sbol_utilities.excel_to_sbol
Module Contents
Functions
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Take an open Excel file, return an SBOL document |
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Initialize sheet configuration dictionary |
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Main wrapper: read from input file, invoke excel_to_sbol, then write to output file |
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Create a composite part from a row in the composites sheet |
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Look up a part by its displayID or its name, searching first by displayID, then by name |
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Extract metadata and build collections |
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Read a row for a basic part and turn it into SBOL Component |
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Attributes
- BASIC_PARTS_COLLECTION = BasicParts
- COMPOSITE_PARTS_COLLECTION = CompositeParts
- FINAL_PRODUCTS_COLLECTION = FinalProducts
- LINEAR_PRODUCTS_COLLECTION = LinearDNAProducts
- constraint_dict
- constraint_pattern
- excel_to_sbol(wb: openpyxl.Workbook, config: dict = None) sbol3.Document
Take an open Excel file, return an SBOL document :param wb: openpyxl pointer to an Excel file :param config: dictionary of sheet parsing configuration variables :return: Document containing all SBOL extracted from Excel sheet
- expand_configuration(values: dict) dict
Initialize sheet configuration dictionary :param values: Dictionary of overrides for defaults :return configuration with all defaults filled in
- is_RC(name)
- main()
Main wrapper: read from input file, invoke excel_to_sbol, then write to output file
- make_combinatorial_derivation(document, display_id, part_lists, reverse_complements, constraints)
- make_composite_component(display_id, part_lists, reverse_complements)
- make_composite_part(document, row, composite_parts, linear_products, final_products, config)
Create a composite part from a row in the composites sheet :param document: Document to add parts to :param row: Excel row to be processed :param composite_parts: collection of parts to add to :param linear_products: collection of linear parts to add to :param final_products: collection of final parts to add to :param config: dictionary of sheet parsing configuration variables
- make_constraint(constraint, part_list)
- part_names(specification)
- part_specifications(row, config)
- partname_to_part(doc: sbol3.Document, name_or_display_id: str)
Look up a part by its displayID or its name, searching first by displayID, then by name
- Parameters
doc – SBOL document to search
name_or_display_id – string to look up
- Returns
object if found, None if not
- read_metadata(wb: openpyxl.Workbook, doc: sbol3.Document, config: dict)
Extract metadata and build collections :param wb: Excel workbook to extract material from :param doc: SBOL document to build collections in :param config: dictionary of sheet parsing configuration variables :return: Tuple of SBOL collections for basic, composite, linear, and final parts
- reverse_complement_pattern
- row_to_basic_part(doc: sbol3.Document, row, basic_parts: sbol3.Collection, linear_products: sbol3.Collection, final_products: sbol3.Collection, config: dict, source_table: dict)
Read a row for a basic part and turn it into SBOL Component :param doc: Document to add parts to :param row: Excel row to be processed :param basic_parts: collection of parts to add to :param linear_products: collection of linear parts to add to :param final_products: collection of final parts to add to :param config: dictionary of sheet parsing configuration variables :param source_table: dictionary mapping source names to namespaces :return: None
- strip_RC(name)
- unresolved_subparts(doc: sbol3.Document, row, config)