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LCSB-BioCore
COBREXA.jl
Commits
e20ba0ec
Unverified
Commit
e20ba0ec
authored
Apr 27, 2022
by
Miroslav Kratochvil
🚴
Committed by
GitHub
Apr 27, 2022
Browse files
Merge pull request #606 from LCSB-BioCore/mo-small-fixes
Small fixes
parents
418186b1
f406440e
Pipeline
#55697
passed with stages
in 24 minutes and 30 seconds
Changes
3
Pipelines
1
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Inline
Side-by-side
src/base/types/Gene.jl
View file @
e20ba0ec
...
...
@@ -7,7 +7,6 @@ id :: String
name :: Maybe{String}
notes :: Dict{String, Vector{String}}
annotation :: Dict{String, Union{Vector{String}, String}}
molar_mass :: Maybe{Float64}
````
"""
mutable struct
Gene
...
...
@@ -15,13 +14,7 @@ mutable struct Gene
name
::
Maybe
{
String
}
notes
::
Notes
annotations
::
Annotations
molar_mass
::
Maybe
{
Float64
}
Gene
(
id
::
String
=
""
;
name
=
nothing
,
notes
=
Notes
(),
annotations
=
Annotations
(),
molar_mass
=
nothing
,
)
=
new
(
id
,
name
,
notes
,
annotations
,
molar_mass
)
Gene
(
id
::
String
=
""
;
name
=
nothing
,
notes
=
Notes
(),
annotations
=
Annotations
())
=
new
(
id
,
name
,
notes
,
annotations
)
end
src/base/types/wrappers/GeckoModel.jl
View file @
e20ba0ec
...
...
@@ -55,10 +55,10 @@ The structure contains fields `columns` that describe the contents of the
coupling columns, `coupling_row_reaction`, `coupling_row_gene_product` and
`coupling_row_mass_group` that describe correspondence of the coupling rows to
original model and determine the coupling bounds, and `inner`, which is the
original wrapped model. Note, `objective` is the objective vector of the model
,
s
pecial care needs to be taken to ensure that its length is
`n_reactions(model)
+
n_genes(model)` when the user modifies it, where
`model` is the GeckoModel in
question.
original wrapped model. Note, `objective` is the objective vector of the model
.
S
pecial care needs to be taken to ensure that its length is
the sum of
`n_reactions(model)` and `
n_genes(model)` when the user modifies it, where
`model` is the GeckoModel in
question.
Implementation exposes the split reactions (available as `reactions(model)`),
but retains the original "
simple
" reactions accessible by [`fluxes`](@ref). All
...
...
test/analysis/gecko.jl
View file @
e20ba0ec
...
...
@@ -46,8 +46,10 @@
)
prot_mass
=
sum
(
ecoli_core_gene_product_masses
[
gid
]
*
c
for
(
gid
,
c
)
in
prot_concens
)
mass_groups
=
gene_product_mass_group_dict
(
gm
,
opt_model
)
@test
isapprox
(
prot_mass
,
total_gene_product_mass
,
atol
=
TEST_TOLERANCE
)
@test
isapprox
(
prot_mass
,
mass_groups
[
"uncategorized"
],
atol
=
TEST_TOLERANCE
)
end
@testset
"GECKO small model"
begin
...
...
cylon-x
🤖
@cylon-x
mentioned in commit
6b346aa0
·
Apr 27, 2022
mentioned in commit
6b346aa0
mentioned in commit 6b346aa02bf682d5c1b2d43bbb9bc7958ae221d9
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