SBGN output (indra.assemblers.sbgn.assembler)

class indra.assemblers.sbgn.assembler.SBGNAssembler(statements=None)

This class assembles an SBGN model from a set of INDRA Statements.

The Systems Biology Graphical Notation (SBGN) is a widely used graphical notation standard for systems biology models. This assembler creates SBGN models following the Process Desctiption (PD) standard, documented at: https://github.com/sbgn/process-descriptions/blob/master/UserManual/sbgn_PD-level1-user-public.pdf. For more information on SBGN, see: http://sbgn.github.io/sbgn/

Parameters

stmts (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to be assembled.

statements

A list of INDRA Statements to be assembled.

Type

list[indra.statements.Statement]

sbgn

The structure of the SBGN model that is assembled, represented as an XML ElementTree.

Type

lxml.etree.ElementTree

add_statements(stmts)

Add INDRA Statements to the assembler’s list of statements.

Parameters

stmts (list[indra.statements.Statement]) – A list of indra.statements.Statement to be added to the statement list of the assembler.

make_model()

Assemble the SBGN model from the collected INDRA Statements.

This method assembles an SBGN model from the set of INDRA Statements. The assembled model is set as the assembler’s sbgn attribute (it is represented as an XML ElementTree internally). The model is returned as a serialized XML string.

Returns

sbgn_str – The XML serialized SBGN model.

Return type

str

print_model(pretty=True, encoding='utf8')

Return the assembled SBGN model as an XML string.

Parameters

pretty (Optional[bool]) – If True, the SBGN string is formatted with indentation (for human viewing) otherwise no indentation is used. Default: True

Returns

sbgn_str – An XML string representation of the SBGN model.

Return type

bytes (str in Python 2)

save_model(file_name='model.sbgn')

Save the assembled SBGN model in a file.

Parameters

file_name (Optional[str]) – The name of the file to save the SBGN network to. Default: model.sbgn