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Flux table importer

IMPORTER
Typing name :  TASK.gws_gena.FluxTableImporter Brick :  gws_gena v

Metabolic flux table importer

FluxTableImporter class

Allows to import a csv or xls file and create a FluxTable resource object. The FluxTable is a generic table of entity IDs (CheBI IDs, Rhea IDs, EC Numbers, User-defined IDs, ...).

The header of you Table can be the following: "reaction_id,target,lower_bound,upper_bound,confidence_score"

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

File

Output

Flux table
Table of metabolic flux measurements

Configuration

file_format

Optional

File format

Type : stringAllowed values : auto  xlsx  xls  csv  tsv  tab  txt  Default value : auto

delimiter

Optional

Delimiter character. Only for parsing CSV files

Type : stringAllowed values : auto  tab  space  ,  ;  Default value : auto

header

Optional

Row to use as the column names. By default the first row is used (i.e. header=0). Set header=-1 to not read column names.

Type : int

format_header_names

Optional

If true, the column and row names are formatted to remove special characters and spaces (only '_' are allowed).

Type : bool

index_column

OptionalAdvanced parameter

Column to use as the row names. By default no index is used (i.e. index_column=-1).

Type : intDefault value : -1

decimal

OptionalAdvanced parameter

Character to recognize as decimal point (e.g. use ‘,’ for European/French data).

Type : stringDefault value : .

nrows

OptionalAdvanced parameter

Number of rows to import. Useful to read piece of data.

Type : int

comment

OptionalAdvanced parameter

Character used to comment lines. Set empty to disable comment lines.

Type : stringDefault value : #

encoding

OptionalAdvanced parameter

Encoding of the file, 'auto' for automatic detection.

Type : stringDefault value : auto

metadata_columns

OptionalAdvanced parameter

Columns data to use to tag the rows of the table

Type : ListMaximum occurrences number : -1

column

OptionalAdvanced parameter

Metadata column to use to tag rows

Type : string

keep_in_table

OptionalAdvanced parameter

Set True to keep the column in the final table; False otherwise

Type : boolDefault value : true

reaction_id_column

Optional

The name of the reaction id column

Type : stringDefault value : reaction_id

target_column_name

Optional

The name of the target column

Type : stringDefault value : target

lower_bound_column_name

Optional

The name of the lower-bound column

Type : stringDefault value : lower_bound

upper_bound_column_name

Optional

The name of the upper-bound column

Type : stringDefault value : upper_bound

confidence_score_column

Optional

The name of the upper-bound column

Type : stringDefault value : confidence_score