Diamond Python bindings for sequence alignment
Project description
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"
)
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