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setup.py
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setup.py
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import os
from setuptools import setup
distmeta = {}
for line in open(os.path.join('ccs_amplicon', '__init__.py')):
try:
field, value = (x.strip() for x in line.split('='))
except ValueError:
continue
if field == '__version_info__':
value = value.strip('[]()')
value = '.'.join(x.strip(' \'"') for x in value.split(','))
else:
value = value.strip('\'"')
distmeta[field] = value
long_description = "See {}".format(distmeta["__homepage__"])
setup(
name="ccs_amplicon",
version=distmeta["__version_info__"],
description="Haplotype polishing and phasing from targetted PacBio sequencing data.",
long_description=long_description,
author=distmeta["__author__"],
author_email=distmeta["__contact__"],
url=distmeta["__homepage__"],
license="MIT",
platforms=["linux"],
packages=["ccs_amplicon"],
include_package_data=True,
python_requires='~=3.0',
install_requires=[
"numpy",
"scikit-learn",
"pandas",
"bokeh",
"pysam",
"click>=7.0",
"markov_clustering>=0.0.5.dev0",
"networkx>=2.0",
"pygraphviz>=1.4rc1",
"biopython",
"edlib",
"tqdm",
"snakemake>=5.0.0"
],
entry_points={
"console_scripts": [
"ccs_amplicon.workflow = ccs_amplicon.runner:cli_handler",
"ccs_amplicon.baminfo = ccs_amplicon.baminfo:cli_handler",
"ccs_amplicon.trim_fasta = ccs_amplicon.trim_fasta:cli_handler",
"ccs_amplicon.clusters = ccs_amplicon.cluster:cli_handler",
"ccs_amplicon.collapse = ccs_amplicon.collapse_homopolymers:cli_handler",
"ccs_amplicon.consensus = ccs_amplicon.consensus:cli_handler",
"ccs_amplicon.distance = ccs_amplicon.distance_matrix:cli_handler",
"ccs_amplicon.embed = ccs_amplicon.embed:cli_handler",
"ccs_amplicon.label = ccs_amplicon.label_haplotype_seqs:cli_handler",
"ccs_amplicon.sanitize_phase = ccs_amplicon.sanitize_phased_vcf:cli_handler",
"ccs_amplicon.seqs_from_clusters = ccs_amplicon.seqs_from_clusters:cli_handler",
"ccs_amplicon.whitelist = ccs_amplicon.whitelist:cli_handler",
"ccs_amplicon.clusterplot = ccs_amplicon.cluster_view:cli_handler",
"ccs_amplicon.filter_clusters = ccs_amplicon.filter_clusters:cli_handler",
"ccs_amplicon.summarize_phasing = ccs_amplicon.phasing_summary:cli_handler",
"ccs_amplicon.strip_primers = ccs_amplicon.strip_primers:cli_handler",
"ccs_amplicon.tag_chimeras = ccs_amplicon.chimerism:cli_handler",
"ccs_amplicon.fq2fa = ccs_amplicon.fq_to_fa:cli_handler"
]
},
classifiers=[
"Development Status :: 3 - Alpha",
"Intended Audience :: Science/Research",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python",
"Topic :: Scientific/Engineering",
"License :: OSI Approved :: MIT License",
],
keywords="bioinformatics"
)