Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Handle inaccurate range number params entries #31

Merged
merged 3 commits into from
Jul 4, 2024
Merged

Handle inaccurate range number params entries #31

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
9c91ee3
handle empty results in forward_ and reverse_ _selection_next_param_r…
Denis-Titov Jul 4, 2024
f77ecdc
handle empty result in calculate_all_parameter_removal_codes_w_num_pa…
Denis-Titov Jul 4, 2024
8403657
modify range_number_params to find feasible starting equations
Denis-Titov Jul 4, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
67 changes: 47 additions & 20 deletions src/data_driven_rate_equation_selection.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -76,11 +76,26 @@ function data_driven_rate_equation_selection(
metab_names,
num_alpha_params,
)
if isempty(starting_param_removal_codes)
@error "Equations for this enzymes with $(num_param_range[1]) parameters do not exist. One reason could be that some parameters are unidentifiable based on the data so upper bound of range_number_params should be reduced. Check number of practically_unidentifiable_params with find_practically_unidentifiable_params(data, param_names)."
return
end

while isempty(starting_param_removal_codes)
num_param_range = ifelse(
forward_model_selection,
(num_param_range[1] - 1, num_param_range[end]),
(num_param_range[1] + 1, num_param_range[end])
)
if num_param_range[1] == num_param_range[end]
@error "Could not find any fesible equations for this enzyme within range_number_params"
end
println("Trying new range_number_params: $num_param_range")
starting_param_removal_codes = DataDrivenEnzymeRateEqs.calculate_all_parameter_removal_codes_w_num_params(
num_param_range[1],
all_param_removal_codes,
param_names,
param_removal_code_names,
metab_names,
num_alpha_params,
)
end

nt_param_removal_codes = starting_param_removal_codes
nt_previous_param_removal_codes = similar(nt_param_removal_codes)
Expand Down Expand Up @@ -347,11 +362,15 @@ function calculate_all_parameter_removal_codes_w_num_params(
end
nt_param_removal_codes =
[NamedTuple{param_removal_code_names}(x) for x in unique(codes_with_num_params)]
filtered_nt_param_removal_codes =
filter_param_removal_codes_to_prevent_wrong_param_combos(
nt_param_removal_codes,
metab_names,
)
if isempty(nt_param_removal_codes)
filtered_nt_param_removal_codes = NamedTuple[]
else
filtered_nt_param_removal_codes =
filter_param_removal_codes_to_prevent_wrong_param_combos(
nt_param_removal_codes,
metab_names,
)
end
return filtered_nt_param_removal_codes
end

Expand Down Expand Up @@ -454,11 +473,15 @@ function forward_selection_next_param_removal_codes(
end
nt_param_removal_codes =
[NamedTuple{param_removal_code_names}(x) for x in unique(next_param_removal_codes)]
filtered_nt_param_removal_codes =
filter_param_removal_codes_to_prevent_wrong_param_combos(
nt_param_removal_codes,
metab_names,
)
if isempty(nt_param_removal_codes)
filtered_nt_param_removal_codes = NamedTuple[]
else
filtered_nt_param_removal_codes =
filter_param_removal_codes_to_prevent_wrong_param_combos(
nt_param_removal_codes,
metab_names,
)
end
return filtered_nt_param_removal_codes
end

Expand All @@ -484,18 +507,22 @@ function reverse_selection_next_param_removal_codes(
end
nt_param_removal_codes =
[NamedTuple{param_removal_code_names}(x) for x in unique(next_param_removal_codes)]
filtered_nt_param_removal_codes =
filter_param_removal_codes_to_prevent_wrong_param_combos(
nt_param_removal_codes,
metab_names,
)
if isempty(nt_param_removal_codes)
filtered_nt_param_removal_codes = NamedTuple[]
else
filtered_nt_param_removal_codes =
filter_param_removal_codes_to_prevent_wrong_param_combos(
nt_param_removal_codes,
metab_names,
)
end
return filtered_nt_param_removal_codes
end

"""Filter removal codes to ensure that if K_S1 = Inf then all K_S1_S2 and all other K containing S1 in qssa cannot be 2, which stands for (K_S1_S2)^2 = K_S1 * K_S2"""
function filter_param_removal_codes_to_prevent_wrong_param_combos(
nt_param_removal_codes,
metab_names::Tuple{Symbol,Vararg{Symbol}}
metab_names::Tuple{Symbol,Vararg{Symbol}},
)
# ensure that if K_S1 = Inf then all K_S1_S2 and all other K containing S1 in qssa cannot be 2, which stands for (K_S1_S2)^2 = K_S1 * K_S2
if any([occursin("allo", string(key)) for key in keys(nt_param_removal_codes[1])])
Expand Down