sbmlsim.combine.sedml.data

Reading NUML, CSV and TSV data from DataDescriptions

Module Contents

Classes

DataDescriptionParser

Class for parsing DataDescriptions.

Attributes

logger

sbmlsim.combine.sedml.data.logger

class sbmlsim.combine.sedml.data.DataDescriptionParser

Bases: object

Class for parsing DataDescriptions.

FORMAT_URN = urn:sedml:format:

FORMAT_NUML = urn:sedml:format:numl

FORMAT_CSV = urn:sedml:format:csv

FORMAT_TSV = urn:sedml:format:tsv

SUPPORTED_FORMATS

classmethod parse(cls, dd, workingDir=None)

Parses single DataDescription.

Returns dictionary of data sources {DataSource.id, slice_data}

Parameters

• dd (libsedml.SedDataDescription) – SED-ML DataDescription

• workingDir – workingDir relative to which the sources are resolved

Returns

Return type

Dict[str, pandas.Series]

classmethod _determine_format(cls, source_path, format=None)

Parameters

• source_path – path of file

• format – format given in the DataDescription

Returns

classmethod _load_csv(cls, path)

Read CSV data from file.

Parameters

path – path of file

Returns

returns pandas DataFrame with data

classmethod _load_tsv(cls, path)

Read TSV data from file.

Parameters

path – path of file

Returns

returns pandas DataFrame with data

classmethod _load_sv(cls, path, separator)

Helper function for loading data file from given source.

CSV files must have a header. Handles file and online resources.

Parameters

path – path of file.

Returns

pandas data frame