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Commit b1db8894 authored by Philippe Veber's avatar Philippe Veber
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update wrt bistro

parent fecafac7
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Showing with 366 additions and 389 deletions
lib/bppsuite.ml
View file @ b1db8894
......@@ -127,19 +127,17 @@ rate_distribution=Constant()
let ne_g = Convergence_hypothesis.neg_of_model hypothesis in
let ne_c = Convergence_hypothesis.nec_of_model hypothesis in
let ne_a = ne_g in
Workflow.shell ~descr:("bppsuite.bppseqgen" ^ descr) [
within_container img (
and_list [
mkdir_p dest;
mkdir_p tmp;
cd tmp;
cmd "cat" ~stdout:config_f [
file_dump (conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~hypothesis ~ne_c ~ne_a ~nb_sites_per_profile) ;
dep nodes ;
];
cmd "bash" [ file_dump (bppseqgen_multi_profiles_script ~config:config_f ~out ~profile_c:profile_c_ok ~seed)];
]
)
Workflow.shell ~descr:("bppsuite.bppseqgen" ^ descr) ~img [
and_list [
mkdir_p dest;
mkdir_p tmp;
cd tmp;
cmd "cat" ~stdout:config_f [
file_dump (conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~hypothesis ~ne_c ~ne_a ~nb_sites_per_profile) ;
dep nodes ;
];
cmd "bash" [ file_dump (bppseqgen_multi_profiles_script ~config:config_f ~out ~profile_c:profile_c_ok ~seed)];
]
]
let alignment run_bppseqgen_multi_profiles : nucleotide_fasta file =
......@@ -167,8 +165,8 @@ let conf_file_bppseqman_fna2faa ~fna =
]
let fna2faa (fna : nucleotide_fasta file) : aminoacid_fasta file =
Workflow.shell ~descr:"bppsuite.fna2faa" [
cmd "bppseqman" ~img [
Workflow.shell ~descr:"bppsuite.fna2faa" ~img [
cmd "bppseqman" [
assign "param" (file_dump (conf_file_bppseqman_fna2faa ~fna)) ;
]
]
......@@ -198,23 +196,23 @@ let conf_file_bppseqman_faa2phy ~faa =
]
let fna2phy ~(fna: nucleotide_fasta file) : nucleotide_phylip file =
Workflow.shell ~descr:"bppsuite.fna2phy_interleaved" [
cmd "bppseqman" ~img [
Workflow.shell ~descr:"bppsuite.fna2phy_interleaved" ~img [
cmd "bppseqman" [
assign "param" (file_dump (conf_file_bppseqman_fna2phy ~fna)) ;
]
]
let faa2phy ~(faa: aminoacid_fasta file) : aminoacid_phylip file =
Workflow.shell ~descr:"bppsuite.faa2phy_interleaved" [
cmd "bppseqman" ~img [
Workflow.shell ~descr:"bppsuite.faa2phy_interleaved" ~img [
cmd "bppseqman" [
assign "param" (file_dump (conf_file_bppseqman_faa2phy ~faa)) ;
]
]
let paste_fna ~(fna_l: nucleotide_fasta file list) : nucleotide_fasta file =
Workflow.shell ~descr:"bppsuite.catfasta" [
cmd "catfasta2phyml.pl" ~stdout:dest ~img (List.concat [
Workflow.shell ~descr:"bppsuite.catfasta" ~img [
cmd "catfasta2phyml.pl" ~stdout:dest (List.concat [
[string "-f" ] ;
List.map fna_l ~f:(fun fna -> dep fna) ;
])
......
lib/convergence_detection.ml
View file @ b1db8894
......@@ -69,8 +69,8 @@ let merge_results ?fna_infos ~(res_by_tools : result list) () : text file =
seq ~sep:" " [opt; dep w]
)
in
Workflow.shell ~descr:"convergence_detection.merge_results" [
cmd "python" ~img:Env.env_py [
Workflow.shell ~descr:"convergence_detection.merge_results" ~img:Env.env_py [
cmd "python" [
file_dump (string Scripts.merge_det_results) ;
opt "-o" ident dest ;
seq ~sep:" " command ;
......@@ -79,8 +79,8 @@ let merge_results ?fna_infos ~(res_by_tools : result list) () : text file =
]
let merge_result_tables ?fna_infos ?oracle ?multinomial ?tdg09 ?identical ?topological ?pcoc ?pcoc_v2 ?pcoc_pcp ?diffsel ?diffseldsparse () : text file =
Workflow.shell ~descr:"convergence_detection.merge_results" [
cmd "python" ~img:Env.env_py [
Workflow.shell ~descr:"convergence_detection.merge_results" ~img:Env.env_py [
cmd "python" [
file_dump (string Scripts.merge_det_results) ;
opt "-o" ident dest ;
option (opt "--multinomial" dep) multinomial ;
......@@ -141,50 +141,46 @@ let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~t
in
let out = dest // "results.svg" in
let inner =
Workflow.shell ~descr:"convergence_detection.plot_results" [
within_container img (
and_list [
mkdir_p dest ;
cmd "python" [
Utils.script_dump Scripts.[ diffsel_script_utils ; plot_data ; plot_convergent_sites ] ;
opt "-msa" dep faa ;
opt "-tsv" dep tsv ;
opt "-tree" dep tree ;
opt "-out" ident out ;
opt "-meth" ident meths ;
option (opt "-t" ident) meths_t ;
option (opt "--t_tsv" dep) t_choices ;
flag string "--all_sites" plot_all_sites ;
]
]
)
]
in
Workflow.select inner ["results.svg"]
let plot_convergent_sites ?(plot_all_sites = true) ~alignment ~detection_results ~tree () =
Workflow.shell ~descr:"plot_convergent_sites.py" [
within_container Env.env_pcoc (
Workflow.shell ~descr:"convergence_detection.plot_results" ~img [
and_list [
mkdir_p dest ;
cmd "python" [
Utils.script_dump Scripts.[ diffsel_script_utils ; plot_data ; plot_convergent_sites ] ;
opt "-tsv" dep detection_results ;
opt "-msa" dep alignment ;
opt "-msa" dep faa ;
opt "-tsv" dep tsv ;
opt "-tree" dep tree ;
opt "-out" ident (dest // "plot.svg") ;
opt "-out" ident out ;
opt "-meth" ident meths ;
option (opt "-t" ident) meths_t ;
option (opt "--t_tsv" dep) t_choices ;
flag string "--all_sites" plot_all_sites ;
]
]
)
]
in
Workflow.select inner ["results.svg"]
let plot_convergent_sites ?(plot_all_sites = true) ~alignment ~detection_results ~tree () =
Workflow.shell ~descr:"plot_convergent_sites.py" ~img:Env.env_pcoc [
and_list [
mkdir_p dest ;
cmd "python" [
Utils.script_dump Scripts.[ diffsel_script_utils ; plot_data ; plot_convergent_sites ] ;
opt "-tsv" dep detection_results ;
opt "-msa" dep alignment ;
opt "-tree" dep tree ;
opt "-out" ident (dest // "plot.svg") ;
flag string "--all_sites" plot_all_sites ;
]
]
]
|> Fn.flip Workflow.select ["plot.svg"]
let recall_precision_curve table =
let img = [ docker_image ~account:"pveber" ~name:"r_basics" ~tag:"20190710" () ] in
Workflow.shell ~descr:"recall_precision_curve" [
cmd "Rscript" ~img [
Workflow.shell ~descr:"recall_precision_curve" ~img [
cmd "Rscript" [
file_dump (string Scripts.recall_precision_curve) ;
dep table ;
dest ;
......
lib/diffsel.ml
View file @ b1db8894
......@@ -61,27 +61,25 @@ let diffsel ~(phy_n:nucleotide_phylip file) ~(tree: _ file) ~(w_every:int) ~(n_c
let n_cycles = if (n_cycles > 200) then 20 else n_cycles in
let script_r = tmp // "DiffselMCMCConvergenceAnalysis.Rmd" in
(*_build/diffsel -t data/samhd1.tree -d data/samhd1.ali -ncond 3 -x 1 10000 myrun*)
Workflow.shell ~descr:("convergence_detection.run_diffsel." ^ descr) [
within_container env (
and_list [
mkdir_p dest;
cd tmp;
cmd "cp" [ file_dump (string Scripts.diffselMCMCConvergenceAnalysis) ; script_r] ;
cmd "cp" [dep phy_n; dest_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep tree; dest_tree]; (* required dep to link the file in the env *)
cmd "cp" [dep phy_n; tmp_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep tree; tmp_tree]; (* required dep to link the file in the env *)
cmd "/diffsel/_build/diffsel" [
opt "-t" ident tmp_tree;
opt "-d" ident tmp_ali ;
opt "-ncond" int 2 ;
opt "-x" seq [ int w_every; string " "; int n_cycles];
option (opt "-seed" int) seed ;
ident chainname_tmp ;
];
cmd "bash" [(file_dump (diffsel_add_iterations_script ~chainname ~ali:tmp_ali ~tree:tmp_tree ~seed))];
]
)
Workflow.shell ~descr:("convergence_detection.run_diffsel." ^ descr) ~img:env [
and_list [
mkdir_p dest;
cd tmp;
cmd "cp" [ file_dump (string Scripts.diffselMCMCConvergenceAnalysis) ; script_r] ;
cmd "cp" [dep phy_n; dest_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep tree; dest_tree]; (* required dep to link the file in the env *)
cmd "cp" [dep phy_n; tmp_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep tree; tmp_tree]; (* required dep to link the file in the env *)
cmd "/diffsel/_build/diffsel" [
opt "-t" ident tmp_tree;
opt "-d" ident tmp_ali ;
opt "-ncond" int 2 ;
opt "-x" seq [ int w_every; string " "; int n_cycles];
option (opt "-seed" int) seed ;
ident chainname_tmp ;
];
cmd "bash" [(file_dump (diffsel_add_iterations_script ~chainname ~ali:tmp_ali ~tree:tmp_tree ~seed))];
]
]
let check_conv run_diffsel : [`diffsel_check_conv] directory =
......@@ -90,24 +88,22 @@ let check_conv run_diffsel : [`diffsel_check_conv] directory =
let trace = Workflow.select run_diffsel ["myrun.trace"] in
let out = dest // "out.html" in
let nb_new_iterations = dest // "new_iterations.txt" in
Workflow.shell ~descr:"convergence_detection.DiffselMCMCConvergenceAnalysis" [
within_container env (
and_list [
mkdir_p tmp ;
mkdir_p dest ;
cd tmp ;
cmd "cp" [ file_dump (string Scripts.diffselMCMCConvergenceAnalysis) ; script] ;
cmd "Rscript" [
string "-e" ;
string {|"rmarkdown::render(\"DiffselMCMCConvergenceAnalysis.Rmd\",|} ;
string {|params=list(set_trace1=\"|} ;
dep trace ;
string {|\"))"|};
] ;
cmd "cp" [string "DiffselMCMCConvergenceAnalysis.html" ; ident out] ;
cmd "cp" [string "new_iterations.txt" ; ident nb_new_iterations]
]
)
Workflow.shell ~descr:"convergence_detection.DiffselMCMCConvergenceAnalysis" ~img:env [
and_list [
mkdir_p tmp ;
mkdir_p dest ;
cd tmp ;
cmd "cp" [ file_dump (string Scripts.diffselMCMCConvergenceAnalysis) ; script] ;
cmd "Rscript" [
string "-e" ;
string {|"rmarkdown::render(\"DiffselMCMCConvergenceAnalysis.Rmd\",|} ;
string {|params=list(set_trace1=\"|} ;
dep trace ;
string {|\"))"|};
] ;
cmd "cp" [string "DiffselMCMCConvergenceAnalysis.html" ; ident out] ;
cmd "cp" [string "new_iterations.txt" ; ident nb_new_iterations]
]
]
let selector run_diffsel : text file =
......@@ -120,25 +116,23 @@ let selector run_diffsel : text file =
let dep_ali = (dep run_diffsel) // "myrun.ali" in
let chainname = (dep run_diffsel) // "myrun" in
let out = dest in
Workflow.shell ~descr:"convergence_detection.parse_diffsel" [
within_container env (
and_list [
mkdir_p tmp ;
cd tmp ;
Workflow.shell ~descr:"convergence_detection.parse_diffsel" ~img:env [
and_list [
mkdir_p tmp ;
cd tmp ;
cmd "cp" [dep_ali; tmp_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep_tree; tmp_tree]; (* required dep to link the file in the env *)
cmd "cp" [dep_ali; tmp_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep_tree; tmp_tree]; (* required dep to link the file in the env *)
(*python diffsel_analyze_result.py [-r /path/to/readdiffsel] [-o output_file] chainname *)
cmd "cp" [ file_dump (string Scripts.diffsel_script_utils) ; package] ;
cmd "cp" [ file_dump (string Scripts.diffsel_analyze_result) ; script] ;
(*python diffsel_analyze_result.py [-r /path/to/readdiffsel] [-o output_file] chainname *)
cmd "cp" [ file_dump (string Scripts.diffsel_script_utils) ; package] ;
cmd "cp" [ file_dump (string Scripts.diffsel_analyze_result) ; script] ;
cmd "python" [
string "diffsel_analyze_result.py" ;
opt "-r" string "/diffsel/_build/readdiffsel" ;
opt "-o" ident out ;
ident chainname ;
]
cmd "python" [
string "diffsel_analyze_result.py" ;
opt "-r" string "/diffsel/_build/readdiffsel" ;
opt "-o" ident out ;
ident chainname ;
]
)
]
]
lib/diffseldsparse.ml
View file @ b1db8894
......@@ -53,30 +53,28 @@ let diffseldsparse
let chainname = dest // "myrun" in
let n_cycles = if (n_cycles > 200) then 200 else n_cycles in
let script_r = tmp // "DiffselMCMCConvergenceAnalysis.Rmd" in
Workflow.shell ~descr:"convergence_detection.run_diffseldsparse" [
within_container img (
and_list [
mkdir_p dest;
cd tmp;
cmd "cp" [ file_dump (string Scripts.diffselMCMCConvergenceAnalysis) ; script_r] ;
cmd "cp" [dep alignment; dest_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep tree; dest_tree]; (* required dep to link the file in the env *)
cmd "cp" [dep alignment; tmp_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep tree; tmp_tree]; (* required dep to link the file in the env *)
cmd "/bayescode/data/diffseldsparse" [
opt "-t" ident tmp_tree;
opt "-d" ident tmp_ali ;
option (opt "-pi" float) pi ;
option (opt "-shiftprob" (fun (mean, invconv) -> seq ~sep:" " [ float mean ; float invconv ])) shiftprob ;
option (opt "-eps" float) eps ;
opt "-ncond" int 2 ;
opt "-x" seq [ int w_every; string " "; int n_cycles];
(* opt "-seed" int seed ; *) (* not yet implemented *)
ident chainname_tmp ;
];
cmd "bash" [(file_dump (diffseldsparse_add_iterations_script ~chainname ~ali:tmp_ali ~tree:tmp_tree))];
]
)
Workflow.shell ~descr:"convergence_detection.run_diffseldsparse" ~img [
and_list [
mkdir_p dest;
cd tmp;
cmd "cp" [ file_dump (string Scripts.diffselMCMCConvergenceAnalysis) ; script_r] ;
cmd "cp" [dep alignment; dest_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep tree; dest_tree]; (* required dep to link the file in the env *)
cmd "cp" [dep alignment; tmp_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep tree; tmp_tree]; (* required dep to link the file in the env *)
cmd "/bayescode/data/diffseldsparse" [
opt "-t" ident tmp_tree;
opt "-d" ident tmp_ali ;
option (opt "-pi" float) pi ;
option (opt "-shiftprob" (fun (mean, invconv) -> seq ~sep:" " [ float mean ; float invconv ])) shiftprob ;
option (opt "-eps" float) eps ;
opt "-ncond" int 2 ;
opt "-x" seq [ int w_every; string " "; int n_cycles];
(* opt "-seed" int seed ; *) (* not yet implemented *)
ident chainname_tmp ;
];
cmd "bash" [(file_dump (diffseldsparse_add_iterations_script ~chainname ~ali:tmp_ali ~tree:tmp_tree))];
]
]
let check_conv run_diffseldsparse : [`diffseldsparse_check_conv] directory =
......@@ -84,43 +82,39 @@ let check_conv run_diffseldsparse : [`diffseldsparse_check_conv] directory =
let trace = Workflow.select run_diffseldsparse ["myrun.trace"] in
let out = dest // "out.html" in
let nb_new_iterations = dest // "new_iterations.txt" in
Workflow.shell ~descr:"convergence_detection.DiffselMCMCConvergenceAnalysis" [
within_container Env.env_r (
and_list [
mkdir_p tmp ;
mkdir_p dest ;
cd tmp ;
cmd "cp" [ file_dump (string Scripts.diffselMCMCConvergenceAnalysis) ; script] ;
cmd "Rscript" [
string "-e" ;
string {|"rmarkdown::render(\"DiffselMCMCConvergenceAnalysis.Rmd\",|} ;
string {|params=list(set_trace1=\"|} ;
dep trace ;
string {|\"))"|};
] ;
cmd "cp" [string "DiffselMCMCConvergenceAnalysis.html" ; ident out] ;
cmd "cp" [string "new_iterations.txt" ; ident nb_new_iterations]
]
)
Workflow.shell ~descr:"convergence_detection.DiffselMCMCConvergenceAnalysis" ~img:Env.env_r [
and_list [
mkdir_p tmp ;
mkdir_p dest ;
cd tmp ;
cmd "cp" [ file_dump (string Scripts.diffselMCMCConvergenceAnalysis) ; script] ;
cmd "Rscript" [
string "-e" ;
string {|"rmarkdown::render(\"DiffselMCMCConvergenceAnalysis.Rmd\",|} ;
string {|params=list(set_trace1=\"|} ;
dep trace ;
string {|\"))"|};
] ;
cmd "cp" [string "DiffselMCMCConvergenceAnalysis.html" ; ident out] ;
cmd "cp" [string "new_iterations.txt" ; ident nb_new_iterations]
]
]
let readdiffseldsparse run =
let tmp_chain = tmp // "myrun" in
Workflow.shell ~descr:"readdiffseldsparse" [
within_container img (
and_list [
mkdir_p tmp ;
cmd "ln" [string "-s" ; (dep run) // "*" ; tmp]; (* required dep to link the file in the env *)
cmd "/bayescode/data/readdiffseldsparse" [
opt "-x" string "300 1 1000" ;
ident tmp_chain ;
] ;
mkdir_p dest ;
cmd "mv" [ tmp // "*pp" ; dest ] ;
]
)
Workflow.shell ~descr:"readdiffseldsparse" ~img [
and_list [
mkdir_p tmp ;
cmd "ln" [string "-s" ; (dep run) // "*" ; tmp]; (* required dep to link the file in the env *)
cmd "/bayescode/data/readdiffseldsparse" [
opt "-x" string "300 1 1000" ;
ident tmp_chain ;
] ;
mkdir_p dest ;
cmd "mv" [ tmp // "*pp" ; dest ] ;
]
]
let posterior_probabilities run_diffseldsparse : text file =
......@@ -130,23 +124,21 @@ let posterior_probabilities run_diffseldsparse : text file =
let dep_ali = (dep run_diffseldsparse) // "myrun.ali" in
let chainname = (dep run_diffseldsparse) // "myrun" in
let out = dest in
Workflow.shell ~descr:"convergence_detection.parse_diffseldsparse" [
within_container img (
and_list [
mkdir_p tmp ;
cd tmp ;
cmd "cp" [dep_ali; tmp_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep_tree; tmp_tree]; (* required dep to link the file in the env *)
cmd "python" [
Utils.script_dump Scripts.[ diffsel_script_utils ; diffseldsparse_analyze_result ] ;
opt "-r" string "/bayescode/data/readdiffseldsparse" ;
opt "-o" ident out ;
ident chainname ;
]
Workflow.shell ~descr:"convergence_detection.parse_diffseldsparse" ~img [
and_list [
mkdir_p tmp ;
cd tmp ;
cmd "cp" [dep_ali; tmp_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep_tree; tmp_tree]; (* required dep to link the file in the env *)
cmd "python" [
Utils.script_dump Scripts.[ diffsel_script_utils ; diffseldsparse_analyze_result ] ;
opt "-r" string "/bayescode/data/readdiffseldsparse" ;
opt "-o" ident out ;
ident chainname ;
]
)
]
]
let%pworkflow results dir =
......
lib/identical.ml
View file @ b1db8894
......@@ -36,16 +36,14 @@ let bppml ?(descr="") ~faa ~tree ~config : _ workflow =
let env = Env.env_bppsuite in
let config_f = dest // "config_bppml.bpp" in
let out = ident dest in
Workflow.shell ~descr:("bppsuite.bppml" ^ descr) [
within_container env (
and_list [
mkdir_p dest;
cmd "cat" ~stdout:config_f [(file_dump (conf_file_bppml ~tree ~faa ~out ~config ))];
cmd "bppml" [
assign "param" config_f;
]
Workflow.shell ~descr:("bppsuite.bppml" ^ descr) ~img:env [
and_list [
mkdir_p dest;
cmd "cat" ~stdout:config_f [(file_dump (conf_file_bppml ~tree ~faa ~out ~config ))];
cmd "bppml" [
assign "param" config_f;
]
)
]
]
let conf_file_bppancestor ~tree ~faa ~out ~config =
......@@ -79,16 +77,14 @@ let bppancestor ?(descr="") ~faa ~tree ~config : _ workflow =
let env = Env.env_bppsuite in
let config_f = dest // "config_bppancestor.bpp" in
let out = ident dest in
Workflow.shell ~descr:("bppsuite.bppancestor" ^ descr) [
within_container env (
and_list [
mkdir_p dest;
cmd "cat" ~stdout:config_f [(file_dump (conf_file_bppancestor ~tree ~faa ~out ~config))];
cmd "bppancestor" [
assign "param" config_f;
]
Workflow.shell ~descr:("bppsuite.bppancestor" ^ descr) ~img:env [
and_list [
mkdir_p dest;
cmd "cat" ~stdout:config_f [(file_dump (conf_file_bppancestor ~tree ~faa ~out ~config))];
cmd "bppancestor" [
assign "param" config_f;
]
)
]
]
let identical ?(descr="") ~(tree_id:_ file) ~(tree_sc:_ file) ~(faa:aminoacid_fasta file) ~prot_model () : [`identical] directory =
......@@ -97,9 +93,9 @@ let identical ?(descr="") ~(tree_id:_ file) ~(tree_sc:_ file) ~(faa:aminoacid_fa
let out2 = dest // "out2.tsv" in
let run_bppancestor = bppancestor ~descr:"" ~tree:tree_id ~faa ~config in
let proba = Workflow.select run_bppancestor ["sites.tsv"] in
Workflow.shell ~descr:("identical."^prot_model^"."^descr) [
Workflow.shell ~descr:("identical."^prot_model^"."^descr) ~img:Env.env_pcoc [
mkdir dest ;
cmd "python" ~img:Env.env_pcoc [
cmd "python" [
file_dump (string Scripts.calc_identical) ;
opt "-t" dep tree_sc;
opt "-a" dep faa;
......
lib/msd.ml
View file @ b1db8894
......@@ -10,29 +10,29 @@ let msd ?(descr="") ~e ~(faa : aminoacid_fasta file) ~(tree_sc : _ file) : [`msd
let tree_nw = dest // "tree.nw" in
let out = dest // "out.tsv" in
let fa_tmp = tmp // "out.tsv" in
Workflow.shell ~descr:("convergence_detection.run_msd."^descr) [
Workflow.shell ~descr:("convergence_detection.run_msd."^descr) ~img [
mkdir_p dest;
mkdir_p tmp;
(*./msd -t 1 -o <nom fichier de sortie> -e 0.05 <phylogénie Newick> <table caractère convergent> <fichier de simulation fasta> *)
cmd "python" ~img [
cmd "python" [
file_dump (string Scripts.parse_input_msd) ;
opt "-i" dep tree_sc;
opt "-o" ident tree_nw;
opt "-m" ident map_table;
];
cmd "cp" ~img [
cmd "cp" [
dep faa;
ident fa_tmp
];
cmd "cat" ~img [
cmd "cat" [
ident fa_tmp
];
cmd "grep" ~img [
cmd "grep" [
string "-c";
string "\">\"";
ident fa_tmp
];
cmd "msd" ~img [
cmd "msd" [
opt "-t" int 1;
opt "-o" ident out ;
opt "-e" float e ;
......@@ -43,8 +43,8 @@ let msd ?(descr="") ~e ~(faa : aminoacid_fasta file) ~(tree_sc : _ file) : [`msd
]
let results run_msd : text file =
Workflow.shell ~descr:"convergence_detection.parse_msd" [
cmd "python" ~img [
Workflow.shell ~descr:"convergence_detection.parse_msd" ~img [
cmd "python" [
file_dump (string Scripts.parse_output_msd) ;
opt "-i" dep (Workflow.select run_msd ["out.tsv"]);
opt "-o" ident dest;
......
lib/multinomial.ml
View file @ b1db8894
......@@ -5,8 +5,8 @@ open File_formats
let multinomial ?(descr="") ~(tree_sc:_ file) ~(faa:aminoacid_fasta file) () : text file =
let img = Env.env_py in
Workflow.shell ~descr:("calc_multinomial."^descr) [
cmd "python" ~img [
Workflow.shell ~descr:("calc_multinomial."^descr) ~img [
cmd "python" [
file_dump (string Scripts.calc_multinomial) ;
opt "-t" dep tree_sc;
opt "-a" dep faa;
......
lib/pcoc.ml
View file @ b1db8894
......@@ -6,8 +6,8 @@ open File_formats
let img = Env.env_pcoc
let pcoc ?(descr = "") ?plot_complete ?gamma ?catx_est ?max_gap_per_pos ?max_gap_per_conv_leaf ~(faa:aminoacid_fasta file) ~(tree:_ workflow) (): [`pcoc] directory =
Workflow.shell ~descr:("convergence_detection.pcoc."^descr) [
cmd "pcoc_det.py" ~img [
Workflow.shell ~descr:("convergence_detection.pcoc."^descr) ~img [
cmd "pcoc_det.py" [
opt "-t" dep tree;
opt "-m" string "-";
opt "-aa" dep faa ;
......@@ -42,9 +42,9 @@ let pcoc_v2 ?(descr = "") ?gamma ~(aa_profiles:aa_profiles) ~(faa:aminoacid_fast
| `Physic_properties -> opt "-est_profiles" ident tmp_profiles
in
Workflow.shell ~descr:("convergence_detection.pcoc_v2."^descr) [
Workflow.shell ~descr:("convergence_detection.pcoc_v2."^descr) ~img:img_v2 [
cmd "cat" ~stdout:tmp_profiles [(file_dump (string Scripts.physic_properties_profiles))];
cmd "pcoc_det.py" ~img:img_v2 [
cmd "pcoc_det.py" [
opt "-t" dep tree;