setup.py

from setuptools import setup, find_packages

import sys
import os
import subprocess
import re


def read(fname):
    return open(os.path.join(os.path.dirname(__file__), fname)).read()


# def check_java():
#     p = subprocess.Popen(['java', '-version'], stderr=subprocess.PIPE)
#     for line in p.stderr:
#         if line.startswith('java version'):
#             return True
#
#     return False
#
#
# def check_bwa():
#     with subprocess.Popen('bwa', shell=True, stderr=subprocess.PIPE) as p:
#         for line in p.stderr:
#             print(line)
#             if line.startswith('Version:'):
#                 print(line)
#                 major, minor, sub = line.strip().split()[1].split('.')
#                 sub = sub.split('-')[0]
#                 digit_pattern = re.compile(r'\D')
#                 sub = filter(None, digit_pattern.split(sub))[0]
#                 if int(major) >= 0 and int(minor) >= 7 and int(sub) >= 12:
#                     return True
#     return False
#
#
# def check_samtools():
#     p = subprocess.Popen(['samtools'], stderr=subprocess.PIPE)
#     for line in p.stderr:
#         if line.startswith('Version:'):
#             major, minor = line.strip().split()[1].split('.')[:2]
#             minor = minor.split('-')[0]
#             if int(major) >= 1 and int(minor) >= 2:
#                 return True
#     return False
#
#
# def check_bcftools():
#     p = subprocess.Popen(['bcftools'], stderr=subprocess.PIPE)
#     for line in p.stderr:
#         if line.startswith('Version:'):
#             major, minor = line.strip().split()[1].split('.')[:2]
#             minor = minor.split('-')[0]
#             if int(major) >= 1 and int(minor) >= 2:
#                 return True
#     return False
#
#
# def check_wgsim():
#     p = subprocess.Popen(['wgsim'], stderr=subprocess.PIPE)
#     for line in p.stderr:
#         if line.startswith('Version:'):
#             major, minor = line.strip().split()[1].split('.')[:2]
#             minor = minor.split('-')[0]
#             if int(major) >= 0 and int(minor) >= 2:
#                 return True
#     return False
#
#
# def check_velvet():
#     p = subprocess.Popen(['velvetg'], stdout=subprocess.PIPE)
#     for line in p.stdout:
#         if line.startswith('Version'):
#             major, minor = line.strip().split()[1].split('.')[:2]
#             minor = minor.split('-')[0]
#             if int(major) >= 1 and int(minor) >= 2:
#                 return True
#     return False
#
#
# def check_exonerate():
#     p = subprocess.Popen(['exonerate'], stdout=subprocess.PIPE)
#     for line in p.stdout:
#         if line.startswith('exonerate from exonerate'):
#             major, minor = line.strip().split()[-1].split('.')[:2]
#             minor = minor.split('-')[0]
#             if int(major) >= 2 and int(minor) >= 2:
#                 return True
#     return False
#
#
# def check_python():
#     return sys.hexversion >= 0x20702f0


if __name__ == '__main__':
    # if not check_python(): sys.exit('Dependency problem: python >= 2.7.2 is required')
    # if not check_bwa(): sys.exit('Dependency problem: bwa >= 0.7.12 not found')
    # if not check_samtools(): sys.exit('Dependency problem: samtools >= 1.2 not found')
    # if not check_bcftools(): sys.exit('Dependency problem: bcftools >= 1.2 not found')
    # if not check_wgsim(): sys.exit('Dependency problem: wgsim not found (required for addsv)')
    # if not check_velvet(): sys.exit('Dependency problem: velvet >= 1.2 not found (required for addsv)')
    # if not check_exonerate(): sys.exit('Dependency problem: exonerate >= 2.2 not found (required for addsv)')
    setup(
        name='bamsurgeon',
        version='1.0',
        author='Adam Ewing',
        description='Collection of tools for adding mutations to BAM files',
        license='MIT',
        keywords=['Python', 'genomics', 'NGS', 'BAM'],
		scripts=[
			'bin/addindel.py',
			'bin/addsnv.py',
			'bin/addsv.py',
			'scripts/bamregions_from_vcf.py',
			'scripts/bamsplit.py',
			'scripts/bamsplit_proportion.py',
			'scripts/bamsplit_multiple.py',
			'scripts/bsrg.py',
			'scripts/covered_segments.py',
			'scripts/dedup.py',
			'scripts/evaluator.py',
			'scripts/makevcf.py',
			'scripts/makevcf_indels.py',
			'scripts/makevcf_sv.py',
			'scripts/postprocess.py',
			'scripts/randomsites.py',
			'scripts/remove_unpaired.py',
			'scripts/rename_reads.py',
			'scripts/seperation.py',
        	'scripts/match_fasta_to_bam.py'],
		packages=find_packages(),
		install_requires=[
            'python<3',
            'pysam>=0.8.1'
    	],
		long_description=read('README.md')
)