cdhit-reader 0.0.4

CD-HIT cluster parser

cdhit-parser

CD-HIT file reader.

Examples

Basic usage

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:

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

Install

pip install cdhit-reader

Author

• Andrea Telatin

License

This project is licensed under the MIT License.

Acknowledgments

This module was based on fasta_reader by Danilo Horta