ont-pyguppy-client-lib 5.1.11

Python bindings for the GuppyClient library.

ont-pyguppy-client-lib

ont-pyguppy-client-lib provides python bindings for connecting to a Guppy basecall server. It allows you to interact with the server to do anything you could normally do using the guppy basecall client. This includes:

• Basecalling

• Barcoding / demultiplexing

• Alignment

For example:

>>> from pyguppy_client_lib.pyclient import PyGuppyClient
>>> caller = PyGuppyClient(
    "127.0.0.1:5555",
    "dna_r9.4.1_450bps_fast",
    alignment_index_file="/path/to/index.mmi",
    bed_file="/path/to/targets.bed"
)
>>> caller.connect()

Getting started

ont-pyguppy-client-lib is available on PyPI and may be installed via pip:

pip install ont-pyguppy-client-lib

ont-pyguppy-client-lib requires an instance of the Guppy basecall server is running. Guppy may be obtained from the Oxford Nanopore Community

The version of ont-pyguppy-client-lib should exactly match the version of Guppy being used. You can find your Guppy version like this:

$ <location of guppy_basecall_server>/guppy_basecall_server --version

For example, this Guppy basecall server is version 4.2.2:

$ ./ont-guppy/bin/guppy_basecall_server --version
: Guppy Basecall Service Software, (C) Oxford Nanopore Technologies,  Limited. Version 4.2.2+effbaf8, client-server API version 3.2.0

Install a specific version of ont-pyguppy-client-lib like this:

pip install ont-pyguppy-client-lib==<version>

Dependencies

ont-pyguppy-client-lib requires numpy in order to run. In order to use included helper functions for reading data from fast5 files it is also necessary to manually install ont-fast5-api:

pip install ont-fast5-api

Documentation and help

Information on the methods available may be viewed through Python’s help command::

>>> from pyguppy_client_lib import pyclient
>>> help(pyclient)
>>> from pyguppy_client_lib import client_lib
>>> help(client_lib)

Interface / Examples

ont-pyguppy-client-lib comprises three Python modules:

1. pyclient A user-friendly wrapper around guppy_client. This is what you should use to interact with a Guppy basecall server.

2. guppy_client A compiled library which provides direct Python bindings to Guppy’s C++ API.

3. helper_functions A set of functions for running a Guppy basecall server and loading reads from fast5 files.

Starting a basecall server

There must be a Guppy basecall server running in order to communicate with it. On most Oxford Nanopore devices a basecall server is always running on port 5555. On other devices, or if you want to run a separate basecall server, you must start one yourself:

from pyguppy_client_lib import helper_functions

# A basecall server requires:
#  * A location to put log files (on your PC)
#  * An initial config file to load
#  * A port to run on
server_args = ["--log_path", "/home/myuser/guppy_server_logs",
               "--config", "dna_r9.4.1_450bps_fast.cfg",
               "--port", 5556]
# The second argument is the directory where the
# guppy_basecall_server executable is found. Update this as
# appropriate.
helper_functions.run_server(server_args, "/home/myuser/ont-guppy/bin")

See the Guppy protocol for more information on server arguments.

Create a client and connect to a server

from pyguppy_client_lib.pyclient import PyGuppyClient

client = PyGuppyClient(
    "127.0.0.1:5555",
    "dna_r9.4.1_450bps_fast"
)
client.connect()

Basecall all the reads in a folder

Note that the helper_functions module requires that ont-fast5-api is installed.:

from pyguppy_client_lib import helper_functions

# Using the client generated in the previous example
results = helper_functions.basecall_with_pyguppy(
    caller,
    <input_folder>
)

Glossary of Terms:

Guppy - Oxford Nanopore Technologies’ production basecaller, which translates electrical signals measured from nanopores into DNA or RNA bases.

Fast5 - an implementation of the HDF5 file format, with specific data schemas for Oxford Nanopore Technologies sequencing data.