pyguppyclient

Python client library for Guppy


Keywords
basecalling, guppy, nanopore, python
License
Other
Install
pip install pyguppyclient==0.0.5

Documentation

pyguppyclient

PyPI version

Full Python client library for communicating with guppy_basecall_server.

$ pip install pyguppyclient

Requirements

Guppy 3.4 or later is required and the guppy_basecall_server must already be running.

$ guppy_basecall_server --config dna_r9.4.1_450bps_fast.cfg -p 5555 -l /tmp/guppy -x 'cuda:0'

Example

The simplest usage is the GuppyBasecallerClient class which takes a config name and provides a basecall method that takes a read and returns a CalledReadData object.

from pyguppyclient import GuppyBasecallerClient, yield_reads

config = "dna_r9.4.1_450bps_fast"
read_file = "reads.fast5"

with GuppyBasecallerClient(config_name=config) as client:
    for read in yield_reads(read_file):
        called = client.basecall(read, trace=True)
        print(read.read_id, called.seq[:50], called.move)

See the example client for the usage of the Caller class that uses multiprocessing to distribute the reading of fast5 files.

$ ./examples/pyguppyclient -t 8 dna_r9.4.1_450bps_fast /data/reads > pyguppyclient.fastq

Developer Quick Start

$ git clone https://github.com/nanoporetech/pyguppyclient.git
$ cd pyguppy-client
$ python3 -m venv venv3
$ source ./venv3/bin/activate
(venv3) $ pip install -r requirements.txt -r development.txt
(venv3) $ python setup.py develop
(venv3) $ make test

Licence and Copyright

(c) 2020 Oxford Nanopore Technologies Ltd.

pyguppyclient is distributed under the terms of the Oxford Nanopore Technologies, Ltd. Public License, v. 1.0. If a copy of the License was not distributed with this file, You can obtain one at http://nanoporetech.com

Research Release

Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of tools. Support for this software will be minimal and is only provided directly by the developers. Feature requests, improvements, and discussions are welcome and can be implemented by forking and pull requests. However much as we would like to rectify every issue and piece of feedback users may have, the developers may have limited resource for support of this software. Research releases may be unstable and subject to rapid iteration by Oxford Nanopore Technologies.