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#!/usr/bin/env python3
"""
Copyright 2020 Kat Holt
Copyright 2020 Ryan Wick (rrwick@gmail.com)
https://github.com/katholt/Kleborate/
This file is part of Kleborate. Kleborate is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by the Free Software Foundation,
either version 3 of the License, or (at your option) any later version. Kleborate is distributed in
the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
details. You should have received a copy of the GNU General Public License along with Kleborate. If
not, see <http://www.gnu.org/licenses/>.
"""
import os
import sys
import subprocess
import distutils.spawn
from setuptools import setup
from setuptools.command.install import install
def readme():
with open('README.md') as f:
return f.read()
# Get the program version from another file.
__version__ = '0.0.0'
exec(open('kleborate/version.py').read())
def check_dir_write_permission(directory):
if os.path.isdir(directory) and not os.access(directory, os.W_OK):
sys.exit('Error: no write permission for ' + directory + ' ' +
'Perhaps you need to use sudo?')
def build_blast_db(data_dir, fasta_filename, seq_type):
fasta_path = os.path.join(data_dir, fasta_filename)
makeblastdb_cmd = ['makeblastdb', '-dbtype', seq_type, '-in', fasta_path]
# Fall back to blastdb version 4 for big endian architectures, as kleborate
# is not yet able to swap bytes appropriately with the new lmdb format of
# the blastdb v5. Note that the content of the distributed data set is
# thus now architecture dependent.
if sys.byteorder == 'big':
makeblastdb_cmd += ['-blastdb_version', '4']
print(' ' + ' '.join(makeblastdb_cmd))
with open(os.devnull, 'w') as devnull:
subprocess.check_call(makeblastdb_cmd, stdout=devnull)
class KleborateInstall(install):
"""
This is a subclass of install where I've added a couple things to the installation process:
* building BLAST databases with makeblastdb
* printing example commands
"""
def run(self):
check_dir_write_permission(self.install_lib)
check_dir_write_permission(self.install_scripts)
# Call the base class run to do the bulk of the installation.
install.run(self)
# Build the BLAST databases now, as the user may not have write permissions to the
# installation directory when running Kleborate.
print('')
data_dir = os.path.join(self.install_lib, 'kleborate', 'data')
if not distutils.spawn.find_executable('makeblastdb'):
print('Warning: could not find makeblastdb, so BLAST databases were not built.')
print('They can be built when you run Kleborate, but this will require write '
'permissions to the data directory:')
print(data_dir)
else:
check_dir_write_permission(data_dir)
print('Building BLAST databases with makeblastdb:')
try:
for fasta in ['CARD_v3.1.13.fasta', 'clb_alleles.fasta', 'rmpA2.fasta',
'iro_alleles.fasta', 'iuc_alleles.fasta', 'rmp_alleles.fasta',
'Klebsiella_pneumoniae.fasta', 'wzi.fasta', 'ybt_alleles.fasta',
'MgrB_and_PmrB.fasta', 'OmpK.fasta', 'QRDR_120.fasta']:
build_blast_db(data_dir, fasta, 'nucl')
except subprocess.CalledProcessError:
print('\n')
print('Warning: makeblastdb failed, so BLAST databases were not built.')
print('They can be built when you run Kleborate, but this will require write '
'permissions to the data directory:')
print(data_dir)
ascii_art = " _ __ _ ______ ____ ____ _____ _______ ______ \n" \
"| | / /| | | ____| _ \ / __ \| __ \ /\|__ __| ____|\n" \
"| |/ / | | | |__ | |_) | | | | |__) | / \ | | | |__ \n" \
"| < | | | __| | _ <| | | | _ / / /\ \ | | | __| \n" \
"| |\ \ | |___| |____| |_) | |__| | | \ \/ ____ \| | | |____ \n" \
"|_| \_\|_____|______|____/ \____/|_| \_\/ \_\_| |______|\n"
print('\n')
print('\033[1m' + ascii_art + '\033[0m') # bold formatting
print('Kleborate is installed and ready to use!')
print('')
print('Example commands:')
print(' kleborate --help')
print(' kleborate -o results.txt -a *.fasta')
print(' kleborate --resistance -o results.txt -a *.fasta')
print(' kleborate --all -o results.txt -a *.fasta')
print('')
setup(name='Kleborate',
version=__version__,
description='Kleborate',
long_description=readme(),
classifiers=['Development Status :: 4 - Beta',
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
'Programming Language :: Python :: 2',
'Programming Language :: Python :: 3',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Scientific/Engineering :: Medical Science Apps.',
'Intended Audience :: Science/Research'],
keywords='microbial genomics sequence typing',
url='https://github.com/katholt/Kleborate',
author='Kathryn Holt',
author_email='',
packages=['kleborate', 'kaptive'],
install_requires=['biopython'],
entry_points={'console_scripts': ['kleborate = kleborate.__main__:main']},
include_package_data=True,
zip_safe=False,
cmdclass={'install': KleborateInstall})
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