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Introduction Version

Transformer Flux Table

TASK
Typing name :  TASK.gws_gena.TransformerFluxTable Brick :  gws_gena v

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/or ec 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]

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

Initial table
2d excel like table

Output

Table
2d excel like table

Configuration

entity_id_column

Optional

The name of the column of entity ids

Type : stringDefault value : id

target_column

Optional

The name of the target column

Type : stringDefault value : target

lower_bound_column

Optional

The name of the lower-bound column

Type : stringDefault value : lower_bound

upper_bound_column

Optional

The name of the upper-bound column

Type : stringDefault value : upper_bound

confidence_score_column

Optional

The name of the confidence score column

Type : stringDefault value : confidence_score