Metadata-Version: 2.1
Name: readfish
Version: 0.0.4
Summary: Adaptive sampling toolkit for MinION
Home-page: https://github.com/LooseLab
Author: Alexander Payne
Author-email: alexander.payne@nottingham.ac.uk
License: UNKNOWN
Platform: UNKNOWN
Requires-Python: >=3.5
Description-Content-Type: text/markdown
Requires-Dist: grpcio
Requires-Dist: requests
Requires-Dist: numpy
Requires-Dist: google
Requires-Dist: protobuf
Requires-Dist: toml
Requires-Dist: jsonschema
Requires-Dist: watchdog
Requires-Dist: pandas
Requires-Dist: mappy
Requires-Dist: biopython
Requires-Dist: pyguppyclient (>=0.0.6)

# <img src="https://raw.githubusercontent.com/LooseLab/ru/rename_cli/examples/images/readfish_logo.jpg">

Installation
---

This toolkit currently requires MinKNOW (minknow-core v3.6) to be installed and `read_until_api_v2` to be installed
separately. We recommend installing in a virtual environment as so:

```bash
# Make a virtual env
python3 -m venv readfish
source ./readfish/bin/activate
pip install git+https://github.com/LooseLab/read_until_api_v2@master
pip install readfish
```

Usage
---
```bash
# check install
$ readfish
usage: readfish [-h] [--version]
                {targets,align,centrifuge,unblock-all,validate,summary} ...

positional arguments:
  {targets,align,centrifuge,unblock-all,validate,summary}
                        Sub-commands
    targets             Run targeted sequencing
    align               ReadFish and Run Until, using minimap2
    centrifuge          ReadFish and Run Until, using centrifuge
    unblock-all         Unblock all reads
    validate            ReadFish TOML Validator
    summary             Summary stats from FASTQ files

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

See '<command> --help' to read about a specific sub-command.

# example run command - change arguments as necessary:
$ readfish targets --experiment-name "Test run" --device MN17073 --toml example.toml --log-file RU_log.log
```


