Docker-in-Docker (DinD) capabilities of public runners deactivated. More info

Commit e8169c33 authored by Philippe Veber's avatar Philippe Veber
Browse files

added rubisco dataset

parent d7bc2f10
module Top = Bistro_utils.Toplevel_eval.Make(struct let np = 8 let mem = 10 end)() module Top = Bistro_utils.Toplevel_eval.Make(struct let np = 8 let mem = 10 end)()
open Top open Top
open Reviewphiltrans open Codepi
let njplot (t : Biotope.Formats.newick Bistro.file) = Sys.command (Printf.sprintf "njplot %s" (path t)) let njplot (t : Biotope.Formats.newick Bistro.file) = Sys.command (Printf.sprintf "njplot %s" (path t))
let n_h0 = 100 let n_h0 = 50
let n_ha = 3 let n_ha = 50
let npairs = 10 let npairs = 10
let tree = Simulation_dataset.Pair_tree { branch_length1 = 3. ; branch_length2 = 3. ; npairs };; let tree = Simulation_dataset.Pair_tree { branch_length1 = 3. ; branch_length2 = 3. ; npairs };;
let sim = Simulation_dataset.convdet_simulation ~tree ~profiles:"example/aa_fitness/263SelectedProfiles.tsv" ~n_h0 ~n_ha () ~ne_s:(8.,8.);; let sim = Simulation_dataset.convdet_simulation ~tree ~profiles:"example/aa_fitness/263SelectedProfiles.tsv" ~n_h0 ~n_ha ();;
let convergent_species = List.init npairs (Printf.sprintf "C%d");; let convergent_species = List.init npairs (Printf.sprintf "C%d");;
let genotype = Gemma.genotype_of_fasta (Simulation_dataset.amino_acid_alignment sim)
let phenotype = Gemma.phenotype_of_tree (Simulation_dataset.tree ~branch_length_unit:`Amino_acid sim);;
let relatedness_matrix = Gemma.calculate_relatedness_matrix ~mode:`Standardized ~genotype ~phenotype;;
let fit = Gemma.univariate_lmm ~lmm:`LRT ~genotype ~phenotype ~relatedness_matrix;;
...@@ -4,7 +4,7 @@ let benchmark d = ...@@ -4,7 +4,7 @@ let benchmark d =
let open Simulation_dataset in let open Simulation_dataset in
Utils.recall_precision_curve Utils.recall_precision_curve
~oracle:(oracle d) ~oracle:(oracle d)
~labels:[|"topological";"multinomial";"gemma_score";"inhouse";"tdg09"|] ~labels:[| "topological"; "multinomial";"gemma_score";"inhouse"; "tdg09" |]
~results:[ ~results:[
topological d ; topological d ;
multinomial_asymptotic_lrt d ; multinomial_asymptotic_lrt d ;
...@@ -17,9 +17,10 @@ let () = ...@@ -17,9 +17,10 @@ let () =
let sim = let sim =
let open Simulation_dataset in let open Simulation_dataset in
convdet_simulation convdet_simulation
~tree:(NHX "example/trees4analyses_db/cyp_coding.Chrysithr_root.nhx") (* ~tree:(NHX "example/trees4analyses_db/cyp_coding.Chrysithr_root.nhx") *)
~tree:(NHX "example/trees_test/orthomam_rooted.nhx")
~profiles:"example/aa_fitness/263SelectedProfiles.tsv" ~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
~n_h0:100 ~n_ha:100 ~ne_s:(2., 2.) () ~n_h0:900 ~n_ha:100 ~ne_s:(2., 2.) ()
in in
let w = benchmark sim in let w = benchmark sim in
let loggers = [ Bistro_utils.Console_logger.create () ] in let loggers = [ Bistro_utils.Console_logger.create () ] in
......
# Rubisco dataset
[reference](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0192697)
This diff is collapsed.
((((Halimione_pedunculata:0.00864425,Halimione_verrucifera:0.00092984)99:0.00537145,(((((Axyris_prostrata:0.01534606,(Ceratocarpus_arenarius:0.02990907,Krascheninnikovia_ceratoides:0.01600814)99:0.01061137)97:0.01138461,((((Suckleya_suckleyana:0.02012189,(Cycloloma_atriplicifolium:0.00640215,(((Chenopodium_cristatum:0.00634437,Dysphania_glomulifera:0.00288888)82:0.00460287,Chenopodium_ambrosioides:0.00969603)22:0.00000102,Chenopodium_botrys:0.00526699)53:0.00107999)78:0.00625852)94:0.00776160,Teloxys_aristata:0.01280784)60:0.00226243,((((Hablitzia_tamnoides:0.01134794,(Aphanisma_blitoides:0.00619394,Patellifolia_patellaris:0.00764319)86:0.00433032)81:0.00373440,(Beta_vulgaris:0.00636735,Beta_nana:0.00208042)100:0.00762631)56:0.00483380,(((((Ptilotus_manglesii:0.01107055,(((Iresine_palmeri:0.00424920,((Gomphrena_elegans:0.00663687,(Pseudoplantago_friesii:0.00419924,Hebanthe_occidentalis:0.00000102)100:0.00949326)96:0.00646777,(((Guilleminea_densa:0.01097833,(Gomphrena_serrata:0.00106511,Gomphrena_haageana:0.00317777)95:0.00215240)73:0.00100613,Blutaparon_vermiculare:0.00106592)93:0.00746116,((Alternanthera_pungens:0.00211324,(Alternanthera_caracasana:0.00105849,Alternanthera_repens:0.00000102)70:0.00000102)100:0.01201192,Tidestromia_lanuginosa:0.02218561)74:0.00114104)66:0.00511913)79:0.00349103)36:0.00101479,Aerva_javanica:0.01510976)17:0.00000102,(Pupalia_lappacea:0.00526750,(((Sericostachys_scandens:0.00745715,(Achyranthes_aspera:0.00105486,Nototrichium_humile:0.00419384)94:0.00318201)42:0.00101179,Pandiaka_angustifolia:0.00633305)14:0.00000102,Calicorema_capitata:0.00209471)10:0.00000102)63:0.00209457)59:0.00062618)100:0.01733079,(((Chamissoa_altissima:0.02775692,((Amaranthus_greggii:0.00000102,Amaranthus_tricolor:0.00105299)83:0.00000102,(Amaranthus_blitum:0.00000102,Amaranthus_hypochondriacus:0.00643206)96:0.00318172)100:0.01451714)100:0.01188603,(Deeringia_amaranthoides:0.01401420,(Hermbstaedtia_glauca:0.01188740,(Celosia_trigyna:0.00334626,Celosia_argentea:0.00847134)100:0.01103714)89:0.00739590)78:0.00290398)96:0.01207656,(Charpentiera_ovata:0.00000102,Charpentiera_obovata:0.00209837)100:0.02101136)51:0.00404498)90:0.00873580,Bosea_yervamora:0.01246853)55:0.00123834,((Nitrophila_occidentalis:0.00423941,Hemichroa_diandra:0.00313045)100:0.00491046,Polycnemum_perenne:0.01602915)100:0.01564853)62:0.00340750,Oreobliton_thesioides:0.02566195)25:0.00231295)6:0.00112808,((((((Halocharis_hispida:0.00853137,(Salsola_vermiculata:0.01173181,(Salsola_implicata:0.00524366,((Salsola_orientalis:0.00000102,Salsola_dshungarica:0.00000102)96:0.00210063,Salsola_micranthera:0.00105274)89:0.00209641)51:0.00000102)96:0.00426190)96:0.00395543,((((Petrosimonia_glaucescens:0.00000102,Petrosimonia_squarrosa:0.00000102)100:0.00322210,Petrosimonia_nigdeensis:0.01301656)94:0.00193353,Petrosimonia_sibirica:0.00758872)91:0.00287087,(((Halimocnemis_villosa:0.00000102,Halimocnemis_karelinii:0.00000102)100:0.01067822,((Salsola_sukaczevii:0.00000102,(Salsola_ferganica:0.00000102,Salsola_heptapotamica:0.00000102)17:0.00000102)30:0.00000102,Climacoptera_lanata:0.00000102)99:0.00316698)85:0.00115767,(Salsola_affinis:0.00480242,Climacoptera_brachiata:0.00210931)82:0.00143556)94:0.00353572)93:0.00540349)77:0.00242058,(Nanophyton_erinaceum:0.01724365,(((((Kochia_americana:0.00536817,Bassia_diffusa:0.00421106)99:0.00431594,((Bassia_dasyphylla:0.00531623,(Maireana_brevifolia:0.00104529,(Sclerolaena_obliquicuspis:0.00315592,(Roycea_divaricata:0.00104718,Dissocarpus_paradoxus:0.00105135)41:0.00000102)64:0.00105266)74:0.00102656)83:0.00214954,((Kochia_densiflora:0.00848085,(Chenoleoides_tomentosa:0.00313108,(Bassia_prostrata:0.01079383,Panderia_pilosa:0.00868129)68:0.00199012)31:0.00000102)96:0.00634913,(Bassia_sedoides:0.00519018,Camphorosma_monspeliaca:0.01051475)97:0.00478526)83:0.00325729)60:0.00095378)100:0.01175947,((Sympegma_regelii:0.00955615,Halothamnus_bottae:0.00439455)53:0.00217134,((((((Salsola_rosacea:0.00167187,Noaea_mucronata:0.00464541)80:0.00215133,Ofaiston_monandrum:0.01030439)94:0.00355407,Rhaphidophyton_regelii:0.00208826)16:0.00000102,Salsola_arbusculiformis:0.00000102)14:0.00000102,Salsola_laricifolia:0.00209005)54:0.00104353,(((Anabasis_brevifolia:0.00000102,Anabasis_truncata:0.00314889)84:0.00104267,(Anabasis_eriopoda:0.00104311,(Anabasis_aphylla:0.00210649,(Anabasis_salsa:0.00000102,Anabasis_elatior:0.00104471)97:0.00209836)94:0.00210361)92:0.00211717)85:0.00209977,(((Girgensohnia_oppositiflora:0.00635314,(Halogeton_glomeratus:0.00638604,(Haloxylon_ammodendron:0.00000102,Haloxylon_persicum:0.00000102)100:0.00421249)47:0.00105843)19:0.00000102,((Haloxylon_tamariscifolium:0.00209455,(Horaninovia_ulicina:0.01192778,Halogeton_arachnoideus:0.00426781)66:0.00206553)12:0.00000102,Iljinia_regelii:0.00000102)8:0.00000102)64:0.00105483,Salsola_foliosa:0.00634975)69:0.00209463)20:0.00000102)94:0.00506880)62:0.00115837)56:0.00324816,(Salsola_arbuscula:0.00211160,(Salsola_kali:0.00104118,((Salsola_chinghaiensis:0.00104318,(Salsola_zaidamica:0.00104394,((Salsola_komarovii:0.00000102,Salsola_ruthenica:0.00000102)15:0.00000102,Salsola_collina:0.00000102)21:0.00000102)28:0.00000102)61:0.00104205,(Salsola_praecox:0.00000102,(Salsola_pellucida:0.00000102,Salsola_paulsenii:0.00000102)17:0.00000102)26:0.00000102)24:0.00000102)87:0.00207039)100:0.00528234)27:0.00105494,Salsola_genistoides:0.00314018)20:0.00104526)6:0.00000102)93:0.01140271,((((((Arthrocnemum_macrostachyum:0.00208856,(Sarcocornia_utahensis:0.00430842,Salicornia_europaea:0.01084361)45:0.00208472)28:0.00214026,((Tecticornia_disarticulata:0.00213150,Sclerostegia_moniliformis:0.00212837)94:0.00426304,(Tecticornia_australasica:0.00105460,((Salicornia_dolichostachya:0.01671719,Halosarcia_indica:0.00632785)54:0.00650166,Pachycornia_triandra:0.00319160)8:0.00000102)4:0.00000102)18:0.00107232)41:0.00217706,((Halostachys_belangeriana:0.00142728,Halopeplis_amplexicaulis:0.00498422)54:0.00319933,(Kalidium_cuspidatum:0.00536000,(Kalidium_caspicum:0.00424783,Kalidium_foliatum:0.00000102)29:0.00000102)84:0.00285700)76:0.00467946)38:0.00134451,Allenrolfea_occidentalis:0.00724180)62:0.00692387,Bienertia_cycloptera:0.01313946)79:0.00702054,((Suaeda_maritima:0.00490738,Suaeda_crassifolia:0.00388120)100:0.01891477,((Suaeda_physophora:0.00588870,Suaeda_microphylla:0.00486985)82:0.00972204,Suaeda_altissima:0.01306847)65:0.00725815)56:0.00443597)80:0.00709752)100:0.01330392,(Agriophyllum_squarrosum:0.01187852,(Corispermum_filifolium:0.00957955,Anthochlamys_multinervis:0.00119607)94:0.00642820)92:0.00603656)35:0.00283291,Acroglochin_chenopodioides:0.01944356)15:0.00152637)14:0.00377071)12:0.00227794,(((Monolepis_nuttalliana:0.00314556,Spinacia_oleracea:0.02411154)100:0.01335566,Chenopodium_foliosum:0.00648643)34:0.00205671,Chenopodium_bonushenricus:0.00310884)39:0.00219374)19:0.00092256)97:0.00745230,Chenopodium_coronopus:0.00690985)99:0.00615396,(Microgynoecium_tibeticum:0.01320943,((((Chenopodium_acuminatum:0.00209272,((Chenopodium_album:0.00000102,Chenopodium_murale:0.00104331)96:0.00314773,Chenopodium_sanctaeclarae:0.00423868)18:0.00000102)5:0.00000102,Chenopodium_frutescens:0.00000102)25:0.00000102,Micromonolepis_pusilla:0.00526085)69:0.00099815,((Einadia_nutans:0.00104063,Rhagodia_drummondi:0.00000102)88:0.00208881,(Chenopodium_desertorum:0.00104282,Chenopodium_auricomum:0.00104393)38:0.00000102)64:0.00321817)100:0.01116813)80:0.00067388)99:0.00433628,(Manochlamys_albicans:0.00519597,Archiatriplex_nanpinensis:0.00861502)61:0.00212072)63:0.00206883)100:0.00649188,(((((Atriplex_parryi:0.00104219,((Atriplex_phyllostegia:0.00104244,Atriplex_serenana:0.00000102)43:0.00000102,Atriplex_powellii:0.00104263)87:0.00209024)11:0.00000102,((Atriplex_lampa:0.00209727,Atriplex_undulata:0.00104916)67:0.00103801,Atriplex_lentiformis:0.00104296)12:0.00000102)38:0.00000102,(((Atriplex_spongiosa:0.00104854,Atriplex_rosea:0.00313774)73:0.00000102,Atriplex_centralasiatica:0.00419604)53:0.00105750,Atriplex_glauca:0.00419623)72:0.00209055)42:0.00104288,Atriplex_coriacea:0.00419172)61:0.00104689,(Atriplex_halimus:0.00208849,Cremnophyton_lanfrancoi:0.00000102)16:0.00000102)28:0.00000102)58:0.00104026,(Atriplex_australasica:0.00000102,Atriplex_patula:0.00000102)62:0.00000102,Atriplex_aucherii:0.00208586);
Achyranthes_aspera C3
Acroglochin_chenopodioides C3
Aerva_javanica C4
Agriophyllum_squarrosum C3
Allenrolfea_occidentalis C3
Alternanthera_caracasana C4
Alternanthera_pungens C4
Alternanthera_repens C4
Amaranthus_blitum C4
Amaranthus_greggii C4
Amaranthus_hypochondriacus C4
Amaranthus_tricolor C4
Anabasis_aphylla C4
Anabasis_brevifolia C4
Anabasis_elatior C4
Anabasis_eriopoda C4
Anabasis_salsa C4
Anabasis_truncata C4
Anthochlamys_multinervis C3
Aphanisma_blitoides C3
Archiatriplex_nanpinensis C3
Arthrocnemum_macrostachyum C3
Atriplex_aucherii C3
Atriplex_australasica C3
Atriplex_centralasiatica C4
Atriplex_coriacea C4
Atriplex_glauca C4
Atriplex_halimus C4
Atriplex_lampa C4
Atriplex_lentiformis C4
Atriplex_parryi C4
Atriplex_patula C3
Atriplex_phyllostegia C4
Atriplex_powellii C4
Atriplex_rosea C4
Atriplex_serenana C4
Atriplex_spongiosa C4
Atriplex_undulata C4
Axyris_prostrata C3
Bassia_dasyphylla C3
Bassia_diffusa C3
Bassia_prostrata C4
Bassia_sedoides C4
Beta_nana C3
Beta_vulgaris C3
Bienertia_cycloptera C4
Blutaparon_vermiculare C4
Bosea_yervamora C3
Calicorema_capitata C3
Camphorosma_monspeliaca C4
Celosia_argentea C3
Celosia_trigyna C3
Ceratocarpus_arenarius C3
Chamissoa_altissima C3
Charpentiera_obovata C3
Charpentiera_ovata C3
Chenoleoides_tomentosa C4
Chenopodium_acuminatum C3
Chenopodium_album C3
Chenopodium_ambrosioides C3
Chenopodium_auricomum C3
Chenopodium_bonushenricus C3
Chenopodium_botrys C3
Chenopodium_coronopus C3
Chenopodium_cristatum C3
Chenopodium_desertorum C3
Chenopodium_foliosum C3
Chenopodium_frutescens C3
Chenopodium_murale C3
Chenopodium_sanctaeclarae C3
Climacoptera_brachiata C4
Climacoptera_lanata C4
Corispermum_filifolium C3
Cremnophyton_lanfrancoi C3
Cycloloma_atriplicifolium C3
Deeringia_amaranthoides C3
Dissocarpus_paradoxus C3
Dysphania_glomulifera C3
Einadia_nutans C3
Girgensohnia_oppositiflora C4
Gomphrena_elegans C3
Gomphrena_haageana C4
Gomphrena_serrata C4
Guilleminea_densa C4
Hablitzia_tamnoides C3
Halimione_pedunculata C3
Halimione_verrucifera C3
Halimocnemis_karelinii C4
Halimocnemis_villosa C4
Halocharis_hispida C4
Halogeton_arachnoideus C4
Halogeton_glomeratus C4
Halopeplis_amplexicaulis C3
Halosarcia_indica C4
Halostachys_belangeriana C3
Halothamnus_bottae C4
Haloxylon_ammodendron C4
Haloxylon_persicum C4
Haloxylon_tamariscifolium C4
Hebanthe_occidentalis C3
Hemichroa_diandra C3
Hermbstaedtia_glauca C3
Horaninovia_ulicina C4
Iljinia_regelii C4
Iresine_palmeri C3
Kalidium_caspicum C3
Kalidium_cuspidatum C3
Kalidium_foliatum C3
Kochia_americana C3
Kochia_densiflora C4
Krascheninnikovia_ceratoides C3
Maireana_brevifolia C3
Manochlamys_albicans C3
Microgynoecium_tibeticum C3
Micromonolepis_pusilla C3
Monolepis_nuttalliana C3
Nanophyton_erinaceum C4
Nitrophila_occidentalis C3
Noaea_mucronata C4
Nototrichium_humile C3
Ofaiston_monandrum C4
Oreobliton_thesioides C3
Pachycornia_triandra C3
Panderia_pilosa C4
Pandiaka_angustifolia C3
Patellifolia_patellaris C3
Petrosimonia_glaucescens C4
Petrosimonia_nigdeensis C4
Petrosimonia_sibirica C4
Petrosimonia_squarrosa C4
Polycnemum_perenne C3
Pseudoplantago_friesii C3
Ptilotus_manglesii C3
Pupalia_lappacea C3
Rhagodia_drummondi C3
Rhaphidophyton_regelii C3
Roycea_divaricata C3
Salicornia_dolichostachya C3
Salicornia_europaea C3
Salsola_affinis C4
Salsola_arbuscula C4
Salsola_arbusculiformis C3
Salsola_chinghaiensis C4
Salsola_collina C4
Salsola_dshungarica C4
Salsola_ferganica C4
Salsola_foliosa C4
Salsola_genistoides C3
Salsola_heptapotamica C4
Salsola_implicata C4
Salsola_kali C4
Salsola_komarovii C4
Salsola_laricifolia C3
Salsola_micranthera C4
Salsola_orientalis C4
Salsola_paulsenii C4
Salsola_pellucida C4
Salsola_praecox C4
Salsola_rosacea C4
Salsola_ruthenica C4
Salsola_sukaczevii C4
Salsola_vermiculata C4
Salsola_zaidamica C4
Sarcocornia_utahensis C3
Sclerolaena_obliquicuspis C3
Sclerostegia_moniliformis C3
Sericostachys_scandens C3
Spinacia_oleracea C3
Suaeda_altissima C4
Suaeda_crassifolia C3
Suaeda_maritima C3
Suaeda_microphylla C4
Suaeda_physophora C3
Suckleya_suckleyana C3
Sympegma_regelii C3
Tecticornia_australasica C3
Tecticornia_disarticulata C3
Teloxys_aristata C3
Tidestromia_lanuginosa C4
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment