Important notice
ont-pyguppy-client-lib has been renamed to ont-pybasecall-client-lib. This project will no longer be updated but is provided in order to support basecall servers up to version 7.2.x. For python bindings to dorado_basecall_server 7.3.0 onwards, please use ont-pybasecall-client-lib.
ont-pyguppy-client-lib
ont-pyguppy-client-lib provides python bindings for connecting to a Dorado basecall server. It allows you to interact with the server to do anything you could normally do using the ont_basecall_client. This includes:
Basecalling
Barcoding / demultiplexing
Alignment
For example:
>>> from pyguppy_client_lib.pyclient import PyGuppyClient
>>> client = PyGuppyClient(
"127.0.0.1:5555",
"dna_r9.4.1_450bps_fast",
align_ref="/path/to/index.mmi",
bed_file="/path/to/targets.bed"
)
>>> client.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 Dorado basecall server is running. ont-dorado-server may be obtained from the Oxford Nanopore Community
The version of ont-pyguppy-client-lib should exactly match the version of ont-dorado-server being used. You can find your ont-dorado-server version like this:
$ <location of dorado_basecall_server>/dorado_basecall_server --version
For example, this Dorado basecall server is version 7.1.1:
$ ./ont-dorado-server/bin/dorado_basecall_server --version : Dorado Basecall Service Software, (C) Oxford Nanopore Technologies, Limited. Version 7.1.1+effbaf8, client-server API version 16.0.0
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 and/or pod5 files it is also necessary to manually install ont-fast5-api and/or pod5:
pip install ont-fast5-api pod5
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:
pyclient A user-friendly wrapper around client_lib. This is what you should use to interact with a Dorado basecall server.
client_lib A compiled library which provides direct Python bindings to Dorado’s C++ GuppyClient API.
helper_functions A set of functions for running a Dorado basecall server and loading reads from fast5 and/or pod5 files.
Starting a basecall server
There must be a Dorado 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
# dorado_basecall_server executable is found. Update this as
# appropriate.
helper_functions.run_server(server_args, "/home/myuser/ont-dorado/bin")
See the the DOCUMENTATION.md file in the ont-dorado-server archive for more information on server arguments.
Basecall and align using PyGuppyClient
from pyguppy_client_lib.pyclient import PyGuppyClient
client = PyGuppyClient(
"127.0.0.1:5555",
"dna_r9.4.1_450bps_fast",
align_ref = "/path/to/align_ref.fasta",
bed_file = "/path/to/bed_file.bed"
)
client.connect()
Note that the helper_functions module requires that ont-fast5-api and/or pod5 is installed.:
from pyguppy_client_lib.helper_functions import basecall_with_pyguppy
# Using the client generated in the previous example
called_reads = basecall_with_pyguppy(
caller,
"/path/to/input_folder"
)
for read in called_reads:
read_id = read['metadata']['read_id']
alignment_genome = read['metadata']['alignment_genome']
sequence = read['datasets']['sequence']
print(f"{read_id} sequence length is {len(sequence)}"
f"alignment_genome is {alignment_genome}")
Basecall and get states, moves and modbases using GuppyClient
In order to retrieve the movement dataset, the move_and_trace_enabled option must be set to True; analogously, for the state_data one, post_out must be turned on. NOTE: You shouldn’t turn on post_out if you don’t need the states, because it generates a LOT of extra output data so it can really hurt performance. Likewise with move_and_trace_enabled, although that’s much less expensive.
options = {'priority': GuppyClient.high_priority,
'client_name': "test_client",
'move_and_trace_enabled': True,
'post_out':True }
client = GuppyClient(port_path, 'dna_r9.4.1_e8.1_modbases_5mc_cg_fast')
result = client.set_params(options)
result = client.connect()
called_reads = basecall_with_pyguppy(client, input_path)
for read in called_reads:
base_mod_context = read['metadata']['base_mod_context']
base_mod_alphabet = read['metadata']['base_mod_alphabet']
sequence = read['datasets']['sequence']
movement = read['datasets']['movement']
state_data = read['datasets']['state_data']
base_mod_probs = read['datasets']['base_mod_probs']
print(f"{read_id} sequence length is {len(sequence)}, "
f"base_mod_context is {base_mod_context}, base_mod_alphabet is {base_mod_alphabet}, "
f"movement size is {movement.shape}, state_data size is {state_data.shape}, "
f"base_mod_probs size is {base_mod_probs.shape}")
Glossary of Terms:
Dorado - 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.
Pod5 - a file format for storing nanopore dna data in an easily accessible way.
1 maintainer
Metadata
1 maintainer
Release files for ont-pyguppy-client-lib 7.2.15
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
Total release size: 55.7 MB
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.8.0 pkginfo/1.10.0 readme-renderer/34.0 requests/2.27.1 requests-toolbelt/1.0.0 urllib3/1.26.16 tqdm/4.64.1 importlib-metadata/4.8.3 keyring/23.4.1 rfc3986/1.5.0 colorama/0.4.5 CPython/3.6.9
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Release files / ont_pyguppy_client_lib-7.2.15-cp38-cp38-macosx_10_15_x86_64.whl
| Download URL | ont_pyguppy_client_lib-7.2.15-cp38-cp38-macosx_10_15_x86_64.whl |
|---|---|
| Size | 4.0 MB |
| Tags | CPython 3.8 macOS 10.15+ x86-64 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.8.0 pkginfo/1.10.0 readme-renderer/34.0 requests/2.27.1 requests-toolbelt/1.0.0 urllib3/1.26.16 tqdm/4.64.1 importlib-metadata/4.8.3 keyring/23.4.1 rfc3986/1.5.0 colorama/0.4.5 CPython/3.6.9
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Release files / ont_pyguppy_client_lib-7.2.15-cp37-cp37m-win_amd64.whl
| Download URL | ont_pyguppy_client_lib-7.2.15-cp37-cp37m-win_amd64.whl |
|---|---|
| Size | 1.6 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Windows x86-64 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.8.0 pkginfo/1.10.0 readme-renderer/34.0 requests/2.27.1 requests-toolbelt/1.0.0 urllib3/1.26.16 tqdm/4.64.1 importlib-metadata/4.8.3 keyring/23.4.1 rfc3986/1.5.0 colorama/0.4.5 CPython/3.6.9
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Release files / ont_pyguppy_client_lib-7.2.15-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | ont_pyguppy_client_lib-7.2.15-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 2.4 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.17+ x86-64 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.8.0 pkginfo/1.10.0 readme-renderer/34.0 requests/2.27.1 requests-toolbelt/1.0.0 urllib3/1.26.16 tqdm/4.64.1 importlib-metadata/4.8.3 keyring/23.4.1 rfc3986/1.5.0 colorama/0.4.5 CPython/3.6.9
|
Release files / ont_pyguppy_client_lib-7.2.15-cp37-cp37m-macosx_10_15_x86_64.whl
| Download URL | ont_pyguppy_client_lib-7.2.15-cp37-cp37m-macosx_10_15_x86_64.whl |
|---|---|
| Size | 4.0 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc macOS 10.15+ x86-64 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.8.0 pkginfo/1.10.0 readme-renderer/34.0 requests/2.27.1 requests-toolbelt/1.0.0 urllib3/1.26.16 tqdm/4.64.1 importlib-metadata/4.8.3 keyring/23.4.1 rfc3986/1.5.0 colorama/0.4.5 CPython/3.6.9
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