unipept 2.1.1 → 2.2.0
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- checksums.yaml +4 -4
- data/.rakeTasks +7 -0
- data/VERSION +1 -1
- data/lib/batch_iterator.rb +16 -0
- data/lib/commands/unipept.rb +25 -1
- data/lib/commands/unipept/api_runner.rb +3 -1
- data/lib/commands/unipept/taxa2tree.rb +74 -0
- data/lib/formatters.rb +104 -32
- data/test.taxa +4 -0
- data/test/commands/unipept/test_pept2ec.rb +9 -9
- data/test/commands/unipept/test_pept2funct.rb +13 -13
- data/test/commands/unipept/test_pept2go.rb +8 -8
- data/test/commands/unipept/test_pept2interpro.rb +24 -24
- data/test/commands/unipept/test_peptinfo.rb +14 -14
- data/test/commands/unipept/test_taxa2tree.rb +68 -0
- data/test/helper.rb +10 -0
- data/test/support/api_stub.rb +60 -0
- data/test/support/resources/pept2ec.json +55 -0
- data/test/support/resources/pept2funct.json +73 -0
- data/test/support/resources/pept2go.json +43 -0
- data/test/support/resources/pept2interpro.json +43 -0
- data/test/support/resources/pept2lca.json +14 -0
- data/test/support/resources/pept2prot.json +422 -0
- data/test/support/resources/pept2taxa.json +194 -0
- data/test/support/resources/peptinfo.json +70 -0
- data/test/support/resources/taxa2tree.json +194 -0
- data/test/support/resources/taxonomy.json +22 -0
- data/unipept.gemspec +18 -3
- metadata +17 -2
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[
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{
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"peptide": "ENFVYIAK",
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"taxon_id": 2711,
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"taxon_name": "Citrus sinensis",
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"taxon_rank": "species"
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"peptide": "ENFVYIAK",
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"taxon_id": 3818,
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"taxon_name": "Arachis hypogaea",
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"taxon_rank": "species"
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"peptide": "ENFVYIAK",
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"taxon_id": 3821,
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"taxon_name": "Cajanus cajan",
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"taxon_rank": "species"
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"peptide": "ENFVYIAK",
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"taxon_id": 3827,
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"taxon_name": "Cicer arietinum",
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"taxon_rank": "species"
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"peptide": "ENFVYIAK",
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"taxon_id": 3847,
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"taxon_name": "Glycine max",
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"taxon_rank": "species"
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"peptide": "ENFVYIAK",
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"taxon_id": 3848,
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"taxon_name": "Glycine soja",
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"taxon_rank": "species"
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{
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"peptide": "ENFVYIAK",
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"taxon_id": 3880,
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"taxon_name": "Medicago truncatula",
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"taxon_rank": "species"
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},
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{
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"peptide": "ENFVYIAK",
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"taxon_id": 3885,
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"taxon_name": "Phaseolus vulgaris",
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"taxon_rank": "species"
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"peptide": "ENFVYIAK",
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"taxon_id": 3900,
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"taxon_name": "Trifolium subterraneum",
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"taxon_rank": "species"
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},
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"peptide": "ENFVYIAK",
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"taxon_id": 3906,
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"taxon_name": "Vicia faba",
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"taxon_rank": "species"
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{
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"peptide": "ENFVYIAK",
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"taxon_id": 4096,
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"taxon_name": "Nicotiana sylvestris",
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"taxon_rank": "species"
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"peptide": "ENFVYIAK",
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"taxon_id": 4097,
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"taxon_name": "Nicotiana tabacum",
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"taxon_rank": "species"
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"peptide": "ENFVYIAK",
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"taxon_id": 16924,
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"taxon_name": "Davidia involucrata",
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"taxon_rank": "species"
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},
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"peptide": "ENFVYIAK",
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"taxon_id": 28930,
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"taxon_name": "Fagus sylvatica",
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"taxon_rank": "species"
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},
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{
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"peptide": "ENFVYIAK",
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"taxon_id": 29760,
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"taxon_name": "Vitis vinifera",
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"taxon_rank": "species"
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},
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"peptide": "ENFVYIAK",
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"taxon_id": 42345,
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"taxon_name": "Phoenix dactylifera",
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"taxon_rank": "species"
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"peptide": "ENFVYIAK",
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"taxon_id": 49451,
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"taxon_name": "Nicotiana attenuata",
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"taxon_rank": "species"
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"peptide": "ENFVYIAK",
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"taxon_id": 55188,
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"taxon_name": "Citrus unshiu",
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"taxon_rank": "species"
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},
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{
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"peptide": "ENFVYIAK",
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"taxon_id": 56857,
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"taxon_name": "Macleaya cordata",
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"taxon_rank": "species"
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{
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"peptide": "ENFVYIAK",
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"taxon_id": 57577,
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"taxon_name": "Trifolium pratense",
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"taxon_rank": "species"
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},
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"peptide": "ENFVYIAK",
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"taxon_id": 85681,
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"taxon_name": "Citrus clementina",
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"taxon_rank": "species"
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},
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{
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"peptide": "ENFVYIAK",
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"taxon_id": 214687,
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"taxon_name": "Musa acuminata subsp. malaccensis",
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"taxon_rank": "subspecies"
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},
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{
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"peptide": "ENFVYIAK",
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"taxon_id": 337451,
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"taxon_name": "Cinnamomum micranthum f. kanehirae",
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"taxon_rank": "forma"
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},
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{
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"peptide": "ENFVYIAK",
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"taxon_id": 561372,
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"taxon_name": "Nyssa sinensis",
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"taxon_rank": "species"
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},
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{
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"peptide": "EGGAGSSTGQR",
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"taxon_id": 5061,
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"taxon_name": "Aspergillus niger",
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"taxon_rank": "species"
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},
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{
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"peptide": "EGGAGSSTGQR",
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"taxon_id": 105351,
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"taxon_name": "Aspergillus awamori",
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"taxon_rank": "species"
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},
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{
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"peptide": "EGGAGSSTGQR",
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"taxon_id": 380704,
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"taxon_name": "Aspergillus niger ATCC 1015",
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"taxon_rank": "no rank"
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},
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{
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"peptide": "EGGAGSSTGQR",
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"taxon_id": 425011,
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"taxon_name": "Aspergillus niger CBS 513.88",
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"taxon_rank": "no rank"
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},
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{
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"peptide": "EGGAGSSTGQR",
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"taxon_id": 1341132,
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"taxon_name": "Aspergillus welwitschiae",
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"taxon_rank": "species"
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},
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{
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"peptide": "EGGAGSSTGQR",
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"taxon_id": 1353007,
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"taxon_name": "Aspergillus phoenicis ATCC 13157",
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"taxon_rank": "no rank"
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},
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{
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"peptide": "EGGAGSSTGQR",
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"taxon_id": 1353008,
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"taxon_name": "Aspergillus niger ATCC 13496",
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"taxon_rank": "no rank"
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},
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{
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"peptide": "EGGAGSSTGQR",
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"taxon_id": 1450533,
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"taxon_name": "Aspergillus niger CBS 101883",
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"taxon_rank": "no rank"
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}
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]
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@@ -0,0 +1,70 @@
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[
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{
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"peptide": "AALTER",
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"total_protein_count": 7,
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"ec": [
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{
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"ec_number": "3.1.3.3",
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"protein_count": 2
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}
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],
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"go": [
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{
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"go_term": "GO:0000287",
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"protein_count": 5
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}
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],
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"ipr": [
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{
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"code": "IPR013221",
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"protein_count": 2
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}
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],
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"taxon_id": 1,
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"taxon_name": "root",
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"taxon_rank": "no rank"
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},
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{
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"peptide": "AALER",
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"total_protein_count": 208,
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"ec": [
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{
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"ec_number": "6.1.1.16",
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"protein_count": 44
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}
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],
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"go": [
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{
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"go_term": "GO:0005737",
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"protein_count": 106
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}
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],
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"ipr": [
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{
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"code": "IPR014729",
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"protein_count": 48
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},
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{
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"code": "IPR009080",
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"protein_count": 45
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},
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{
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"code": "IPR015803",
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"protein_count": 44
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}
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],
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"taxon_id": 1,
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"taxon_name": "root",
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"taxon_rank": "no rank"
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},
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{
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"peptide": "AAEVALVGTEK",
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"total_protein_count": 0,
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"ec": [],
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"go": [],
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"ipr": [],
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"taxon_id": 1,
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"taxon_name": "root",
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"taxon_rank": "no rank"
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}
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]
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{
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"id": 1,
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"name": "Organism",
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"rank": "root",
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"data": {
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"count": 4,
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"self_count": 0
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},
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"children": [
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{
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"id": 2,
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"name": "Bacteria",
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"rank": "superkingdom",
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"data": {
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"count": 4,
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"self_count": 0
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},
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"children": [
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{
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"id": 28,
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"name": "halophilic eubacterium",
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"rank": "species",
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"data": {
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"count": 1,
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"self_count": 1
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},
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"children": []
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},
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{
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"id": 1224,
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"name": "Proteobacteria",
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"rank": "phylum",
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"data": {
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"count": 3,
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"self_count": 0
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},
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"children": [
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{
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"id": 68525,
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"name": "delta/epsilon subdivisions",
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"rank": "subphylum",
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"data": {
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"count": 1,
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"self_count": 0
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},
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"children": [
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{
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"id": 28221,
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"name": "Deltaproteobacteria",
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"rank": "class_",
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"data": {
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"count": 1,
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"self_count": 0
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},
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"children": [
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{
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"id": 29,
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|
+
"name": "Myxococcales",
|
|
59
|
+
"rank": "order",
|
|
60
|
+
"data": {
|
|
61
|
+
"count": 1,
|
|
62
|
+
"self_count": 0
|
|
63
|
+
},
|
|
64
|
+
"children": [
|
|
65
|
+
{
|
|
66
|
+
"id": 80812,
|
|
67
|
+
"name": "Sorangiineae",
|
|
68
|
+
"rank": "suborder",
|
|
69
|
+
"data": {
|
|
70
|
+
"count": 1,
|
|
71
|
+
"self_count": 0
|
|
72
|
+
},
|
|
73
|
+
"children": [
|
|
74
|
+
{
|
|
75
|
+
"id": 49,
|
|
76
|
+
"name": "Polyangiaceae",
|
|
77
|
+
"rank": "family",
|
|
78
|
+
"data": {
|
|
79
|
+
"count": 1,
|
|
80
|
+
"self_count": 0
|
|
81
|
+
},
|
|
82
|
+
"children": [
|
|
83
|
+
{
|
|
84
|
+
"id": 55,
|
|
85
|
+
"name": "Polyangium",
|
|
86
|
+
"rank": "genus",
|
|
87
|
+
"data": {
|
|
88
|
+
"count": 1,
|
|
89
|
+
"self_count": 1
|
|
90
|
+
},
|
|
91
|
+
"children": []
|
|
92
|
+
}
|
|
93
|
+
]
|
|
94
|
+
}
|
|
95
|
+
]
|
|
96
|
+
}
|
|
97
|
+
]
|
|
98
|
+
}
|
|
99
|
+
]
|
|
100
|
+
}
|
|
101
|
+
]
|
|
102
|
+
},
|
|
103
|
+
{
|
|
104
|
+
"id": 28211,
|
|
105
|
+
"name": "Alphaproteobacteria",
|
|
106
|
+
"rank": "class_",
|
|
107
|
+
"data": {
|
|
108
|
+
"count": 1,
|
|
109
|
+
"self_count": 0
|
|
110
|
+
},
|
|
111
|
+
"children": [
|
|
112
|
+
{
|
|
113
|
+
"id": 204458,
|
|
114
|
+
"name": "Caulobacterales",
|
|
115
|
+
"rank": "order",
|
|
116
|
+
"data": {
|
|
117
|
+
"count": 1,
|
|
118
|
+
"self_count": 0
|
|
119
|
+
},
|
|
120
|
+
"children": [
|
|
121
|
+
{
|
|
122
|
+
"id": 76892,
|
|
123
|
+
"name": "Caulobacteraceae",
|
|
124
|
+
"rank": "family",
|
|
125
|
+
"data": {
|
|
126
|
+
"count": 1,
|
|
127
|
+
"self_count": 0
|
|
128
|
+
},
|
|
129
|
+
"children": [
|
|
130
|
+
{
|
|
131
|
+
"id": 75,
|
|
132
|
+
"name": "Caulobacter",
|
|
133
|
+
"rank": "genus",
|
|
134
|
+
"data": {
|
|
135
|
+
"count": 1,
|
|
136
|
+
"self_count": 1
|
|
137
|
+
},
|
|
138
|
+
"children": []
|
|
139
|
+
}
|
|
140
|
+
]
|
|
141
|
+
}
|
|
142
|
+
]
|
|
143
|
+
}
|
|
144
|
+
]
|
|
145
|
+
},
|
|
146
|
+
{
|
|
147
|
+
"id": 28216,
|
|
148
|
+
"name": "Betaproteobacteria",
|
|
149
|
+
"rank": "class_",
|
|
150
|
+
"data": {
|
|
151
|
+
"count": 1,
|
|
152
|
+
"self_count": 0
|
|
153
|
+
},
|
|
154
|
+
"children": [
|
|
155
|
+
{
|
|
156
|
+
"id": 80840,
|
|
157
|
+
"name": "Burkholderiales",
|
|
158
|
+
"rank": "order",
|
|
159
|
+
"data": {
|
|
160
|
+
"count": 1,
|
|
161
|
+
"self_count": 0
|
|
162
|
+
},
|
|
163
|
+
"children": [
|
|
164
|
+
{
|
|
165
|
+
"id": 88,
|
|
166
|
+
"name": "Leptothrix",
|
|
167
|
+
"rank": "genus",
|
|
168
|
+
"data": {
|
|
169
|
+
"count": 1,
|
|
170
|
+
"self_count": 0
|
|
171
|
+
},
|
|
172
|
+
"children": [
|
|
173
|
+
{
|
|
174
|
+
"id": 89,
|
|
175
|
+
"name": "Leptothrix discophora",
|
|
176
|
+
"rank": "species",
|
|
177
|
+
"data": {
|
|
178
|
+
"count": 1,
|
|
179
|
+
"self_count": 1
|
|
180
|
+
},
|
|
181
|
+
"children": []
|
|
182
|
+
}
|
|
183
|
+
]
|
|
184
|
+
}
|
|
185
|
+
]
|
|
186
|
+
}
|
|
187
|
+
]
|
|
188
|
+
}
|
|
189
|
+
]
|
|
190
|
+
}
|
|
191
|
+
]
|
|
192
|
+
}
|
|
193
|
+
]
|
|
194
|
+
}
|