mcdoe: main.jl annotate

annotate main.jl @ 1:4a5c94d1d8bb draft

planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit a920127294bcfcb708881e28144a77a5c10d46d2

author	padge
date	Wed, 31 Aug 2022 12:13:10 +0000
parents	cc0957c46408
children	d5832ac370e3

rev	line source
0 cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	1 using Pkg
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	2 Pkg.add("Plots");
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	3 Pkg.add("Distributions");
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	4 Pkg.add("LinearAlgebra");
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	5 Pkg.add("Combinatorics");
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	6 Pkg.add("BioCCP");
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	7 Pkg.add("ArgParse");
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	8 Pkg.add("XLSX");
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	9 Pkg.add("DataFrames");
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	10 Pkg.add("Weave");
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	11 Pkg.add("DataStructures");
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	12 Pkg.add("PrettyTables");
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	13
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	14 using Random
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	15 using Plots
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	16 using Distributions
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	17 using LinearAlgebra
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	18 using Combinatorics
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	19 using BioCCP
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	20 using ArgParse
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	21 using XLSX
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	22 using DataFrames
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	23 using Weave
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	24 using DataStructures
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	25 using PrettyTables
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	26
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	27 global current_dir = pwd()
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	28 include("MultiplexCrisprDOE.jl");
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	29
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	30 function main(args)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	31
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	32 aps = ArgParseSettings("MultiplexCrisprDOE")
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	33
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	34 @add_arg_table! aps begin
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	35 "gfd" #, "gRNA_freq_dist"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	36 action = :command # adds a command which will be read from an argument
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	37 help = "gRNA/Cas9 frequencies"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	38 "ged" #, "gRNA_edit_dist"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	39 action = :command
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	40 help = "gRNA/Cas9 editing efficiencies"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	41 "sim" # simulation
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	42 action = :command
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	43 help = "simulation-based approaches for computing the minimal plant library size that guarantees full combinatorial coverage (and other relevant statistics)"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	44 "ccp" # bioccp
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	45 action = :command
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	46 help = "BioCCP-based approaches for computing the minimal plant library size that guarantees full combinatorial coverage (and other relevant statistics)"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	47 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	48
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	49 @add_arg_table! aps["gfd"] begin # add command arg_table: same as usual, but invoked on s["grna"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	50 "m"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	51 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	52 help = "plant library size"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	53 "sd"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	54 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	55 help = "the standard deviation on the gRNA abundances (in terms of absolute or relative frequency)"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	56 "l"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	57 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	58 help = "minimal gRNA abundance (in terms of absolute or relative frequency)"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	59 "u"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	60 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	61 help = "maximal gRNA abundance (in terms of absolute or relative frequency)"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	62 "n" #, "--n_gRNA_total"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	63 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	64 help = "the total number of gRNAs in the experiment"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	65 "--normalize"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	66 action = :store_true
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	67 # arg_type = Bool
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	68 # default = true
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	69 help = "if provided, the gRNA abundances (absolute frequencies) are converted into relative frequencies"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	70 "--visualize"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	71 action = :store_true
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	72 # arg_type = Bool
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	73 # default = false
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	74 help = "if provided, a histogram of all gRNA abundances is plotted"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	75 "--out_file"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	76 arg_type = String
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	77 default = "gRNA_reads"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	78 help = "Output excel file prefix"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	79 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	80
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	81 @add_arg_table! aps["ged"] begin # add command arg_table: same as usual, but invoked on s["grna"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	82 "f_act"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	83 arg_type = Float16
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	84 help = "fraction of all gRNAs that is active"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	85 "eps_edit_act"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	86 arg_type = Float16
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	87 help = "Average genome editing efficiency for active gRNAs - mean of the genome editing efficiency distribution for active gRNAs"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	88 "eps_edit_inact"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	89 arg_type = Float16
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	90 help = "Average genome editing efficiency for inactive gRNAs - mean of the genome editing efficiency distribution for inactive gRNAs"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	91 "sd_act"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	92 arg_type = Float16
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	93 help = "standard deviation of the genome editing efficiency distributions for active and inactive gRNAs"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	94 "n_gRNA_total"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	95 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	96 help = "the total number of gRNAs in the experiment"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	97 "--visualize"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	98 action = :store_true
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	99 # arg_type = Bool
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	100 # default = false
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	101 help = "if provided a histogram of all genome editing efficiency is plotted"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	102 "--out_file"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	103 arg_type = String
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	104 default = "gRNA_edit"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	105 help = "Output excel file prefix"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	106 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	107
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	108 @add_arg_table! aps["sim"] begin
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	109 "M" #, "--mode"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	110 # action = :command
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	111 # dest_name = "M"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	112 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	113 range_tester = x -> 1 <= x <= 4
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	114 help = """Select simulation mode (1: simulate_Nₓ₁; 2: simulate_Nₓ₂; 3: simulate_Nₓ₃; 4: simulate_Nₓ₂_countKOs)"""
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	115 "x"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	116 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	117 help = "number of target genes in the experiment"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	118 "g"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	119 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	120 help = "number of gRNAs designed per target gene"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	121 "r"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	122 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	123 help = "number of gRNA sequences per combinatorial gRNA/Cas construct"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	124 "t"#, "--n_gRNA_total"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	125 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	126 help = "total number of gRNAs in the experiment"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	127 "f"#, "--p_gRNA_freq"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	128 arg_type = String #Vector{Float64}
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	129 help = "vector with relative frequencies for all gRNAs in the construct library (normalized!)"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	130 "e"#, "--p_gRNA_edit"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	131 arg_type = String #Vector{Float64}
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	132 help = "vector with genome editing efficiencies for all gRNAs"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	133 "E"#, "--ϵ_KO"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	134 arg_type=Float16
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	135 help = "global knockout efficiency; fraction of mutations leading to effective gene knockout"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	136 "--i", "--iter"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	137 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	138 default = 500
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	139 help = "number of CRISPR/Cas experiments that are simulated"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	140 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	141
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	142 @add_arg_table! aps["ccp"] begin
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	143 "M"#, "--mode"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	144 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	145 range_tester = x -> 1 <= x <= 9
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	146 help = """Select BioCCP mode (1: BioCCP_Nₓ₁; 2: BioCCP_Nₓ₂; 3: BioCCP_Nₓ₃; 4: BioCCP_Pₓ₁; 5: BioCCP_Pₓ₂ ;
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	147 6: BioCCP_Pₓ₃; 7: BioCCP_γₓ₁; 8: BioCCP_γₓ₂; 9: BioCCP_γₓ₃)"""
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	148 "x"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	149 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	150 help = "number of target genes in the experiment"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	151 "N"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	152 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	153 help = "(Minimum) plant library size"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	154 "--s", "--step"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	155 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	156 default = 5
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	157 range_tester = x -> 1 <= x <= 10
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	158 help = "Step size for plant library size (optional for calculating expected combinatorial coverage / plant library size)"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	159 "--MN", "--max_pl_size"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	160 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	161 default = 4000
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	162 help = "Maximum plant library size (optional for calculating expected combinatorial coverage / plant library size)"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	163 "g"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	164 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	165 help = "number of gRNAs designed per target gene"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	166 "r"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	167 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	168 help = "number of gRNA sequences per combinatorial gRNA/Cas construct"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	169 "t"#, "--n_gRNA_total"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	170 arg_type = Int
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	171 help = "total number of gRNAs in the experiment"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	172 "f"#, "--p_gRNA_freq"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	173 arg_type = String #Vector{Float64}
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	174 help = "File containing vector with relative frequencies for all gRNAs in the construct library (normalized!)"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	175 "e"#, "--p_gRNA_edit"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	176 arg_type = String #Vector{Float64}
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	177 help = "File containing vector with genome editing efficiencies for all gRNAs"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	178 "E"#, "--ϵ_KO"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	179 arg_type=Float16
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	180 help = "global knockout efficiency; fraction of mutations leading to effective gene knockout"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	181 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	182
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	183 parsed_args = parse_args(args, aps)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	184 command_args = parsed_args[parsed_args["%COMMAND%"]]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	185 println(command_args)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	186
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	187 tool_info = OrderedDict()
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	188 args_info = OrderedDict()
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	189 grna_dict = Dict()
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	190 out_dict = Dict()
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	191 if parsed_args["%COMMAND%"] == "gfd"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	192 tool_info["method"] = "gRNA_ frequency _distribution"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	193 tool_info["description"] = "Generates vector with frequencies in the combinatorial "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	194 "gRNA/Cas9 construct library for all gRNAs"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	195 tool_info["mode"] = ""
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	196 tool_info["mode_description"] = ""
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	197 args_info["Plant library size"] = command_args["m"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	198 args_info["SD on the gRNA abundances"] = command_args["sd"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	199 args_info["Minimal gRNA abundance"] = command_args["l"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	200 args_info["Maximal gRNA abundance"] = command_args["u"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	201 args_info["Total number of gRNAs"] = command_args["n"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	202 args_info["Convert gRNA abundances to relative frequencies"] = string(command_args["normalize"])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	203 args_info["Plot gRNA abundances"] = string(command_args["visualize"])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	204
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	205 m = command_args["m"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	206 sd = command_args["sd"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	207 l = command_args["l"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	208 u = command_args["u"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	209 n_gRNA_total = command_args["n"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	210 norm = command_args["normalize"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	211 viz = command_args["visualize"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	212
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	213 println(string(norm))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	214 println(string(viz))
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	215
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	216 p_gRNA_reads = gRNA_frequency_distribution(m, sd, l, u, n_gRNA_total; normalize = norm, visualize = false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	217 grna_dict["p_gRNA_reads"] = p_gRNA_reads
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	218
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	219 # println(p_gRNA_reads)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	220 # write to excel file
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	221 fn = command_args["out_file"] * ".xlsx"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	222 labels = ["gRNA_read"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	223 columns = Vector()
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	224 push!(columns, p_gRNA_reads)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	225 XLSX.openxlsx(fn, mode="w") do xf
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	226 sheet = xf[1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	227 XLSX.writetable!(sheet, columns, labels)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	228 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	229
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	230 out_dict["output file"] = fn
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	231
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	232 elseif parsed_args["%COMMAND%"] == "ged"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	233 tool_info["method"] = "gRNA_ edit _distribution"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	234 tool_info["description"] = "Generates vector with genome editing efficiencies "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	235 "for all the gRNAs in the experiment"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	236 tool_info["mode"] = ""
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	237 tool_info["mode_description"] = ""
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	238 args_info["Fraction of active gRNAs"] = command_args["f_act"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	239 args_info["Average genome editing efficiency of active gRNAs"] = command_args["eps_edit_act"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	240 args_info["Average genome editing efficiency of inactive gRNAs"] = command_args["eps_edit_inact"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	241 args_info["Standard deviation"] = command_args["sd_act"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	242 args_info["Total number of gRNAs"] = command_args["n_gRNA_total"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	243 args_info["Plot genome editing efficiency"] = string(command_args["visualize"])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	244
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	245 f_act = command_args["f_act"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	246 eps_edit_act = command_args["eps_edit_act"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	247 eps_edit_inact = command_args["eps_edit_inact"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	248 sd_act = command_args["sd_act"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	249 n_gRNA_total = command_args["n_gRNA_total"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	250 viz = ["visualize"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	251
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	252 p_gRNA_edit = gRNA_edit_distribution(f_act, eps_edit_act, eps_edit_inact, sd_act, n_gRNA_total; visualize=false)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	253 grna_dict["p_gRNA_edit"] = p_gRNA_edit
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	254 # write to excel file
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	255 fn = command_args["out_file"] * ".xlsx"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	256 labels = ["gRNA_edit_efficiency"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	257 columns = Vector()
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	258 push!(columns, p_gRNA_edit)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	259 XLSX.openxlsx(fn, mode="w") do xf
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	260 sheet = xf[1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	261 XLSX.writetable!(sheet, columns, labels)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	262 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	263
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	264 out_dict["output file"] = fn
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	265
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	266 elseif parsed_args["%COMMAND%"] == "sim" \|\| parsed_args["%COMMAND%"] == "ccp"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	267
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	268 filename = command_args["f"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	269 sheet = 1
1 4a5c94d1d8bb planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit a920127294bcfcb708881e28144a77a5c10d46d2 padge parents: 0 diff changeset	270 data = DataFrame(XLSX.readtable(filename, sheet))
0 cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	271 p_gRNA_reads = data[!,"gRNA_read"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	272 p_gRNA_reads_normalized = p_gRNA_reads/sum(p_gRNA_reads) # normalize
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	273 f = p_gRNA_reads_normalized
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	274 grna_dict["p_gRNA_reads"] = f
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	275
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	276 filename = command_args["e"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	277 sheet = 1
1 4a5c94d1d8bb planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit a920127294bcfcb708881e28144a77a5c10d46d2 padge parents: 0 diff changeset	278 data = DataFrame(XLSX.readtable(filename, sheet))
0 cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	279 p_gRNA_edit = data[!,"gRNA_edit_efficiency"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	280 e = p_gRNA_edit
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	281 grna_dict["p_gRNA_edit"] = e
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	282
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	283 x = command_args["x"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	284 g = command_args["g"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	285 r = command_args["r"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	286 t = command_args["t"] # n_gRNA_total
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	287 E = command_args["E"] # ϵ_KO # iter = 500
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	288
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	289 args_info["# of target genes in the experiment"] = command_args["x"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	290 args_info["# of gRNAs designed per target gene"] = command_args["g"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	291 args_info["# of gRNAs / combi gRNA/Cas construct"] = command_args["r"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	292 args_info["Total number of gRNAs"] = command_args["t"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	293 args_info["Relative frequencies for all gRNAs"] = command_args["f"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	294 args_info["Genome editing efficiencies for all gRNAs"] = command_args["e"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	295 args_info["Global knockout efficiency"] = command_args["E"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	296
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	297 if parsed_args["%COMMAND%"] == "sim"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	298 tool_info["method"] = "simulation"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	299 tool_info["description"] = "simulation-based approaches for computing the minimal "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	300 "plant library size that guarantees full combinatorial "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	301 "coverage (and other relevant statistics)"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	302 i = command_args["i"] # iter = 500
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	303 args_info["# of simulated experiments"] = command_args["i"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	304
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	305 if command_args["M"] == 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	306 tool_info["mode"] = "simulate_Nx1"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	307 tool_info["mode_description"] = "Computes the expected value and the standard deviation "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	308 "of the minimal plant library size for full coverage of "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	309 "all single gene knockouts (E[Nx,1] and σ[Nx,1]) using simulation"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	310 E_sim, sd_sim = simulate_Nₓ₁(x, g, r, t, f, e, E; iter=i)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	311 out_dict["E_sim"] = E_sim
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	312 out_dict["sd_sim"] = sd_sim
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	313
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	314 elseif command_args["M"] == 2
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	315 tool_info["mode"] = "simulate_Nx2"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	316 tool_info["mode_description"] = "Computes the expected value and the standard deviation of "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	317 "the minimal plant library size for full coverage of "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	318 "all pairwise combinations of gene knockouts in a "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	319 "multiplex CRISPR/Cas experiment (E[Nx,2] and σ[Nx,2]) using simulation"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	320
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	321 E_sim, sd_sim = simulate_Nₓ₂(x, g, r, t, f, e, E; iter=i)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	322 out_dict["E_sim"] = E_sim
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	323 out_dict["sd_sim"] = sd_sim
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	324
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	325 elseif command_args["M"] == 3
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	326 tool_info["mode"] = "simulate_Nx3"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	327 tool_info["mode_description"] = "Computes the expected value and the standard deviation of "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	328 "the minimal plant library size for full coverage of "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	329 "all triple combinations of gene knockouts in a "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	330 "multiplex CRISPR/Cas experiment (E[Nx,3] and σ[Nx,3]) using simulation"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	331
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	332 E_sim, sd_sim = simulate_Nₓ₃(x, g, r, t, f, e, E; iter=i)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	333 out_dict["E_sim"] = E_sim
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	334 out_dict["sd_sim"] = sd_sim
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	335
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	336 elseif command_args["M"] == 4
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	337 tool_info["mode"] = "simulate_Nx2_countKOs"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	338 tool_info["mode_description"] = "Counts of the number of knockouts per plant in the experiment"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	339
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	340 n_KOs_vec = simulate_Nₓ₂_countKOs(x, g, r, t, f, e, E; iter=i)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	341 out_dict["n_KOs_vec"] = n_KOs_vec
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	342
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	343 # write to excel file
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	344 fn = "countKOs.xlsx"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	345 labels = ["countKOs"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	346 columns = Vector()
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	347 push!(columns, n_KOs_vec)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	348 XLSX.openxlsx(fn, mode="w") do xf
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	349 sheet = xf[1]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	350 XLSX.writetable!(sheet, columns, labels)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	351 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	352
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	353 out_dict["output file"] = fn
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	354
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	355 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	356
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	357 elseif parsed_args["%COMMAND%"] == "ccp"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	358 tool_info["method"] = "BioCCP"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	359 tool_info["description"] = "BioCCP-based approaches for computing the minimal "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	360 "plant library size that guarantees full combinatorial "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	361 "coverage (and other relevant statistics)"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	362
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	363 N = command_args["N"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	364 if haskey(command_args,"s") && haskey(command_args,"MN")
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	365 s = command_args["s"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	366 MN = command_args["MN"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	367 args_info["Step size"] = command_args["s"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	368 args_info["Maximum Plant library size"] = command_args["MN"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	369 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	370 args_info["Plant library size"] = command_args["N"]
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	371
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	372
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	373 if command_args["M"] == 1
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	374 tool_info["mode"] = "BioCCP_Nx1"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	375 tool_info["mode_description"] = "Computes the expected value and the standard deviation of "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	376 "the minimal plant library size for full coverage of all "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	377 "single gene knockouts (E[Nx,1] and σ[Nx,1]) using BioCCP"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	378
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	379 E_sim, sd_sim = BioCCP_Nₓ₁(x, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	380 out_dict["E_sim"] = E_sim
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	381 out_dict["sd_sim"] = sd_sim
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	382
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	383 elseif command_args["M"] == 2
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	384 tool_info["mode"] = "BioCCP_Nx2"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	385 tool_info["mode_description"] = "Computes the expected value and the standard deviation of "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	386 "the minimal plant library size for full coverage of all "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	387 "pairwise combinations of gene knockouts in a multiplex "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	388 "CRISPR/Cas experiment (E[Nx,2] and σ[Nx,2]) using BioCCP"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	389
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	390 E_sim, sd_sim = BioCCP_Nₓ₂(x, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	391 out_dict["E_sim"] = E_sim
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	392 out_dict["sd_sim"] = sd_sim
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	393
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	394 elseif command_args["M"] == 3
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	395 tool_info["mode"] = "BioCCP_Nx3"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	396 tool_info["mode_description"] = "Computes the expected value and the standard deviation of "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	397 "the minimal plant library size for full coverage of all triple combinations of "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	398 "gene knockouts in a multiplex CRISPR/Cas experiment (E[Nx,3] and σ[Nx,3]) using BioCCP"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	399
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	400 E_sim, sd_sim = BioCCP_Nₓ₃(x, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	401 out_dict["E_sim"] = E_sim
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	402 out_dict["sd_sim"] = sd_sim
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	403
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	404 elseif command_args["M"] == 4
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	405 tool_info["mode"] = "BioCCP_Px1"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	406 tool_info["mode_description"] = "Computes the probability of full coverage of "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	407 "all single gene knockouts (Px,1) for an experiment with given "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	408 "plant library size using BioCCP"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	409
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	410 if s != nothing && MN != nothing
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	411 plant_library_sizes = N:s:MN
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	412 else
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	413 plant_library_sizes = N
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	414 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	415 PT = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	416 global N_95_P = nothing
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	417 for N in plant_library_sizes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	418 Pr = BioCCP_Pₓ₁(x, N, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	419 push!(PT, Pr)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	420 if Pr < 0.95
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	421 N_95_P = N
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	422 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	423 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	424 # P = BioCCP_Pₓ₁(x, N, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	425 out_dict["P_sim"] = PT
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	426 out_dict["N_95_P"] = N_95_P
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	427 out_dict["pls"] = plant_library_sizes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	428
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	429 elseif command_args["M"] == 5
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	430 tool_info["mode"] = "BioCCP_Px2"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	431 tool_info["mode_description"] = "Computes the probability of full coverage of "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	432 "all pairwise combinations of gene knockouts (Px,2) "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	433 "for an experiment with given plant library size using BioCCP"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	434
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	435 if s != nothing && MN != nothing
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	436 plant_library_sizes = N:s:MN
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	437 else
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	438 plant_library_sizes = N
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	439 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	440 PT = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	441 global N_95_P = nothing
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	442 for N in plant_library_sizes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	443 Pr = BioCCP_Pₓ₂(x, N, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	444 push!(PT, Pr)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	445 if Pr < 0.95
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	446 N_95_P = N
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	447 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	448 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	449 # P = BioCCP_Pₓ₂(x, N, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	450 out_dict["P_sim"] = PT
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	451 out_dict["N_95_P"] = N_95_P
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	452 out_dict["pls"] = plant_library_sizes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	453
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	454 elseif command_args["M"] == 6
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	455 tool_info["mode"] = "BioCCP_Px3"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	456 tool_info["mode_description"] = "Computes the probability of full coverage of all "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	457 "triple combinations of gene knockouts (Px,3) for an experiment "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	458 "with given plant library size using BioCCP"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	459
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	460 if s != nothing && MN != nothing
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	461 plant_library_sizes = N:s:MN
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	462 else
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	463 plant_library_sizes = N
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	464 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	465 PT = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	466 global N_95_P = nothing
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	467 for N in plant_library_sizes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	468 Pr = BioCCP_Pₓ₃(x, N, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	469 push!(PT, Pr)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	470 if Pr < 0.95
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	471 N_95_P = N
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	472 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	473 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	474 # P = BioCCP_Pₓ₃(x, N, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	475 out_dict["P_sim"] = PT
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	476 out_dict["N_95_P"] = N_95_P
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	477 out_dict["pls"] = plant_library_sizes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	478
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	479 elseif command_args["M"] == 7
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	480 tool_info["mode"] = "BioCCP_γx1"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	481 tool_info["mode_description"] = "Computes the expected coverage of all "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	482 "single gene knockouts (E[γx,1]) for an experiment "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	483 "with given plant library size using BioCCP"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	484 if s != nothing && MN != nothing
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	485 plant_library_sizes = N:s:MN
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	486 else
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	487 plant_library_sizes = N
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	488 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	489 exp_cov = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	490 global N_95 = nothing
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	491 for N in plant_library_sizes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	492 E_cov = BioCCP_γₓ₁(x, N, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	493 push!(exp_cov, E_cov)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	494 if E_cov < 0.95
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	495 N_95 = N
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	496 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	497 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	498 # E_sim, sd_sim = BioCCP_γₓ₁(x, N, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	499 out_dict["E_cov"] = exp_cov
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	500 out_dict["N_95"] = N_95
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	501 out_dict["pls"] = plant_library_sizes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	502
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	503 elseif command_args["M"] == 8
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	504 tool_info["mode"] = "BioCCP_γx2"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	505 tool_info["mode_description"] = "Computes the expected coverage of all "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	506 "pairwise combinations of gene knockouts (E[γx,2]) for an experiment with "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	507 "given plant library size using BioCCP"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	508
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	509 if s != nothing && MN != nothing
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	510 plant_library_sizes = N:s:MN
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	511 else
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	512 plant_library_sizes = N
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	513 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	514 exp_cov = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	515 global N_95 = nothing
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	516 for N in plant_library_sizes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	517 E_cov = BioCCP_γₓ₂(x, N, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	518 push!(exp_cov, E_cov)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	519 if E_cov < 0.95
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	520 N_95 = N
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	521 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	522 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	523 # E_sim, sd_sim = BioCCP_γₓ₂(x, N, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	524 out_dict["E_cov"] = exp_cov
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	525 out_dict["N_95"] = N_95
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	526 out_dict["pls"] = plant_library_sizes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	527
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	528 elseif command_args["M"] == 9
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	529 tool_info["mode"] = "BioCCP_γx3"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	530 tool_info["mode_description"] = "Computes the expected coverage of all "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	531 "triple combinations of gene knockouts (E[γx,3]) for an experiment with "*
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	532 "given plant library size using BioCCP"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	533
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	534 if s != nothing && MN != nothing
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	535 plant_library_sizes = N:s:MN
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	536 else
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	537 plant_library_sizes = N
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	538 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	539 exp_cov = []
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	540 global N_95 = nothing
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	541 for N in plant_library_sizes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	542 E_cov = BioCCP_γₓ₃(x, N, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	543 push!(exp_cov, E_cov)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	544 if E_cov < 0.95
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	545 N_95 = N
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	546 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	547 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	548 # E_sim, sd_sim = BioCCP_γₓ₃(x, N, g, r, t, f, e, E)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	549 out_dict["E_cov"] = exp_cov
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	550 out_dict["N_95"] = N_95
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	551 out_dict["pls"] = plant_library_sizes
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	552
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	553 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	554 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	555 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	556
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	557 println(parsed_args)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	558 println("Parsed args:")
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	559 for (key,val) in parsed_args
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	560 println(" $key => $(repr(val))")
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	561 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	562 println()
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	563 println("Command: ", parsed_args["%COMMAND%"])
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	564 # h1 = histogram(grna_dict["p_gRNA_reads"], label="",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	565 # xlabel="Number of reads per gRNA",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	566 # linecolor="white",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	567 # normalize=:probability,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	568 # xtickfontsize=10,ytickfontsize=10,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	569 # color=:mediumturquoise, size=(600,350), bins = 25,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	570 # ylabel="Relative frequency",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	571 # title="gRNA frequency distribution")
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	572
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	573 # h2 = histogram(grna_dict["p_gRNA_edit"],
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	574 # normalize = :probability,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	575 # linecolor = "white",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	576 # label="",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	577 # color=:turquoise4,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	578 # xtickfontsize=10,ytickfontsize=10, xlim = (0, 1),
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	579 # xticks=(0:0.1:1),
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	580 # bins = 150,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	581 # xlabel="gRNA editing efficiency",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	582 # ylabel="Relative frequency",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	583 # title="gRNA genome editing effiency distribution")
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	584
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	585 # p_plot = plot(plant_library_sizes, Pₓ₂, label="Pₓ₂",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	586 # title="Probability of full combinatorial coverage with respect to plant library size",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	587 # xlabel="N", ylabel="Pₓₖ",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	588 # xticks = (0:500:50000, string.(0:500:50000)),
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	589 # size=(900,400), color=:turquoise4, linewidth=2)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	590 # hline!([0.95], linestyle=:dash, color=:grey, label="Pₓₖ = 0.95", legend=:bottomright)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	591
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	592 # exp_plot = plot(plant_library_sizes, expected_γₓ₂,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	593 # label="E[γₓ₂]", title="Expected combinatorial coverage w.r.t. plant library size",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	594 # xlabel="N", ylabel="E[γₓₖ]",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	595 # xticks = (0:500:50000, string.(0:500:50000)),
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	596 # size=(800,400), color=:turquoise4, linewidth=2)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	597 # hline!([0.95], linestyle=:dash, color=:grey, label="E[γₓₖ] = 0.95", legend=:bottomright)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	598
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	599
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	600 ENV["GKSwstype"]="nul"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	601 weave(string(@__DIR__) * "/report.jmd",
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	602 args = (parsed_args = parsed_args,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	603 tool_info = tool_info,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	604 args_info = args_info,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	605 grna_dict = grna_dict,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	606 #h1 = h1, h2 = h2,
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	607 output = out_dict);
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	608 doctype = "md2html", out_path = :pwd)
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	609 ENV["GKSwstype"]="gksqt"
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	610 end
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	611
cc0957c46408 "planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit b6c1b1860eee82b06ed4a592d1f9eee6886be318-dirty" padge parents: diff changeset	612 main(ARGS)

Mercurial > repos > padge > mcdoe

annotate main.jl @ 1:4a5c94d1d8bb draft