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Introduction Version

Medium table importer

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

Culture medium table importer

MediumTableImporter class

Allows to import a csv or xls file and create a MediumTable object resource. The MediumTable is a table representing a culture medium composition.

Your file must have:

  • a column with the compound name
  • a column with the chebi id

For example:

entity chebi_id
2-oxoglutarate CHEBI:16810
glutamine CHEBI:18050

Input

File

Output

Medium table
Table of culture medium composition

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

entity_column

Optional

The name of the column containing the entity names

Type : stringDefault value : entity

chebi_column

Optional

The name of the column containing the list of chebi ids

Type : stringDefault value : chebi_id