def validate_fasta_file(file_content, session_dir, file_name):
if file_content is None or file_name is None or session_dir is None:
return None
else:
if ".zip" in file_name:
file_content = tools.decode_zip_content(file_content)
else:
file_content = tools.decode_content(file_content)
output_dir = Path(session_dir)
fasta_path = tools.get_child_path(output_dir, file_name)
if ".zip" in file_name:
tools.save_to_file(file_content, fasta_path, 'wb')
else:
tools.save_to_file(file_content, fasta_path)
error_message = pangtreebuild.fasta_file_is_valid(fasta_path)
if len(error_message) == 0:
return {
"is_correct": True,
"filename": file_name,
"error": error_message
}
else:
return {
"is_correct": False,
"filename": file_name,
"error": error_message
}
def validate_blosum_file(file_content, missing_symbol, fasta_provider_choice, file_name):
if file_content is None or file_name is None:
return None
if fasta_provider_choice == "Symbol" and missing_symbol != "":
symbol = missing_symbol
else:
symbol = None
if file_content is None:
blosum_file_content = tools.read_file_to_stream(pangtreebuild.get_default_blosum_path())
file_source_info = "default BLOSUM file"
else:
blosum_file_content = StringIO(tools.decode_content(file_content))
file_source_info = f"provided BLOSUM file: {file_name}"
error_message = pangtreebuild.blosum_file_is_valid(blosum_file_content, symbol)
if len(error_message) == 0:
symbol_info = f"It contains symbol for missing nucleotides/proteins: {symbol}." if symbol else ""
validation_message = f"The {file_source_info} is correct. " + symbol_info
return {"is_correct": True,
"filename": file_name,
"symbol": symbol,
"validation_message": validation_message}
else:
validation_message = f"Error in {file_source_info} or symbol for missing nucleotides/proteins: {symbol}. " \
f"Reason: {error_message}"
return {"is_correct": False,
"filename": file_name,
"symbol": symbol,
"validation_message": validation_message}
def read_pangenome_upload(upload_content) -> PangenomeJSON:
if not upload_content:
raise PreventUpdate()
if upload_content.startswith("data:application/json;base64"):
jsonified_pangenome = tools.decode_content(upload_content)
else:
jsonified_pangenome = upload_content
return tools.unjsonify_jsonpangenome(jsonified_pangenome)
def validate_metadata_file(file_content, file_name):
if file_content is None or file_name is None:
return None
else:
file_content = tools.decode_content(file_content)
error_message = pangtreebuild.multialignment_file_is_valid(file_content, file_name)
if len(error_message) == 0:
return {"is_correct": True, "filename": file_name, "error": error_message}
else:
return {"is_correct": False, "filename": file_name, "error": error_message}
def validate_metadata_file(file_content, file_name):
if file_content is None or file_name is None:
return None
file_content = tools.decode_content(file_content)
error_message = pangtreebuild.metadata_file_is_valid(
file_content, file_name)
is_file_correct = True if len(error_message) == 0 else False
return {
"is_correct": is_file_correct,
"filename": file_name,
"error": error_message
}
def run_pangenome(run_processing_btn_click, session_state: Dict,
session_dir: str, datatype: str, multialignment_content: str,
multialignment_filename: str, fasta_provider_choice: str,
fasta_content: str, fasta_filename: str, missing_symbol: str,
consensus_choice: str, output_config: List[str],
metadata_content: str, metadata_filename: str,
hbmin_value: float, stop_value: float, p_value: float):
if run_processing_btn_click == 0:
raise PreventUpdate()
if session_state is None:
session_state = {}
if session_dir is None:
session_dir = tools.create_output_dir()
else:
session_dir = Path(session_dir)
current_processing_output_dir_name = tools.get_child_path(
session_dir, tools.get_current_time())
tools.create_dir(current_processing_output_dir_name)
if multialignment_filename and "maf" in multialignment_filename:
multialignment = Maf(StringIO(
tools.decode_content(multialignment_content)),
file_name=multialignment_filename)
elif multialignment_filename and "po" in multialignment_filename:
multialignment = Po(StringIO(
tools.decode_content(multialignment_content)),
file_name=multialignment_filename)
else:
session_state[
"error"] = "Cannot create Poagraph. Only MAF and PO files are supported."
return session_state
missing_symbol = MissingBase(
missing_symbol) if missing_symbol != "" else MissingBase()
fasta_path = None
if fasta_provider_choice == "NCBI":
fasta_provider = FromNCBI(use_cache=True)
elif fasta_provider_choice == "File":
fasta_path = tools.get_child_path(current_processing_output_dir_name,
fasta_filename).resolve()
save_mode = "wb" if "zip" in fasta_filename else "w"
if "zip" in fasta_filename:
fasta_decoded_content = tools.decode_zip_content(fasta_content)
else:
fasta_decoded_content = tools.decode_content(fasta_content)
tools.save_to_file(fasta_decoded_content, fasta_path, save_mode)
fasta_provider = FromFile(fasta_path)
blosum_path = pangtreebuild.get_default_blosum_path()
blosum_contents = tools.read_file_to_stream(blosum_path)
blosum = Blosum(blosum_contents, blosum_path)
metadata = MetadataCSV(StringIO(tools.decode_content(metadata_content)),
metadata_filename) if metadata_content else None
pangenomejson = pangtreebuild.run_pangtreebuild(
output_dir=current_processing_output_dir_name,
datatype=DataType[datatype],
multialignment=multialignment,
fasta_provider=fasta_provider,
blosum=blosum,
consensus_choice=consensus_choice,
output_po=True if "po" in output_config else False,
output_fasta=True if "fasta" in output_config else False,
output_newick=True if "newick" in output_config else False,
missing_symbol=missing_symbol,
metadata=metadata,
hbmin=Hbmin(hbmin_value) if hbmin_value else None,
stop=Stop(stop_value) if stop_value else None,
p=P(p_value) if p_value else None,
fasta_path=fasta_filename if fasta_filename else None,
include_nodes=True # if "nodes" in output_config else False
)
pangenome_json_str = to_json(pangenomejson)
current_processing_output_zip = tools.dir_to_zip(
current_processing_output_dir_name)
current_processing_short_name = "/".join(
str(current_processing_output_zip).split("/")[-2:])
return {
"last_output_zip": current_processing_short_name,
"jsonpangenome": pangenome_json_str,
"error": ""
}, True
