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Commit f0a5fa14 authored by Carine Rey's avatar Carine Rey Committed by LANORE Vincent
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clean up in hyp

parent 12dab7be
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Showing with 8 additions and 11 deletions
Makefile
View file @ f0a5fa14
......@@ -74,9 +74,8 @@ real:
.PHONY: analyses_we
analyses_we:
cd example && \
reviewphiltrans validation --outdir outdir_analyses_we --tree-dir trees_analyses_weekend --profile-fn aa_fitness/263SelectedProfiles.tsv --np 28 --preview --ns 1000 --fast && \
reviewphiltrans validation --outdir outdir_analyses_we --tree-dir trees_analyses_weekend --profile-fn aa_fitness/263SelectedProfiles.tsv --np 28 --ns 1000 --fast && \
reviewphiltrans validation --outdir outdir_analyses_we --tree-dir trees_analyses_weekend --profile-fn aa_fitness/263SelectedProfiles.tsv --np 28 --ns 1000 && \
reviewphiltrans validation --outdir outdir_analyses_we_0907 --tree-dir trees_analyses_weekend --profile-fn aa_fitness/263SelectedProfiles.tsv --np 24 --ns 2000 --fast --seed 2167988076475850536 && \
reviewphiltrans validation --outdir outdir_analyses_we_0907 --tree-dir trees_analyses_weekend --profile-fn aa_fitness/263SelectedProfiles.tsv --np 24 --ns 2000 --seed 2167988076475850536 && \
mv dag.dot daganalyses_we.dot
.PHONY: analyses_night
......
example/trees_analyses_weekend/ensemblV92.mammals.not_random_scenario_1.bl_1.nhx deleted 100644 → 0
View file @ 12dab7be
(ornithorhynchus_anatinus:0.1278[&&NHX:Condition=0],(((sarcophilus_harrisii:0.06813[&&NHX:Condition=0],notamacropus_eugenii:0.07663[&&NHX:Condition=0]):0.00305[&&NHX:Condition=0],monodelphis_domestica:0.07637[&&NHX:Condition=0]):0.04008[&&NHX:Condition=0],(((loxodonta_africana:0.06161[&&NHX:Condition=0],procavia_capensis:0.07695[&&NHX:Condition=0]):0.01578[&&NHX:Condition=0],echinops_telfairi:0.09765[&&NHX:Condition=0]):0.02562[&&NHX:Condition=0],((dasypus_novemcinctus:0.07725[&&NHX:Condition=1],choloepus_hoffmanni:0.0787[&&NHX:Condition=1]):0.02781[&&NHX:Condition=1:Transition=1],(((((oryctolagus_cuniculus:0.07649[&&NHX:Condition=0],ochotona_princeps:0.09226[&&NHX:Condition=0]):0.02465[&&NHX:Condition=0],((((((cavia_aperea:0.01305[&&NHX:Condition=1],cavia_porcellus:0.00765[&&NHX:Condition=1]):0.06702[&&NHX:Condition=1],chinchilla_lanigera:0.06971[&&NHX:Condition=1]):0.00361[&&NHX:Condition=1],octodon_degus:0.07621[&&NHX:Condition=1]):0.00219[&&NHX:Condition=1:Transition=1],((heterocephalus_glaber_female:0.00045[&&NHX:Condition=0],heterocephalus_glaber_male:0.00082[&&NHX:Condition=0]):0.05583[&&NHX:Condition=0],fukomys_damarensis:0.05811[&&NHX:Condition=0]):0.01878[&&NHX:Condition=0]):0.02107[&&NHX:Condition=0],ictidomys_tridecemlineatus:0.08987[&&NHX:Condition=0]):0.00443[&&NHX:Condition=0],(dipodomys_ordii:0.10007[&&NHX:Condition=0],(jaculus_jaculus:0.09418[&&NHX:Condition=0],(nannospalax_galili:0.08691[&&NHX:Condition=0],(((((cricetulus_griseus_chok1gshd:0.00024[&&NHX:Condition=0],cricetulus_griseus_crigri:0.00077[&&NHX:Condition=0]):0.04865[&&NHX:Condition=0],mesocricetus_auratus:0.05241[&&NHX:Condition=0]):0.01641[&&NHX:Condition=0],peromyscus_maniculatus_bairdii:0.06366[&&NHX:Condition=0]):0.00279[&&NHX:Condition=0],microtus_ochrogaster:0.07073[&&NHX:Condition=0]):0.01053[&&NHX:Condition=0],(rattus_norvegicus:0.06307[&&NHX:Condition=1],(mus_pahari:0.03682[&&NHX:Condition=1],(mus_caroli:0.02056[&&NHX:Condition=1],(mus_spretus:0.01046[&&NHX:Condition=1],(mus_musculus_casteij:0.00509[&&NHX:Condition=1],(mus_musculus_pwkphj:0.00538[&&NHX:Condition=1],(mus_musculus_nzohlltj:0.00134[&&NHX:Condition=1],((mus_musculus_c57bl6nj:0.00064[&&NHX:Condition=1],mus_musculus:0.0001[&&NHX:Condition=1]):0.00094[&&NHX:Condition=1],((mus_musculus_lpj:0.00058[&&NHX:Condition=1],mus_musculus_129s1svimj:0.00049[&&NHX:Condition=1]):0.00094[&&NHX:Condition=1],(((((mus_musculus_c3hhej:0.00038[&&NHX:Condition=1],mus_musculus_cbaj:0.00054[&&NHX:Condition=1]):0.00026[&&NHX:Condition=1],mus_musculus_dba2j:0.00112[&&NHX:Condition=1]):0.00027[&&NHX:Condition=1],(mus_musculus_aj:0.00037[&&NHX:Condition=1],mus_musculus_balbcj:0.00091[&&NHX:Condition=1]):0.0001[&&NHX:Condition=1]):0.00028[&&NHX:Condition=1],mus_musculus_akrj:0.00075[&&NHX:Condition=1]):0.0001[&&NHX:Condition=1],(mus_musculus_wsbeij:0.00183[&&NHX:Condition=1],(mus_musculus_nodshiltj:0.00145[&&NHX:Condition=1],mus_musculus_fvbnj:0.00095[&&NHX:Condition=1]):0.00046[&&NHX:Condition=1]):0.0001[&&NHX:Condition=1]):0.0001[&&NHX:Condition=1]):0.00028[&&NHX:Condition=1]):0.0001[&&NHX:Condition=1]):0.00301[&&NHX:Condition=1]):0.00044[&&NHX:Condition=1]):0.00566[&&NHX:Condition=1]):0.01055[&&NHX:Condition=1]):0.01672[&&NHX:Condition=1]):0.02326[&&NHX:Condition=1]):0.01744[&&NHX:Condition=1:Transition=1]):0.01323[&&NHX:Condition=0]):0.00918[&&NHX:Condition=0]):0.00747[&&NHX:Condition=0]):0.00124[&&NHX:Condition=0]):0.00365[&&NHX:Condition=0]):0.00185[&&NHX:Condition=0],tupaia_belangeri:0.09888[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0],(((propithecus_coquereli:0.0424[&&NHX:Condition=0],microcebus_murinus:0.0412[&&NHX:Condition=0]):0.02776[&&NHX:Condition=0],otolemur_garnettii:0.07575[&&NHX:Condition=0]):0.0073[&&NHX:Condition=0],(carlito_syrichta:0.0799[&&NHX:Condition=0],((((saimiri_boliviensis_boliviensis:0.02639[&&NHX:Condition=0],cebus_capucinus:0.02594[&&NHX:Condition=0]):0.00278[&&NHX:Condition=0],callithrix_jacchus:0.03[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0],aotus_nancymaae:0.02501[&&NHX:Condition=0]):0.02357[&&NHX:Condition=0],((((((pan_paniscus:0.00307[&&NHX:Condition=0],pan_troglodytes:0.00247[&&NHX:Condition=0]):0.0043[&&NHX:Condition=0],homo_sapiens:0.00661[&&NHX:Condition=0]):0.00176[&&NHX:Condition=0],gorilla_gorilla:0.00868[&&NHX:Condition=0]):0.00836[&&NHX:Condition=0],pongo_abelii:0.01726[&&NHX:Condition=0]):0.00283[&&NHX:Condition=0],nomascus_leucogenys:0.01961[&&NHX:Condition=0]):0.01078[&&NHX:Condition=0],(((rhinopithecus_roxellana:0.0021[&&NHX:Condition=1],rhinopithecus_bieti:0.00301[&&NHX:Condition=1]):0.00939[&&NHX:Condition=1],colobus_angolensis_palliatus:0.01232[&&NHX:Condition=1]):0.00505[&&NHX:Condition=1:Transition=1],(chlorocebus_sabaeus:0.0117[&&NHX:Condition=0],(((mandrillus_leucophaeus:0.00665[&&NHX:Condition=0],cercocebus_atys:0.0058[&&NHX:Condition=0]):0.00064[&&NHX:Condition=0],papio_anubis:0.00666[&&NHX:Condition=0]):0.0012[&&NHX:Condition=0],((macaca_mulatta:0.00233[&&NHX:Condition=0],macaca_fascicularis:0.00215[&&NHX:Condition=0]):0.00095[&&NHX:Condition=0],macaca_nemestrina:0.00418[&&NHX:Condition=0]):0.00433[&&NHX:Condition=0]):0.00401[&&NHX:Condition=0]):0.00475[&&NHX:Condition=0]):0.01388[&&NHX:Condition=0]):0.0176[&&NHX:Condition=0]):0.02753[&&NHX:Condition=0]):0.00099[&&NHX:Condition=0]):0.01976[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0],((erinaceus_europaeus:0.10146[&&NHX:Condition=0],sorex_araneus:0.10725[&&NHX:Condition=0]):0.004[&&NHX:Condition=0],((((tursiops_truncatus:0.06798[&&NHX:Condition=0],(((capra_hircus:0.01127[&&NHX:Condition=0],ovis_aries:0.01107[&&NHX:Condition=0]):0.01687[&&NHX:Condition=0],bos_taurus:0.02703[&&NHX:Condition=0]):0.05573[&&NHX:Condition=0],(vicugna_pacos:0.08218[&&NHX:Condition=0],sus_scrofa:0.07611[&&NHX:Condition=0]):0.00086[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0]):0.01334[&&NHX:Condition=0],equus_caballus:0.0817[&&NHX:Condition=0]):0.0044[&&NHX:Condition=0],(pteropus_vampyrus:0.07973[&&NHX:Condition=1],myotis_lucifugus:0.08293[&&NHX:Condition=1]):0.00724[&&NHX:Condition=1:Transition=1]):0.0001[&&NHX:Condition=0],(felis_catus:0.06559[&&NHX:Condition=0],((mustela_putorius_furo:0.05565[&&NHX:Condition=0],ailuropoda_melanoleuca:0.0549[&&NHX:Condition=0]):0.00652[&&NHX:Condition=0],canis_familiaris:0.05998[&&NHX:Condition=0]):0.00575[&&NHX:Condition=0]):0.01641[&&NHX:Condition=0]):0.01276[&&NHX:Condition=0]):0.00018[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0]):0.00274[&&NHX:Condition=0]):0.01154[&&NHX:Condition=0]):0.00682[&&NHX:Condition=0]);
\ No newline at end of file
example/trees_analyses_weekend/ensembl_3tr.nhx deleted 100644 → 0
View file @ 12dab7be
(ornithorhynchus_anatinus:0.1278[&&NHX:Condition=0],(((sarcophilus_harrisii:0.06813[&&NHX:Condition=0],notamacropus_eugenii:0.07663[&&NHX:Condition=0]):0.00305[&&NHX:Condition=0],monodelphis_domestica:0.07637[&&NHX:Condition=0]):0.04008[&&NHX:Condition=0],(((loxodonta_africana:0.06161[&&NHX:Condition=0],procavia_capensis:0.07695[&&NHX:Condition=0]):0.01578[&&NHX:Condition=0],echinops_telfairi:0.09765[&&NHX:Condition=0]):0.02562[&&NHX:Condition=0],((dasypus_novemcinctus:0.07725[&&NHX:Condition=0],choloepus_hoffmanni:0.0787[&&NHX:Condition=0]):0.02781[&&NHX:Condition=0],(((((oryctolagus_cuniculus:0.07649[&&NHX:Condition=0],ochotona_princeps:0.09226[&&NHX:Condition=0]):0.02465[&&NHX:Condition=0],((((((cavia_aperea:0.01305[&&NHX:Condition=1],cavia_porcellus:0.00765[&&NHX:Condition=1]):0.06702[&&NHX:Condition=1],chinchilla_lanigera:0.06971[&&NHX:Condition=1]):0.00361[&&NHX:Condition=1],octodon_degus:0.07621[&&NHX:Condition=1]):0.00219[&&NHX:Condition=1],((heterocephalus_glaber_female:0.00045[&&NHX:Condition=1],heterocephalus_glaber_male:0.00082[&&NHX:Condition=1]):0.05583[&&NHX:Condition=1],fukomys_damarensis:0.05811[&&NHX:Condition=1]):0.01878[&&NHX:Condition=1]):0.02107[&&NHX:Condition=1],ictidomys_tridecemlineatus:0.08987[&&NHX:Condition=1]):0.00443[&&NHX:Condition=1:Transition=1],(dipodomys_ordii:0.10007[&&NHX:Condition=0],(jaculus_jaculus:0.09418[&&NHX:Condition=0],(nannospalax_galili:0.08691[&&NHX:Condition=0],(((((cricetulus_griseus_chok1gshd:0.00024[&&NHX:Condition=0],cricetulus_griseus_crigri:0.00077[&&NHX:Condition=0]):0.04865[&&NHX:Condition=0],mesocricetus_auratus:0.05241[&&NHX:Condition=0]):0.01641[&&NHX:Condition=0],peromyscus_maniculatus_bairdii:0.06366[&&NHX:Condition=0]):0.00279[&&NHX:Condition=0],microtus_ochrogaster:0.07073[&&NHX:Condition=0]):0.01053[&&NHX:Condition=0],(rattus_norvegicus:0.06307[&&NHX:Condition=0],(mus_pahari:0.03682[&&NHX:Condition=0],(mus_caroli:0.02056[&&NHX:Condition=0],(mus_spretus:0.01046[&&NHX:Condition=0],(mus_musculus_casteij:0.00509[&&NHX:Condition=0],(mus_musculus_pwkphj:0.00538[&&NHX:Condition=0],(mus_musculus_nzohlltj:0.00134[&&NHX:Condition=0],((mus_musculus_c57bl6nj:0.00064[&&NHX:Condition=0],mus_musculus:0.0001[&&NHX:Condition=0]):0.00094[&&NHX:Condition=0],((mus_musculus_lpj:0.00058[&&NHX:Condition=0],mus_musculus_129s1svimj:0.00049[&&NHX:Condition=0]):0.00094[&&NHX:Condition=0],(((((mus_musculus_c3hhej:0.00038[&&NHX:Condition=0],mus_musculus_cbaj:0.00054[&&NHX:Condition=0]):0.00026[&&NHX:Condition=0],mus_musculus_dba2j:0.00112[&&NHX:Condition=0]):0.00027[&&NHX:Condition=0],(mus_musculus_aj:0.00037[&&NHX:Condition=0],mus_musculus_balbcj:0.00091[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0]):0.00028[&&NHX:Condition=0],mus_musculus_akrj:0.00075[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0],(mus_musculus_wsbeij:0.00183[&&NHX:Condition=0],(mus_musculus_nodshiltj:0.00145[&&NHX:Condition=0],mus_musculus_fvbnj:0.00095[&&NHX:Condition=0]):0.00046[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0]):0.00028[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0]):0.00301[&&NHX:Condition=0]):0.00044[&&NHX:Condition=0]):0.00566[&&NHX:Condition=0]):0.01055[&&NHX:Condition=0]):0.01672[&&NHX:Condition=0]):0.02326[&&NHX:Condition=0]):0.01744[&&NHX:Condition=0]):0.01323[&&NHX:Condition=0]):0.00918[&&NHX:Condition=0]):0.00747[&&NHX:Condition=0]):0.00124[&&NHX:Condition=0]):0.00365[&&NHX:Condition=0]):0.00185[&&NHX:Condition=0],tupaia_belangeri:0.09888[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0],(((propithecus_coquereli:0.0424[&&NHX:Condition=0],microcebus_murinus:0.0412[&&NHX:Condition=0]):0.02776[&&NHX:Condition=0],otolemur_garnettii:0.07575[&&NHX:Condition=0]):0.0073[&&NHX:Condition=0],(carlito_syrichta:0.0799[&&NHX:Condition=0],((((saimiri_boliviensis_boliviensis:0.02639[&&NHX:Condition=0],cebus_capucinus:0.02594[&&NHX:Condition=0]):0.00278[&&NHX:Condition=0],callithrix_jacchus:0.03[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0],aotus_nancymaae:0.02501[&&NHX:Condition=0]):0.02357[&&NHX:Condition=0],((((((pan_paniscus:0.00307[&&NHX:Condition=1],pan_troglodytes:0.00247[&&NHX:Condition=1]):0.0043[&&NHX:Condition=1],homo_sapiens:0.00661[&&NHX:Condition=1]):0.00176[&&NHX:Condition=1],gorilla_gorilla:0.00868[&&NHX:Condition=1]):0.00836[&&NHX:Condition=1],pongo_abelii:0.01726[&&NHX:Condition=1]):0.00283[&&NHX:Condition=1],nomascus_leucogenys:0.01961[&&NHX:Condition=1]):0.01078[&&NHX:Condition=1:Transition=1],(((rhinopithecus_roxellana:0.0021[&&NHX:Condition=0],rhinopithecus_bieti:0.00301[&&NHX:Condition=0]):0.00939[&&NHX:Condition=0],colobus_angolensis_palliatus:0.01232[&&NHX:Condition=0]):0.00505[&&NHX:Condition=0],(chlorocebus_sabaeus:0.0117[&&NHX:Condition=0],(((mandrillus_leucophaeus:0.00665[&&NHX:Condition=0],cercocebus_atys:0.0058[&&NHX:Condition=0]):0.00064[&&NHX:Condition=0],papio_anubis:0.00666[&&NHX:Condition=0]):0.0012[&&NHX:Condition=0],((macaca_mulatta:0.00233[&&NHX:Condition=0],macaca_fascicularis:0.00215[&&NHX:Condition=0]):0.00095[&&NHX:Condition=0],macaca_nemestrina:0.00418[&&NHX:Condition=0]):0.00433[&&NHX:Condition=0]):0.00401[&&NHX:Condition=0]):0.00475[&&NHX:Condition=0]):0.01388[&&NHX:Condition=0]):0.0176[&&NHX:Condition=0]):0.02753[&&NHX:Condition=0]):0.00099[&&NHX:Condition=0]):0.01976[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0],((erinaceus_europaeus:0.10146[&&NHX:Condition=0],sorex_araneus:0.10725[&&NHX:Condition=0]):0.004[&&NHX:Condition=0],((((tursiops_truncatus:0.06798[&&NHX:Condition=1],(((capra_hircus:0.01127[&&NHX:Condition=1],ovis_aries:0.01107[&&NHX:Condition=1]):0.01687[&&NHX:Condition=1],bos_taurus:0.02703[&&NHX:Condition=1]):0.05573[&&NHX:Condition=1],(vicugna_pacos:0.08218[&&NHX:Condition=1],sus_scrofa:0.07611[&&NHX:Condition=1]):0.00086[&&NHX:Condition=1]):0.0001[&&NHX:Condition=1]):0.01334[&&NHX:Condition=1:Transition=1],equus_caballus:0.0817[&&NHX:Condition=0]):0.0044[&&NHX:Condition=0],(pteropus_vampyrus:0.07973[&&NHX:Condition=0],myotis_lucifugus:0.08293[&&NHX:Condition=0]):0.00724[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0],(felis_catus:0.06559[&&NHX:Condition=0],((mustela_putorius_furo:0.05565[&&NHX:Condition=0],ailuropoda_melanoleuca:0.0549[&&NHX:Condition=0]):0.00652[&&NHX:Condition=0],canis_familiaris:0.05998[&&NHX:Condition=0]):0.00575[&&NHX:Condition=0]):0.01641[&&NHX:Condition=0]):0.01276[&&NHX:Condition=0]):0.00018[&&NHX:Condition=0]):0.0001[&&NHX:Condition=0]):0.00274[&&NHX:Condition=0]):0.01154[&&NHX:Condition=0]):0.00682[&&NHX:Condition=0]);
\ No newline at end of file
lib/pipeline.ml
View file @ f0a5fa14
......@@ -171,9 +171,8 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n
[]
else
[
[H0_NeG3 ;
H0_NeG4 ;
HaPC_NeG3;
[(*H0_NeG3 ;HaPC_NeG3; *)
H0_NeG4;
HaPC_NeG4;
H0_NeG2;
HaPC_NeG2;
......@@ -182,14 +181,14 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n
(if no_Ne then
[]
else
[HaPC_NeG5_NeC_div2 ;
[(*HaPC_NeG5_NeC_div2 ;
HaPC_NeG5_NeC_x2 ;
H0_NeG5_NeC_div2 ;
H0_NeG5_NeC_x2 ;
HaPC_NeG1_NeC_5 ;
HaPC_NeG5_NeC_1 ;
H0_NeG1_NeC_5 ;
H0_NeG5_NeC_1 ;
H0_NeG5_NeC_1 ;*)
HaPC_NeG1_NeC_4 ;
HaPC_NeG4_NeC_1 ;
H0_NeG1_NeC_4 ;
......@@ -213,7 +212,7 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n
let concat_H0HaPC = {Dataset.model_prefix="H0_NeG5+HaPC_NeG5"; tree_prefix; is_real = false; dataset = Ready_dataset.paste dataset_H0_NeG5.dataset dataset_HaPC_NeG5.dataset; seed=(dataset_H0_NeG5.seed + dataset_HaPC_NeG5.seed |> Hashtbl.hash) } in
let dataset_concat_hypos = if use_concat then [concat_H0HaPC;] else [] in
let dataset_with_indels = if add_indels then [indel_H0_NeG5 ; indel_HaPC_NeG5] else [] in
List.concat [ dataset_basis_hyps; dataset_per_hypo ; dataset_concat_hypos; dataset_with_indels ]
List.concat [ (*dataset_basis_hyps;*) dataset_per_hypo ; dataset_concat_hypos; dataset_with_indels ]
let derive_sim ~tree_dir ~trees ~profile ~preview ~use_concat ~ns ~no_Ne ~no_HaPC ~ne_test ~add_indels ~seed =
List.map trees ~f:(fun tree ->
......@@ -377,6 +376,7 @@ let derive_profile ?(indir = "") ?(ns = 0) ~preview ~fast_mode ~no_Ne ~ne_test ~
let repo_of_post_analyses_simu = Post_analyses.repo_of_post_analyses_simu ~post_analyses_simu in
let profile_prefix = profile.profile_n in
let repo_post_analyses_all_trees = Post_analyses.repo_post_analyses_all_trees_of_all_post_analyses_per_tree ~all_post_analyses_per_tree ~profile_prefix in
let repo_post_analyses_all_trees = [] in
let repo_post_analyses_all_trees = if only_simu then
[]
else
......
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