CD-HIT cluster parser
Project description
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
License
This project is licensed under the MIT License.
Acknowledgments
This module was based on fasta_reader by Danilo Horta
Project details
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