Added config for chimp

misc-scripts/xref_mapping/xref_config.ini

@@ -270,7 +270,7 @@ release_uri     =
 data_uri        = file:Codelink/GEHC_Amersham_CodeLink_RWG_300031.fna
 
 [source EntrezGene::MULTI]
-# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, 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, oryctolagus_cuniculus, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
+# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, 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, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
 name            = EntrezGene
 download        = Y
 order           = 10
@@ -281,7 +281,7 @@ release_uri     =
 data_uri        = ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz
 
 [source GO::MULTI]
-# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, felis_catus, gallus_gallus, gasterosteus_aculeatus, loxodonta_africana, macaca_mulatta, monodelphis_domestica, myotis_lucifugus, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri
+# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, felis_catus, gallus_gallus, gasterosteus_aculeatus, loxodonta_africana, macaca_mulatta, monodelphis_domestica, myotis_lucifugus, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri
 name            = GO
 download        = Y
 order           = 60
@@ -516,7 +516,7 @@ release_uri     =
 data_uri        = file:Illumina_V2/Human-6_v2_sequence.csv
 
 [source Interpro::MULTI]
-# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, 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, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
+# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, 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, ornithorhynchus_anatinus, oryctolagus_cuniculus, pan_troglodytes, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
 name            = Interpro
 download        = Y
 order           = 30
@@ -724,6 +724,17 @@ parser          = RefSeqParser
 release_uri     = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
 data_uri        = ftp://ftp.ncbi.nih.gov/refseq/M_musculus/mRNA_Prot/mouse.rna.fna.gz
 
+[source RefSeq_dna::pan_troglodytes]
+# Used by pan_troglodytes
+name            = RefSeq_dna
+download        = Y
+order           = 20
+priority        = 2
+prio_descr      = refseq
+parser          = RefSeqGPFFParser
+release_uri     = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
+data_uri        = ftp://ftp.ncbi.nih.gov/genomes/Pan_troglodytes/RNA/rna.gbk.gz
+
 [source RefSeq_dna::rattus_norvegicus]
 # Used by rattus_norvegicus
 name            = RefSeq_dna
@@ -866,6 +877,17 @@ parser          = RefSeqGPFFParser
 release_uri     = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
 data_uri        = ftp://ftp.ncbi.nih.gov/refseq/M_musculus/mRNA_Prot/mouse.protein.gpff.gz
 
+[source RefSeq_peptide::pan_troglodytes]
+# Used by pan_troglodytes
+name            = RefSeq_peptide
+download        = Y
+order           = 20
+priority        = 1
+prio_descr      =
+parser          = RefSeqGPFFParser
+release_uri     = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
+data_uri        = ftp://ftp.ncbi.nih.gov/genomes/Pan_troglodytes/protein/protein.gbk.gz
+
 [source RefSeq_peptide::rattus_norvegicus]
 # Used by rattus_norvegicus
 name            = RefSeq_peptide
@@ -1124,7 +1146,7 @@ parser          = UniProtParser
 release_uri     = 
 
 [source Uniprot/SPTREMBL::MULTI]
-# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, 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, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
+# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, 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, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
 name            = Uniprot/SPTREMBL
 download        = Y
 order           = 20
@@ -1145,7 +1167,7 @@ parser          = UniProtParser
 release_uri     = 
 
 [source Uniprot/SWISSPROT::MULTI]
-# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, 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, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
+# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, 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, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
 name            = Uniprot/SWISSPROT
 download        = Y
 order           = 20
@@ -1177,7 +1199,7 @@ release_uri     =
 data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/integr8/uniprot/proteomes/17.D_melanogaster.dat.gz
 
 [source Uniprot/Varsplic::MULTI]
-# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, monodelphis_domestica, mus_musculus, myotis_lucifugus, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
+# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, monodelphis_domestica, mus_musculus, myotis_lucifugus, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
 name            = Uniprot/Varsplic
 download        = Y
 order           = 30
@@ -1297,7 +1319,7 @@ release_uri     =
 data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz
 
 [source ncRNA::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, rattus_norvegicus, spermophilus_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, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, rattus_norvegicus, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, ornithorhynchus_anatinus
 name            = ncRNA
 download        = Y
 order           = 70
@@ -1751,6 +1773,19 @@ source          = UniProt::protein_id
 source          = Uniprot::EMBL
 source          = ncRNA::MULTI
 
+[species pan_troglodytes]
+taxonomy_id     = 9598
+aliases         = pantroglodytes, ptroglodytes, chimpanzee, chimp
+source          = EntrezGene::MULTI
+source          = GO::MULTI
+source          = Interpro::MULTI
+source          = RefSeq_dna::pan_troglodytes
+source          = RefSeq_peptide::pan_troglodytes
+source          = Uniprot/SPTREMBL::MULTI
+source          = Uniprot/SWISSPROT::MULTI
+source          = Uniprot/Varsplic::MULTI
+source          = ncRNA::MULTI
+
 [species rattus_norvegicus]
 taxonomy_id     = 10116
 aliases         = rat, rattusnorvegicus, rnovegicus