Phenotype table importer
Phenotype table importer importer
PhenotypeTableImporter class
Allows to import a csv or xls file and create a PhenotypeTable resource object.
The PhenotypeTable is a generic table of entity IDs (CheBI IDs, Rhea IDs, EC Numbers, User-defined IDs, ...).
Input
Output
Configuration
file_format
File format
stringauto xlsx xls csv tsv tab txt autodelimiter
Delimiter character. Only for parsing CSV files
stringauto tab space , ; autoheader
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.
intformat_header_names
If true, the column and row names are formatted to remove special characters and spaces (only '_' are allowed).
boolindex_column
Column to use as the row names. By default no index is used (i.e. index_column=-1).
int-1decimal
Character to recognize as decimal point (e.g. use ‘,’ for European/French data).
string.nrows
Number of rows to import. Useful to read piece of data.
intcomment
Character used to comment lines. Set empty to disable comment lines.
string#encoding
Encoding of the file, 'auto' for automatic detection.
stringautometadata_columns
Columns data to use to tag the rows of the table
List-1column
Metadata column to use to tag rows
stringkeep_in_table
Set True to keep the column in the final table; False otherwise
boolentity_column
The name of the column of entities
stringentitychebi_id_column
The name of the chebi id column
stringchebi_idtarget_column_name
The name of the target column
stringtargetlower_bound_column_name
The name of the lower-bound column
stringlower_boundupper_bound_column_name
The name of the upper-bound column
stringupper_boundconfidence_score_column
The name of the upper-bound column
stringconfidence_score