro::MULTI
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
+source          = TRNASCAN_SE::MULTI
+source          = RNAMMER::MULTI
 
 
 
@@ -4392,10 +4472,9 @@ source          = RefSeq_dna::MULTI-fungi
 source          = RefSeq_peptide::MULTI-fungi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = RFAM::MULTI
-source          = TRNASCAN-SE::MULTI-asp
-source          = RNAMMER::MULTI-asp
 source          = PHIbase::MULTI
+source          = ncRNA::EG
+source          = misc_EG::EG
 
 [species phytophthora_infestans]
 taxonomy_id     = 403677
@@ -4459,6 +4538,7 @@ source          = Uniprot/SWISSPROT::MULTI
 source          = PHIbase::MULTI
 source          = ncRNA::EG
 
+
 [species fusarium_oxysporum]
 taxonomy_id     = 426428
 taxonomy_id     = 59765
@@ -4475,6 +4555,7 @@ source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = PHIbase::MULTI
 source          = ncRNA::EG
+source          = misc_EG::EG
 
 [species gibberella_zeae]
 taxonomy_id     = 229533
@@ -4491,6 +4572,7 @@ source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = PHIbase::MULTI
 source          = ncRNA::EG
+source          = misc_EG::EG
 
 [species nomascus_leucogenys]
 taxonomy_id     = 61853