def write_sbol(filled_library,
filled_library_metadata,
filled_description,
molecule_type=BIOPAX_DNA,
part_column="Part Name",
sequence_column="Sequence",
description_column="Description (Optional)",
role_column="Role",
length_column="length (bp)"):
"""
the function reads an excel spreadsheet and converts it into valid sbol
Parameters
----------
filled_library : DATAFRAME
Dataframe containing the library part data
filled_metadata : DATAFRAME
Dataframe containing the metadata
filled_description : DATAFRAME
Dataframe containing the description data
molecule_type : STRING, default = BIOPAX_DNA
Molecule type
part_column : STRING, default = "Part Name"
Name of the dataframe column that contains the part names
sequence_column : STRING, default = "Sequence"
Name of the dataframe column that contains the sequence
description_column : STRING, default = "Description (Optional)"
Name of the dataframe column that contains the library description
role_column : STRING, default = "Role"
Name of the dataframe column that contains the Role
length_column : STRING, default = "length (bp)"
Name of the dataframe column that contains the sequence length
Returns
-------
doc: SBOL Document
Document containing all components and sequences
Example
-------
Doc = write_sbol(filled_library, filled_library_metadata, filled_description)
"""
doc = Document()
Config.setOption('sbol_typed_uris', False)
#Define SBOL object and components
#Parts Library
molecule_type = BIOPAX_DNA #Change later
part_column = "Part Name"
sequence_column = "Sequence"
description_column = "Description (Optional)"
role_column = "Role"
length_column = "length (bp)"
for index, row in filled_library.iterrows():
component = ComponentDefinition(row[part_column], molecule_type)
component.roles = ontology[row[role_column]]
component.name = row[part_column]
if not (pd.isnull(row[description_column])):
component.description = row[description_column]
doc.addComponentDefinition(component)
row[sequence_column] = "".join(row[sequence_column].split())
row[sequence_column] = row[sequence_column].replace(u"\ufeff", "")
row[sequence_column] = row[sequence_column].lower()
if len(row[sequence_column]) != row[length_column]:
logging.warning(
f"The length of the sequence {row[part_column]} does not coincide with the length in the corresponding column 'length (bp)'"
)
sequence = Sequence(f"{row[part_column]}_sequence",
row[sequence_column], SBOL_ENCODING_IUPAC)
doc.addSequence(sequence)
component.sequences = sequence
#Metadata
doc.description = str(filled_description.values)
doc.name = filled_library_metadata.iloc[0, 1]
doc.write('SBOL_testcollection.xml')
return (doc)
def get_sbol(self, construct_id='BASIC_construct', validate=False):
"""Get the SBOL string representation of the construct.
The object outputted is SBOL document which can be written
to a file using the "writeString" method.
WARNING: validation needs internet connexion.
:param construct_id: Construct object ID
:type construct_id: str
:param validate: perform online SBOL validation
:type validate: bool
:return: SBOL object
:rtype: <sbol.Document>
"""
_SBOL_ROLE_ASSOC = {
'misc': SO_MISC,
'promoter': SO_PROMOTER,
'rbs': SO_RBS,
'cds': SO_CDS,
'ori': SO_CIRCULAR
}
setHomespace('https://localhost')
doc = Document()
# Check duplicated part
part_seen = set()
dup_part_ids = set()
for part in self._parts:
if part.id not in part_seen:
part_seen.add(part.id)
else:
dup_part_ids.add(part.id)
components = []
for part in self._parts:
# Deal with duplicated part
if part.get_sbol_id() in dup_part_ids:
i = 0
part_id = f'{part.get_sbol_id()}_{i}'
while part_id in doc.componentDefinitions:
i += 1
part_id = f'{part.get_sbol_id()}_{i}'
else:
part_id = part.get_sbol_id()
# Build part
component = ComponentDefinition(part_id)
component.roles = _SBOL_ROLE_ASSOC[part.biological_role]
component.sequence = Sequence(part_id, part.seq)
doc.addComponentDefinition(component)
components.append(component)
plasmid = ComponentDefinition(construct_id)
doc.addComponentDefinition(plasmid)
plasmid.assemblePrimaryStructure(components)
if validate:
logging.info(doc.validate())
return doc