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LCSB-BioCore
COBREXA.jl
Commits
17c91878
Unverified
Commit
17c91878
authored
Jan 10, 2022
by
Miroslav Kratochvil
🚴
Committed by
GitHub
Jan 10, 2022
Browse files
Merge pull request #553 from LCSB-BioCore/mk-explain-ko-mod
explain the multi-gene knockouts better
parents
221fd108
19a68da0
Pipeline
#51182
failed with stages
in 5 minutes and 13 seconds
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src/analysis/modifications/knockout.jl
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17c91878
...
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@@ -2,7 +2,19 @@
knockout(gene_ids::Vector{String})
A modification that zeroes the bounds of all reactions that would be knocked
out by the specified genes (effectively disables the reactions).
out by the combination of specified genes (effectively disabling the
reactions).
A slightly counter-intuitive behavior may occur if knocking out multiple genes:
Because this only changes the reaction bounds, multiple gene knockouts _must_
be specified in a single call to [`knockout`](@ref), because the modifications
have no way to remember which genes are already knocked out and which not.
In turn, having a reaction that can be catalyzed either by Gene1 or by Gene2,
specifying `modifications = [knockout(["
Gene1
", "
Gene2
"])]` does indeed disable
the reaction, but `modifications = [knockout("
Gene1
"), knockout("
Gene2
")]` does
_not_ disable the reaction (although reactions that depend either only on Gene1
or only on Gene2 are disabled).
"""
knockout
(
gene_ids
::
Vector
{
String
})
=
(
model
,
optmodel
)
->
_do_knockout
(
model
,
optmodel
,
gene_ids
)
...
...
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