Module that creates Nextclade command and captures Nextclade output.
capture_output(command)
Runs Nextclade CLI and captures the output.
Parameters:
-
command
(str)
–
The Nextclade CLI command.
Returns:
-
DataFrame
–
A DataFrame of the Nextclade analysis TSV output.
Source code in src/vargram/wranglers/_nextclade_cli.py
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89 | def capture_output(command):
"""Runs Nextclade CLI and captures the output.
Parameters
----------
command : str
The Nextclade CLI command.
Returns
-------
pandas.DataFrame
A DataFrame of the Nextclade analysis TSV output.
"""
try:
if len(command) != 2: # Reference FASTA is provided
subprocess.run(command, check=True)
analysis_arg_ind = command.index("-t") + 1
analysis_file_path = command[analysis_arg_ind]
else: # Name of Nextclade reference is provided
analysis_arg_ind = command[1].index("-t") + 1
analysis_file_path = command[1][analysis_arg_ind]
for line in command:
subprocess.run(line, check=True)
# Reading Nextclade analysis TSV output
analysis_dataframe = pd.read_csv(analysis_file_path, delimiter='\t')
# Removing index column
analysis_dataframe.drop('index', axis=1, inplace=True)
return analysis_dataframe
except subprocess.CalledProcessError as e:
print(f"Error running Nextclade: {e}")
except FileNotFoundError:
print("Nextclade executable not found. Make sure it is included in the system $PATH.")
except Exception as e:
print(f"An unexpected error occurred: {e}")
|
create_command(**kwargs)
Creates Nextclade command based on user input.
Parameters:
-
input
(dict)
–
Dictionary containing the user input to nextclade().
-
secure_analysis_dir
(str)
–
Secure temporary directory to store Nexclade analysis TSV output.
-
secure_ref_dir
(str)
–
Secure temporary directory to store reference sequence from Nextclade.
Returns:
-
list
–
A list whose elements constitute the Nextclade command.
Source code in src/vargram/wranglers/_nextclade_cli.py
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51 | def create_command(**kwargs):
"""Creates Nextclade command based on user input.
Parameters
----------
input : dict
Dictionary containing the user input to nextclade().
secure_analysis_dir : str
Secure temporary directory to store Nexclade analysis TSV output.
secure_ref_dir : str
Secure temporary directory to store reference sequence from Nextclade.
Returns
-------
list
A list whose elements constitute the Nextclade command.
"""
# Getting user input
input = kwargs["input"]
seq = input["seq"]
ref = input["ref"]
# Getting nextread-created directories
secure_analysis_dir = kwargs["secure_analysis_dir"]
secure_ref_dir = kwargs["secure_ref_dir"]
# Creating command based on user input
if os.path.isfile(ref): # Reference FASTA is provided
nextclade_command = f"nextclade run -r {ref} -t {os.path.join(secure_analysis_dir, 'analysis.tsv')}".split()
if "gene" in input: # Gene annotation is provided
gene = input["gene"]
nextclade_command = nextclade_command + ["-m", gene]
nextclade_command = nextclade_command + [seq]
gene_path = gene
else: # Name of Nextclade reference is provided
secure_ref_dir = kwargs["secure_analysis_dir"]
# Get dataset first and then run the command
gene_path = os.path.join(secure_ref_dir, 'genome_annotation.gff3')
first_command = f"nextclade dataset get -n {ref} -o {secure_ref_dir}".split()
second_command = f"nextclade run -r {os.path.join(secure_ref_dir, 'reference.fasta')} -m {gene_path} -t {os.path.join(secure_analysis_dir, 'analysis.tsv')} {seq}".split()
nextclade_command = [first_command, second_command]
return nextclade_command, gene_path
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