Task to transform table into Flux table
TransformerFluxTable class
Allows to transform a Table with the right columns names to create a Flux Table.
The Flux Table
is a generic table of entity IDs (CheBI IDs, Rhea IDs, EC Numbers, User-defined IDs, ...).
It's a table of experimentally measured (or user-defined) metabolic fluxes
The header of you Table can be the following: "reaction_id,target,lower_bound,upper_bound,confidence_score"
- The first column is the list of
reaction ids
and/orec numbers
[required]
. They uniquely identify each reaction of a network. - The next columns are:
- target: the value of the flux measured experimentally (e.g.
mol/gDW/h
)[required]
- upper_bound: the upper bound of the flux (e.g.
mol/gDW/h
)[required]
- lower_bound: the lower bound of the flux (e.g.
mol/gDW/h
)[required]
- confidence_score: the confidence score of the flux
[required]
- target: the value of the flux measured experimentally (e.g.
For example:
id | target | lower_bound | lower_bound | confidence_score |
---|---|---|---|---|
RHEA_62620_1_11_1_24 | 0.234 | 0 | 1000 | 1.0 |
6.3.1.2 | -1.234 | -5 | 0 | 1.0 |
This Task manages multiple simulations. So if you have different values of target,lower_bound,upper_bound; set them as a list like this: reaction_id,target,lower_bound,upper_bound,confidence_score reaction1,"[0.04, 0.045, 0.035]","[0.01, 0.008, -0.02]","[0.03, -0.003, 0.001]","[1, 1, 1]"
Input
Output
Configuration
entity_id_column
The name of the column of entity ids
string
id
target_column
The name of the target column
string
target
lower_bound_column
The name of the lower-bound column
string
lower_bound
upper_bound_column
The name of the upper-bound column
string
upper_bound
confidence_score_column
The name of the confidence score column
string
confidence_score