diamond4py 0.0.2rc1

Diamond Python bindings for sequence alignment

diamond4py

This is python binding for diamond--a sequence alignment BLAST software implements in C++.

install

• from source code

git clone https://github.com/GCS-ZHN/diamond4py.git
cd diamond4py
conda create -n diamond4py python=3.8
# zlib is required by diamond.
conda install -c anaconda zlib
pip install -v .

• from pypi

pip install diamond4py

Usage

from diamond4py import Diamond

# create a object
diamond = Diamond(
    database="database.dmnd",
    n_threads=4
)

# make db if you don't create it or just download one from websites
diamond.makedb("database.fasta")
print(diamond.version)

# print database statistic info
diamond.dbinfo()

# run blast for proteins
diamond.blastp(
    query="test_proteins.fasta",
    out="test_output"
)