Change to xref_config.ini for flycatcher

misc-scripts/xref_mapping/xref_config.ini

@@ -885,7 +885,7 @@ release_uri     =
 data_uri        = http://www.dbass.soton.ac.uk/dbass3/download.aspx?item=genes
 
 [source EntrezGene::MULTI]
-# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, 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_abelii,  rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,phaeodactylum_tricornutum,thalassiosira_pseudonana, lepisosteus_oculatus
+# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, ficedula_albicollis, 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_abelii,  rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,phaeodactylum_tricornutum,thalassiosira_pseudonana, lepisosteus_oculatus
 name            = EntrezGene
 download        = Y
 order           = 10
@@ -931,7 +931,7 @@ release_uri     =
 data_uri        = ftp://fantom.gsc.riken.jp/FANTOM3/DDBJ/DDBJ_fantom3_HTC_accession.txt.gz
 
 [source GO::MULTI]
-# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, drosophila_grimshawi, drosophila_willistoni, drosophila_ananassae, drosophila_yakuba, drosophila_simulans, drosophila_sechellia, drosophila_erecta, drosophila_persimilis, drosophila_mojavensis, drosophila_virilis, 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_abelii, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri,phaeodactylum_tricornutum,thalassiosira_pseudonana, lepisosteus_oculatus
+# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, drosophila_grimshawi, drosophila_willistoni, drosophila_ananassae, drosophila_yakuba, drosophila_simulans, drosophila_sechellia, drosophila_erecta, drosophila_persimilis, drosophila_mojavensis, drosophila_virilis, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, ficedula_albicollis, 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_abelii, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri,phaeodactylum_tricornutum,thalassiosira_pseudonana, lepisosteus_oculatus
 name            = GO
 download        = Y
 order           = 80
@@ -1345,7 +1345,7 @@ release_uri     =
 data_uri        = file:Mus_musculus/Segments/Seg_xrefs.txt
 
 [source Interpro::MULTI]
-# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, 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, microcebus_murinus, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, ottolemur_garnetti, pan_troglodytes,pongo_abelii, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, sorex_araneus, ictidomys_tridecemlineatus,sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,thalassiosira_pseudonana, phaeodactylum_tricornutum, lepisosteus_oculatus
+# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, ficedula_albicollis, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, ixodes__scapularis, loxodonta_africana, macaca_mulatta, microcebus_murinus, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, ottolemur_garnetti, pan_troglodytes,pongo_abelii, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, sorex_araneus, ictidomys_tridecemlineatus,sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,thalassiosira_pseudonana, phaeodactylum_tricornutum, lepisosteus_oculatus
 name            = Interpro
 download        = Y
 order           = 70
@@ -1733,7 +1733,7 @@ release_uri     = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-rel
 data_uri        = ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_mammalian/vertebrate_mammalian*.rna.fna.gz
 
 [source RefSeq_dna::MULTI-vertebrate_other]
-# Used by anolis_carolinensis, ciona_intestinalis, ciona_savignyi, gasterosteus_aculeatus, oryzias_latipes, taeniopygia_guttata, takifugu_rubripes, xenopus_tropicalis
+# Used by anolis_carolinensis, ciona_intestinalis, ciona_savignyi, ficedula_albicollis, gasterosteus_aculeatus, oryzias_latipes, taeniopygia_guttata, takifugu_rubripes, xenopus_tropicalis
 name            = RefSeq_dna
 download        = Y
 order           = 20
@@ -2370,7 +2370,7 @@ release_uri     = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-rel
 data_uri        = ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_mammalian/vertebrate_mammalian*.protein.gpff.gz
 
 [source RefSeq_peptide::MULTI-vertebrate_other]
-# Used by anolis_carolinensis, ciona_intestinalis, ciona_savignyi, gasterosteus_aculeatus, oryzias_latipes, taeniopygia_guttata, takifugu_rubripes, xenopus_tropicalis
+# Used by anolis_carolinensis, ciona_intestinalis, ciona_savignyi, ficedula_albicollis, gasterosteus_aculeatus, oryzias_latipes, taeniopygia_guttata, takifugu_rubripes, xenopus_tropicalis
 name            = RefSeq_peptide
 download        = Y
 order           = 20
@@ -3686,7 +3686,7 @@ parser          = UniProtAltParser
 release_uri     =
 
 [source Uniprot/SPTREMBL::MULTI]
-# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, 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_abelii, rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana, lepisosteus_oculatus
+# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, ficedula_albicollis, 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_abelii, rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana, lepisosteus_oculatus
 name            = Uniprot/SPTREMBL
 download        = Y
 order           = 20
@@ -3721,7 +3721,7 @@ parser          = UniProtAltParser
 release_uri     =
 
 [source Uniprot/SWISSPROT::MULTI]
-# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, 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_abelii, rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana, lepisosteus_oculatus
+# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, felis_catus, ficedula_albicollis, 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_abelii, rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana, lepisosteus_oculatus
 name            = Uniprot/SWISSPROT
 download        = Y
 order           = 20
@@ -4078,7 +4078,7 @@ release_uri     =
 data_uri        = ftp://ftp.jgi-psf.org/pub/JGI_data/Ciona/v1.0/ciona.prot.fasta.gz
 
 [source RFAM::MULTI]
-# Used by bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_pseudoobscura, erinaceus_europaeus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_abelii, rattus_norvegicus, ictidomys_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, ornithorhynchus_anatinus
+# Used by bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_pseudoobscura, erinaceus_europaeus, ficedula_albicollis, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_abelii, rattus_norvegicus, ictidomys_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, ornithorhynchus_anatinus
 name            = RFAM
 download        = Y
 order           = 70
@@ -4102,7 +4102,7 @@ data_uri        = script:object_type=>gene,project=>ensemblgenomes,copy_descript
 
 
 [source miRBase::MULTI]
-# Used by bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, erinaceus_europaeus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_abelii, rattus_norvegicus, ictidomys_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, ornithorhynchus_anatinus
+# Used by bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, erinaceus_europaeus, ficedula_albicollis, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_abelii, rattus_norvegicus, ictidomys_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, ornithorhynchus_anatinus
 name            = miRBase
 download        = Y
 order           = 70
@@ -5994,6 +5994,24 @@ source          = RFAM::MULTI
 source		= miRBase::MULTI
 source 		= ArrayExpress::MULTI
 
+[species ficedula_albicollis]
+taxonomy_id     = 59894
+aliases         = flycatcher, falbicollis, falb
+source          = EntrezGene::MULTI
+source          = GO::MULTI
+source          = goslim_goa::MULTI
+source          = InterproGO::MULTI
+source          = Interpro::MULTI
+source          = RefSeq_dna::MULTI-vertebrate_other
+source          = RefSeq_peptide::MULTI-vertebrate_other
+source          = Uniprot/SPTREMBL::MULTI
+source          = Uniprot/SWISSPROT::MULTI
+source          = Uniprot/SWISSPROT::DIRECT
+source          = UniParc::MULTI
+source          = RFAM::MULTI
+source          = miRBase::MULTI
+source          = ArrayExpress::MULTI
+
 [species gadus_morhua]
 taxonomy_id     = 8049
 aliases         = cod,gmorhua,gadus_morhua,gmor,atlantic_cod,gadmor