Metadata-Version: 2.1
Name: cdhit-reader
Version: 0.0.4
Summary: CD-HIT cluster parser
Home-page: https://github.com/telatin/cdhit-parser
Download-URL: https://github.com/telatin/cdhit-parser
Author: Andrea Telatin
Author-email: andrea.telatin@gmail.com
Maintainer: Andrea Telatin
Maintainer-email: andrea.telatin@gmail.com
License: MIT
Keywords: cd-hit,clustering,reader
Platform: Windows
Platform: MacOS
Platform: Linux
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Description-Content-Type: text/markdown
Provides-Extra: cli
License-File: LICENSE.md

# cdhit-parser

CD-HIT file reader.

## Examples

Basic usage

```python
input = "cluster.fa.clstr"
for cluster in read_cdhit(input):
    print(f"{cluster.name} refSequence={cluster.refname} size={len(cluster)}")

    for member in cluster.sequences:
        print(f" {member.name} ({member.length}) identity={member.identity}% {'(Reference sequence)' if member.is_ref else ''}")
```

Load all clusters in to a list:
```python

# Load all clusters to a list
clusters = read_cdhit(input).read_items()
```
## Install

```bash
pip install cdhit-reader
```

## Author

* [Andrea Telatin](https://github.com/telatin)

## License

This project is licensed under the MIT License.

## Acknowledgments

This module was based on [fasta_reader](https://github.com/EBI-Metagenomics/fasta-reader-py) by [Danilo Horta](https://github.com/horta)



