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Commit b06665bd authored by Ian Longden's avatar Ian Longden
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use ncRNA database now instead of the species files, which had to be manually copied over

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misc-scripts/xref_mapping/xref_config.ini
+ 42
− 301
View file @ b06665bd
......@@ -2073,286 +2073,17 @@ parser = comes via ncRNAParser
release_uri =
data_uri =
[source ncRNA::bos_taurus]
[source ncRNA::MULTI]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
parser = ncRNA_DBParser
release_uri =
data_uri = file:Bos_taurus/ncRNA/ncRNA.txt
[source ncRNA::canis_familiaris]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Canis_familiaris/ncRNA/ncRNA.txt
[source ncRNA::ciona_intestinalis]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Ciona_intestinalis/ncRNA/ncRNA.txt
[source ncRNA::ciona_savignyi]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Ciona_savignyi/ncRNA/ncRNA.txt
[source ncRNA::danio_rerio]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Danio_rerio/ncRNA/ncRNA.txt
[source ncRNA::dasypus_novemcinctus]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Dasypus_novemcinctus/ncRNA/ncRNA.txt
[source ncRNA::equus_caballus]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Equus_caballus/ncRNA/ncRNA.txt
[source ncRNA::erinaceus_europaeus]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Erinaceus_europaeus/ncRNA/ncRNA.txt
[source ncRNA::gallus_gallus]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Gallus_gallus/ncRNA/ncRNA.txt
[source ncRNA::gasterosteus_aculeatus]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Gasterosteus_aculeatus/ncRNA/ncRNA.txt
[source ncRNA::gorilla_gorilla]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Gorilla_gorilla/ncRNA/ncRNA.txt
data_uri = script:host=>genebuild7,port=>3306,dbname=>sw4_ncRNA_Xrefs,
[source ncRNA::homo_sapiens]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Homo_sapiens/ncRNA/ncRNA.txt
[source ncRNA::loxodonta_africana]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Loxodonta_africana/ncRNA/ncRNA.txt
[source ncRNA::macaca_mulatta]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Macaca_mulatta/ncRNA/ncRNA.txt
[source ncRNA::monodelphis_domestica]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Monodelphis_domestica/ncRNA/ncRNA.txt
[source ncRNA::mus_musculus]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Mus_musculus/ncRNA/ncRNA.txt
[source ncRNA::myotis_lucifugus]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Myotis_lucifugus/ncRNA/ncRNA.txt
[source ncRNA::ochotona_princeps]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Ochotona_princeps/ncRNA/ncRNA.txt
[source ncRNA::oryctolagus_cuniculus]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Oryctolagus_cuniculus/ncRNA/ncRNA.txt
[source ncRNA::oryzias_latipes]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Oryzias_latipes/ncRNA/ncRNA.txt
[source ncRNA::pan_troglodytes]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Pan_troglodytes/ncRNA/ncRNA.txt
[source ncRNA::pongo_pygmaeus]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:pongo_pygmaeus/ncRNA/ncRNA.txt
[source ncRNA::rattus_norvegicus]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Rattus_norvegicus/ncRNA/ncRNA.txt
[source ncRNA::spermophilus_tridecemlineatus]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Spermophilus_tridecemlineatus/ncRNA/ncRNA.txt
[source ncRNA::takifugu_rubripes]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Takifugu_rubripes/ncRNA/ncRNA.txt
[source ncRNA::tupaia_belangeri]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Tupaia_belangeri/ncRNA/ncRNA.txt
[source ncRNA::xenopus_tropicalis]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Xenopus_tropicalis/ncRNA/ncRNA.txt
[source ncRNA::ornithorhynchus_anatinus]
name = ncRNA
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:Ornithorhynchus_anatinus/ncRNA/ncRNA.txt
[source wormpep_id::caenorhabditis_elegans]
# Used by caenorhabditis_elegans
......@@ -2567,7 +2298,7 @@ source = UniGene::bos_taurus
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::bos_taurus
source = ncRNA::MULTI
[species caenorhabditis_elegans]
taxonomy_id = 6239
......@@ -2598,7 +2329,7 @@ source = UniGene::canis_familiaris
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::canis_familiaris
source = ncRNA::MULTI
[species ciona_intestinalis]
taxonomy_id = 7719
......@@ -2617,7 +2348,7 @@ source = cint_aniseed_jgi_v1::ciona_intestinalis
source = cint_aniseed_jgi_v2::ciona_intestinalis
source = cint_jgi_v1::ciona_intestinalis
source = cint_jgi_v2::ciona_intestinalis
source = ncRNA::ciona_intestinalis
source = ncRNA::MULTI
[species ciona_savignyi]
taxonomy_id = 51511
......@@ -2633,7 +2364,7 @@ source = UniGene::ciona_savignyi
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::ciona_savignyi
source = ncRNA::MULTI
[species danio_rerio]
taxonomy_id = 7955
......@@ -2651,7 +2382,7 @@ source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ZFIN_ID::danio_rerio
source = ncRNA::danio_rerio
source = ncRNA::MULTI
[species dasypus_novemcinctus]
taxonomy_id = 9361
......@@ -2663,7 +2394,7 @@ source = Interpro::MULTI
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::dasypus_novemcinctus
source = ncRNA::MULTI
[species dipodomys_ordii]
taxonomy_id = 10020
......@@ -2677,6 +2408,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::MULTI
[species drosophila_melanogaster]
taxonomy_id = 7227
......@@ -2700,6 +2432,7 @@ source = Interpro::MULTI
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::MULTI
[species erinaceus_europaeus]
taxonomy_id = 9365
......@@ -2714,7 +2447,7 @@ source = UniGene::MULTI
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::erinaceus_europaeus
source = ncRNA::MULTI
[species equus_caballus]
taxonomy_id = 9796
......@@ -2729,7 +2462,7 @@ source = UniGene::equus_caballus
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::equus_caballus
source = ncRNA::MULTI
[species felis_catus]
taxonomy_id = 9685
......@@ -2741,6 +2474,7 @@ source = Interpro::MULTI
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::MULTI
[species gallus_gallus]
taxonomy_id = 9031
......@@ -2756,7 +2490,7 @@ source = UniGene::gallus_gallus
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::gallus_gallus
source = ncRNA::MULTI
[species gasterosteus_aculeatus]
taxonomy_id = 69293
......@@ -2771,7 +2505,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::gasterosteus_aculeatus
source = ncRNA::MULTI
[species gorilla_gorilla]
taxonomy_id = 9593
......@@ -2785,7 +2519,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::gorilla_gorilla
source = ncRNA::MULTI
[species homo_sapiens]
......@@ -2818,7 +2552,7 @@ source = RefSeq_peptide::homo_sapiens
source = UniGene::homo_sapiens
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::homo_sapiens
source = ncRNA::MULTI
source = UCSC::homo_sapiens
source = HGNC_curated_transcript::homo_sapiens
......@@ -2832,7 +2566,7 @@ source = Interpro::MULTI
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::loxodonta_africana
source = ncRNA::MULTI
[species macaca_mulatta]
taxonomy_id = 9544
......@@ -2845,7 +2579,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian
source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ncRNA::macaca_mulatta
source = ncRNA::MULTI
[species monodelphis_domestica]
taxonomy_id = 13616
......@@ -2859,7 +2593,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::monodelphis_domestica
source = ncRNA::MULTI
[species mus_musculus]
taxonomy_id = 10090
......@@ -2889,7 +2623,7 @@ source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
#source = Uniprot/Varsplic::MULTI
#source = Vega_mouse_transcript::mus_musculus # removed use Vega_transcript
source = ncRNA::mus_musculus
source = ncRNA::MULTI
source = UCSC::mus_musculus
[species myotis_lucifugus]
......@@ -2905,7 +2639,7 @@ source = UniGene::myotis_lucifugus
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::myotis_lucifugus
source = ncRNA::MULTI
[species ochotona_princeps]
taxonomy_id = 9978
......@@ -2919,7 +2653,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::ochotona_princeps
source = ncRNA::MULTI
[species ornithorhynchus_anatinus]
taxonomy_id = 9258
......@@ -2935,7 +2669,7 @@ source = Uniprot/Varsplic::MULTI
source = Oxford_FGU_Oa_tscript::ornithorhynchus_anatinus
source = Oxford_FGU_Oa_gene::ornithorhynchus_anatinus
source = Platypus_olfactory_receptor::ornithorhynchus_anatinus
source = ncRNA::ornithorhynchus_anatinus
source = ncRNA::MULTI
[species oryctolagus_cuniculus]
taxonomy_id = 9986
......@@ -2947,7 +2681,7 @@ source = Interpro::MULTI
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::oryctolagus_cuniculus
source = ncRNA::MULTI
[species oryzias_latipes]
taxonomy_id = 8090
......@@ -2964,7 +2698,7 @@ source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = UniProt::protein_id
source = Uniprot::EMBL
source = ncRNA::oryzias_latipes
source = ncRNA::MULTI
[species pan_troglodytes]
taxonomy_id = 9598
......@@ -2978,7 +2712,7 @@ source = RefSeq_peptide::pan_troglodytes
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::pan_troglodytes
source = ncRNA::MULTI
[species pongo_pygmaeus]
taxonomy_id = 9600
......@@ -2994,7 +2728,7 @@ source = UniGene::MULTI
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::pongo_pygmaeus
source = ncRNA::MULTI
[species procavia_capensis]
taxonomy_id = 9813
......@@ -3008,6 +2742,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::MULTI
[species pteropus_vampyrus]
......@@ -3022,6 +2757,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::MULTI
[species rattus_norvegicus]
taxonomy_id = 10116
......@@ -3040,7 +2776,7 @@ source = UniGene::rattus_norvegicus
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::rattus_norvegicus
source = ncRNA::MULTI
[species saccharomyces_cerevisiae]
taxonomy_id = 4932
......@@ -3069,7 +2805,7 @@ source = UniGene::MULTI
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::spermophilus_tridecemlineatus
source = ncRNA::MULTI
[species taeniopygia_guttata]
taxonomy_id = 59729
......@@ -3084,6 +2820,7 @@ source = UniGene::taeniopygia_guttata
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::MULTI
[species takifugu_rubripes]
taxonomy_id = 31033
......@@ -3098,7 +2835,7 @@ source = UniGene::takifugu_rubripes
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::takifugu_rubripes
source = ncRNA::MULTI
[species tarsius_syrichta]
taxonomy_id = 9478
......@@ -3112,6 +2849,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::MULTI
[species tetraodon_nigroviridis]
taxonomy_id = 99883
......@@ -3125,7 +2863,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
#source = ncRNA::tetraodon_nigroviridis
source = ncRNA::MULTI
source = Genoscope_pred_gene::tetraodon_nigroviridis
source = Genoscope_pred_transcript::tetraodon_nigroviridis
source = Genoscope_pred_translation::tetraodon_nigroviridis
......@@ -3145,7 +2883,7 @@ source = UniGene::MULTI
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::tupaia_belangeri
source = ncRNA::MULTI
[species tursiops_truncatus]
taxonomy_id = 9739
......@@ -3159,6 +2897,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::MULTI
[species vicugna_pacos]
taxonomy_id = 30538
......@@ -3172,6 +2911,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::MULTI
[species choloepus_hoffmanni]
taxonomy_id = 9358
......@@ -3185,6 +2925,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::MULTI
[species xenopus_tropicalis]
taxonomy_id = 8364
......@@ -3200,4 +2941,4 @@ source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = Xenopus_Jamboree::xenopus_tropicalis
source = ncRNA::xenopus_tropicalis
source = ncRNA::MULTI
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