def example_02a_download_result_as_tsv(document_id: int):
"""
Download the raw file as a TSV.
"""
client = PipebioClient()
# Either login with hardcoded variables or use environment variables:
# e.g.
# client.login(<my-email>, <my-password>, <my-token>)
# or:
# PIPE_EMAIL=<my-email> PIPE_PASSWORD=<my-password> PIPE_TOKEN=<my-token> python login.py
client.login()
# Display who we are logged in as.
user = client.authentication.user
print('\nLogged in as {}. \n'.format(user['firstName'], user['lastName']))
# Set the download name and folder.
destination_filename = "download.tsv"
destination_location = Util.get_executed_file_location()
absolute_location = os.path.join(destination_location, '..',
f'Downloads/{destination_filename}')
client.sequences.download(document_id, destination=absolute_location)
return absolute_location
def example_02c_download_result_to_biological_format(document_id):
"""
Download the format in Genbank, Fasta, Fastq, Ab1 etc.
"""
client = PipebioClient()
# Either login with hardcoded variables or use environment variables:
# e.g.
# client.login(<my-email>, <my-password>, <my-token>)
# or:
# PIPE_EMAIL=<my-email> PIPE_PASSWORD=<my-password> PIPE_TOKEN=<my-token> python login.py
client.login()
# Display who we are logged in as.
user = client.authentication.user
print('\nLogged in as {}. \n'.format(user['firstName'], user['lastName']))
# Specify a target folder on this computer to download the file to.
destination_folder = Util.get_executed_file_location()
return client.export(document_id, ExportFormat.GENBANK.value,
destination_folder)
def example_02d_download_original_file(document_id: int,
destination_filename: str = None
) -> str:
"""
Download the original, un-parsed file.
"""
client = PipebioClient()
# Either login with hardcoded variables or use environment variables.
# PIPE_EMAIL=<my-email> PIPE_PASSWORD=<my-password> PIPE_TOKEN=<my-token> python login.py
client.login()
# Display who we are logged in as.
user = client.authentication.user
print('\nLogged in as {}. \n'.format(user['firstName'], user['lastName']))
# Set the download name and folder.
destination_filename = "download.tsv" if destination_filename is None else destination_filename
destination_location = Util.get_executed_file_location()
absolute_location = os.path.join(destination_location,
f'../Downloads/{destination_filename}')
return client.entities.download_original_file(document_id,
absolute_location)