cdhit-reader 0.0.6

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

Demo applications

Cluster stats

The module ships a demo program called cdhit-reader.py.

Compare two fasta files

:warning: This requires cd-hit installed and available in the system path.

cdhit-compare allows to compare two fasta files and print the sequences that are in common, those which are only present in one of the files or those which are redundant.

Example:

cdhit-compare data/input1.faa data/input2.faa

will produce:

input1_ IBJJOHBJ_00007
input2_ IBJJOHBJ_00007
input2_ IBJJOHBJ_00002
both    IBJJOHBJ_00003:_IBJJOHBJ_00003
both    IBJJOHBJ_00005:_IBJJOHBJ_00005
both    IBJJOHBJ_00004:_IBJJOHBJ_00004
dupl    IBJJOHBJ_00001:IBJJOHBJ_000F1

where records starting with file1 or file2 are only present in one of the files, records starting with both are present in both files (one per file), records starting with dupl are duplicates (two in one of the files), and records starting with multi are present multiple times in at least one of the datasets

Author

• Andrea Telatin

License

This project is licensed under the MIT License.

Acknowledgments

This module was based on fasta_reader by Danilo Horta