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Commit 33ae6905 authored by Monika Komorowska's avatar Monika Komorowska
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changed source definition for RNAMMER and TRNASCAN_SE

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misc-scripts/xref_mapping/xref_config.ini
+ 125
− 47
View file @ 33ae6905
......@@ -237,6 +237,7 @@ source = Uniprot/SWISSPROT::MULTI
source = RFAM::MULTI
source = miRBase::MULTI
#source = Uniprot/Varsplic::MULTI
source = WikiGene::MULTI
[source VB_Community_Annotation::aedes_aegypti]
# Used by aedes_aegypti
......@@ -3130,7 +3131,7 @@ download = Y
order = 70
priority = 1
prio_descr =
parser = RFAMParser
parser = RFAMParser_E
release_uri =
data_uri = ftp://ftp.sanger.ac.uk/pub/databases/Rfam/CURRENT/Rfam.seed.gz
......@@ -3179,15 +3180,6 @@ parser = comes via official naming
release_uri =
data_uri =
[source ncRNA::EG]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNA_DBParser
release_uri =
data_uri = script:host=>mysql-eg-pan-1,port=>4276,dbname=>ncRNA_Xrefs,
[source RFAM_gene_name]
# Used homo_sapiens,mus_musculus
......@@ -3215,24 +3207,25 @@ data_uri =
[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
download = Y
order = 70
priority = 1
prio_descr =
parser =
parser = CoreXrefParser
release_uri =
data_uri =
data_uri = script:biotype=>rRNA,object_type=>gene,project=>ensemblgenomes,
[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
download = Y
order = 70
priority = 1
prio_descr =
parser =
parser = CoreXrefParser
release_uri =
data_uri =
data_uri = script:biotype=>tRNA,object_type=>gene,project=>ensemblgenomes,
[source misc_EG::EG]
# Used by EnsemblGenomes to maintain sources of xrefs which don't have a proper parser yet.
......@@ -3922,7 +3915,10 @@ source = RefSeq_dna::MULTI-fungi
source = RefSeq_peptide::MULTI-fungi
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species aspergillus_oryzae]
......@@ -4024,7 +4020,10 @@ source = RefSeq_dna::MULTI-fungi
source = RefSeq_peptide::MULTI-fungi
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
source = PHIbase::MULTI
......@@ -4041,7 +4040,10 @@ source = RefSeq_dna::MULTI-fungi
source = RefSeq_peptide::MULTI-fungi
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
source = PHIbase::MULTI
......@@ -4057,7 +4059,10 @@ source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species schistosoma_mansoni]
......@@ -4072,11 +4077,12 @@ source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species leishmania_major]
taxonomy_id = 5664
taxonomy_id = 347515
......@@ -4108,7 +4114,10 @@ source = Uniprot/SWISSPROT::MULTI
source = RefSeq_dna::MULTI-protozoa
source = RefSeq_peptide::MULTI-protozoa
source = PHIbase::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species gibberella_moniliformis]
......@@ -4125,7 +4134,10 @@ source = RefSeq_peptide::MULTI-fungi
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = PHIbase::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species hyaloperonospora_arabidopsidis]
......@@ -4160,7 +4172,10 @@ source = RefSeq_dna::MULTI-fungi
source = RefSeq_peptide::MULTI-fungi
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species ustilago_maydis]
......@@ -4177,7 +4192,10 @@ source = RefSeq_peptide::MULTI-fungi
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = PHIbase::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species puccinia_triticina]
......@@ -4194,7 +4212,10 @@ source = RefSeq_peptide::MULTI-fungi
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = PHIbase::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species bos_taurus]
......@@ -4368,7 +4389,10 @@ source = RefSeq_dna::MULTI-protozoa
source = RefSeq_peptide::MULTI-protozoa
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species dipodomys_ordii]
......@@ -5145,7 +5169,10 @@ source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species plasmodium_vivax]
......@@ -5160,7 +5187,10 @@ source = RefSeq_dna::MULTI-complete
source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
......@@ -5178,7 +5208,10 @@ source = RefSeq_dna::MULTI-complete
source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
......@@ -5194,7 +5227,10 @@ source = RefSeq_dna::MULTI-complete
source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
......@@ -5210,7 +5246,10 @@ source = RefSeq_dna::MULTI-complete
source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species plasmodium_berghei]
......@@ -5226,7 +5265,10 @@ source = RefSeq_dna::MULTI-complete
source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species thalassiosira_pseudonana]
......@@ -5242,7 +5284,10 @@ source = RefSeq_dna::MULTI-complete
source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species ictidomys_tridecemlineatus]
......@@ -5430,7 +5475,10 @@ source = RefSeq_peptide::MULTI-fungi
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = PHIbase::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species phytophthora_infestans]
......@@ -5447,7 +5495,10 @@ source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = PHIbase::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species phytophthora_sojae]
......@@ -5463,7 +5514,10 @@ source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = PHIbase::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species phytophthora_ramorum]
......@@ -5479,7 +5533,10 @@ source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = PHIbase::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species nectria_haematococca]
......@@ -5496,7 +5553,10 @@ source = RefSeq_peptide::MULTI-fungi
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = PHIbase::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
[species fusarium_oxysporum]
taxonomy_id = 426428
......@@ -5513,7 +5573,10 @@ source = RefSeq_peptide::MULTI-fungi
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = PHIbase::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species tuber_melanosporum]
......@@ -5601,7 +5664,10 @@ source = RefSeq_peptide::MULTI-fungi
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = PHIbase::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species nomascus_leucogenys]
......@@ -5687,7 +5753,10 @@ source = RefSeq_dna::MULTI-Plants
source = RefSeq_peptide::MULTI-Plants
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = goslim_goa::EG
[species oryza_brachyantha]
......@@ -5701,7 +5770,10 @@ source = RefSeq_dna::MULTI-Plants
source = RefSeq_peptide::MULTI-Plants
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
#source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = goslim_goa::EG
[species setaria_italica]
......@@ -5715,7 +5787,10 @@ source = RefSeq_dna::MULTI-Plants
source = RefSeq_peptide::MULTI-Plants
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
#source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = goslim_goa::EG
[species solanum_lycopersicum]
......@@ -5729,7 +5804,10 @@ source = RefSeq_dna::MULTI-Plants
source = RefSeq_peptide::MULTI-Plants
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
#source = ncRNA::EG
source = RFAM::EG
source = miRBase
source = RNAMMER::MULTI
source = TRNASCAN_SE::MULTI
source = goslim_goa::EG
[species amphimedon_queenslandica]
......
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