commented out Uniprot/Varsplic and all the array type sources

misc-scripts/xref_mapping/xref_config.ini

@@ -1536,14 +1536,14 @@ parser          = UCSCParser
 
 [source UCSC::homo_sapiens]
 # Used by homo_sapiens
-name            = UCSC_hg18
+name            = UCSC_hg19
 download        = Y
 order           = 70
 priority        = 1
 prio_descr      =
 parser          = UCSCParser
-release_uri     = ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/README.txt
-data_uri        = ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownGene.txt.gz
+release_uri     = ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/README.txt
+data_uri        = ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz
 
 [source UCSC::mus_musculus]
 # Used by mus_musculus
@@ -2373,7 +2373,7 @@ source          = RefSeq_peptide::apis_mellifera
 source          = UniGene::apis_mellifera
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 
 [species bos_taurus]
 taxonomy_id     = 9913
@@ -2403,7 +2403,7 @@ source          = RefSeq_peptide::MULTI-invertebrate
 source          = UniGene::caenorhabditis_elegans
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = wormpep_id::caenorhabditis_elegans
 source          = wormpep_id::caenorhabditis_elegans#01
 
@@ -2419,7 +2419,7 @@ source          = RefSeq_peptide::canis_familiaris
 source          = UniGene::canis_familiaris
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species ciona_intestinalis]
@@ -2454,7 +2454,7 @@ source          = RefSeq_peptide::MULTI-vertebrate_other
 source          = UniGene::ciona_savignyi
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species culex_pipiens]
@@ -2466,13 +2466,13 @@ source          = GO::MULTI
 source          = Interpro::MULTI
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::culex_pipiens
 
 [species danio_rerio]
 taxonomy_id     = 7955
 aliases         = danio, daniorerio, drerio, zebrafish
-source          = AgilentProbe::danio_rerio
+#source          = AgilentProbe::danio_rerio
 source          = EntrezGene::MULTI
 source          = GO::danio_rerio
 source          = InterproGO::MULTI
@@ -2483,7 +2483,7 @@ source          = RefSeq_peptide::danio_rerio
 source          = UniGene::danio_rerio
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ZFIN_ID::danio_rerio
 source          = ncRNA::MULTI
 
@@ -2496,7 +2496,7 @@ source          = InterproGO::MULTI
 source          = Interpro::MULTI
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species dipodomys_ordii]
@@ -2510,7 +2510,7 @@ source          = RefSeq_dna::MULTI-vertebrate_mammalian
 source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species drosophila_melanogaster]
@@ -2534,7 +2534,7 @@ source          = InterproGO::MULTI
 source          = Interpro::MULTI
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species erinaceus_europaeus]
@@ -2549,7 +2549,7 @@ source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = UniGene::MULTI
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species equus_caballus]
@@ -2564,7 +2564,7 @@ source          = RefSeq_peptide::equus_caballus
 source          = UniGene::equus_caballus
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species felis_catus]
@@ -2576,7 +2576,7 @@ source          = InterproGO::MULTI
 source          = Interpro::MULTI
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species gallus_gallus]
@@ -2592,7 +2592,7 @@ source          = RefSeq_peptide::gallus_gallus
 source          = UniGene::gallus_gallus
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species gasterosteus_aculeatus]
@@ -2607,7 +2607,7 @@ source          = RefSeq_dna::gasterosteus_aculeatus
 source          = RefSeq_peptide::MULTI-vertebrate_other
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species gorilla_gorilla]
@@ -2621,17 +2621,17 @@ source          = RefSeq_dna::MULTI-vertebrate_mammalian
 source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 
 [species homo_sapiens]
 taxonomy_id     = 9606
 aliases         = homosapiens, hsapiens, human
-source          = AgilentCGH::homo_sapiens
-source          = AgilentProbe::homo_sapiens
+#source          = AgilentCGH::homo_sapiens
+#source          = AgilentProbe::homo_sapiens
 source          = CCDS::homo_sapiens
-source          = Codelink::homo_sapiens
+#source          = Codelink::homo_sapiens
 source          = DBASS5::homo_sapiens
 source          = DBASS3::homo_sapiens
 source          = EntrezGene::MULTI
@@ -2644,8 +2644,8 @@ source          = HGNC::homo_sapiens#01
 source          = HGNC::homo_sapiens#02
 source          = IMGT/GENE_DB::homo_sapiens
 source          = IPI::homo_sapiens
-source          = Illumina_V1::homo_sapiens
-source          = Illumina_V2::homo_sapiens
+#source          = Illumina_V1::homo_sapiens
+#source          = Illumina_V2::homo_sapiens
 source          = Interpro::MULTI
 source          = MIM::homo_sapiens
 #source          = OTTT::homo_sapiens  # got from merge
@@ -2656,7 +2656,7 @@ source          = UniGene::homo_sapiens
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 source          = ncRNA::MULTI
-source          = UCSC::homo_sapiens
+#source          = UCSC::homo_sapiens            ADD WHEN STABLE ID'S ADDED FOR NEW ASEMBLY
 source          = HGNC_curated_transcript::homo_sapiens
 
 [species ixodes_scapularis]
@@ -2670,7 +2670,7 @@ source          = Interpro::MULTI
 source          = UniGene::ixodes_scapularis
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 
 [species loxodonta_africana]
 taxonomy_id     = 9785
@@ -2681,7 +2681,7 @@ source          = InterproGO::MULTI
 source          = Interpro::MULTI
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species macaca_mulatta]
@@ -2709,16 +2709,16 @@ source          = RefSeq_dna::MULTI-vertebrate_mammalian
 source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = UniGene::monodelphis_domestica
 source          = ncRNA::MULTI
 
 [species mus_musculus]
 taxonomy_id     = 10090
 aliases         = mmusculus, mouse, musmusculus
-source          = AgilentProbe::mus_musculus
+#source          = AgilentProbe::mus_musculus
 source          = CCDS::mus_musculus
-source          = Codelink::mus_musculus
+#source          = Codelink::mus_musculus
 source          = EntrezGene::MULTI
 source          = GO::mus_musculus
 source          = GO::mus_musculus#01
@@ -2754,7 +2754,7 @@ source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = UniGene::myotis_lucifugus
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species ochotona_princeps]
@@ -2768,7 +2768,7 @@ source          = RefSeq_dna::MULTI-vertebrate_mammalian
 source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species ornithorhynchus_anatinus]
@@ -2781,7 +2781,7 @@ source          = RefSeq_dna::MULTI-vertebrate_mammalian
 source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = Oxford_FGU_Oa_tscript::ornithorhynchus_anatinus
 source          = Oxford_FGU_Oa_gene::ornithorhynchus_anatinus
 source          = Platypus_olfactory_receptor::ornithorhynchus_anatinus
@@ -2796,7 +2796,7 @@ source          = InterproGO::MULTI
 source          = Interpro::MULTI
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species oryzias_latipes]
@@ -2811,7 +2811,7 @@ source          = RefSeq_peptide::MULTI-vertebrate_other
 source          = UniGene::MULTI
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = UniProt::protein_id
 source          = Uniprot::EMBL
 source          = ncRNA::MULTI
@@ -2827,7 +2827,7 @@ source          = RefSeq_dna::pan_troglodytes
 source          = RefSeq_peptide::pan_troglodytes
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species pongo_pygmaeus]
@@ -2843,7 +2843,7 @@ source          = RefSeq_peptide::pongo_pygmaeus
 source          = UniGene::MULTI
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species procavia_capensis]
@@ -2857,7 +2857,7 @@ source          = RefSeq_dna::MULTI-vertebrate_mammalian
 source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 
@@ -2872,14 +2872,14 @@ source          = RefSeq_dna::MULTI-vertebrate_mammalian
 source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species rattus_norvegicus]
 taxonomy_id     = 10116
 aliases         = rat, rattusnorvegicus, rnovegicus
-source          = AgilentProbe::rattus_norvegicus
-source          = Codelink::rattus_norvegicus
+#source          = AgilentProbe::rattus_norvegicus
+#source          = Codelink::rattus_norvegicus
 source          = EntrezGene::MULTI
 source          = GO::rattus_norvegicus
 source          = InterproGO::MULTI
@@ -2891,7 +2891,7 @@ source          = RefSeq_peptide::rattus_norvegicus
 source          = UniGene::rattus_norvegicus
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species saccharomyces_cerevisiae]
@@ -2906,7 +2906,7 @@ source          = RefSeq_peptide::MULTI-fungi
 source          = SGD::saccharomyces_cerevisiae
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 
 [species spermophilus_tridecemlineatus]
 taxonomy_id     = 43179
@@ -2920,7 +2920,7 @@ source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = UniGene::MULTI
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species taeniopygia_guttata]
@@ -2935,7 +2935,7 @@ source          = RefSeq_peptide::MULTI-vertebrate_other
 source          = UniGene::taeniopygia_guttata
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species takifugu_rubripes]
@@ -2950,7 +2950,7 @@ source          = RefSeq_peptide::MULTI-vertebrate_other
 source          = UniGene::takifugu_rubripes
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species tarsius_syrichta]
@@ -2964,7 +2964,7 @@ source          = RefSeq_dna::MULTI-vertebrate_mammalian
 source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species tetraodon_nigroviridis]
@@ -2978,7 +2978,7 @@ source          = RefSeq_dna::MULTI-vertebrate_other
 source          = RefSeq_peptide::MULTI-vertebrate_other
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 source          = Genoscope_pred_gene::tetraodon_nigroviridis
 source          = Genoscope_pred_transcript::tetraodon_nigroviridis
@@ -2998,7 +2998,7 @@ source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = UniGene::MULTI
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species tursiops_truncatus]
@@ -3012,7 +3012,7 @@ source          = RefSeq_dna::MULTI-vertebrate_mammalian
 source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species vicugna_pacos]
@@ -3026,7 +3026,7 @@ source          = RefSeq_dna::MULTI-vertebrate_mammalian
 source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species choloepus_hoffmanni]
@@ -3040,7 +3040,7 @@ source          = RefSeq_dna::MULTI-vertebrate_mammalian
 source          = RefSeq_peptide::MULTI-vertebrate_mammalian
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = ncRNA::MULTI
 
 [species xenopus_tropicalis]
@@ -3055,6 +3055,6 @@ source          = RefSeq_peptide::MULTI-vertebrate_other
 source          = UniGene::xenopus_tropicalis
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
-source          = Uniprot/Varsplic::MULTI
+#source          = Uniprot/Varsplic::MULTI
 source          = Xenopus_Jamboree::xenopus_tropicalis
 source          = ncRNA::MULTI