add CP004009.1 as a cannonical C, make primer degenerate for yjaA_2b

clermontpcr/_version.py

@@ -1 +1 @@
-__version__ = '0.1.1'
+__version__ = '0.2.0'

clermontpcr/clermontpcr.py

@@ -334,7 +334,7 @@ def main(args):
     chuA_2  = "TGCCGCCAGTACCAAAGACA"
     # yjaH
     yjaA_1b = "CAAACGTGAAGTGTCAGGAG"
-    yjaA_2b = "AATGCGTTCCTCAACCTGTG"
+    yjaA_2b = "AAT[GA]CGTTCCTCAACCTGTG"
     # TspE4.C2
     TspE4_C2 = "CACTATTCGTAAGGTCATCC"
     TspE4C2_2b = "AGTTTATCGCTGCGGGTCGC"

setup.py

@@ -18,19 +18,6 @@
 
 here = path.abspath(path.dirname(__file__))
 
-# Get the long description from the README file
-# with open(path.join(here, 'README.md'), encoding='utf-8') as f:
-#     long_description = f.read()
-
-# # from pyani
-# with open(path.join(here, 'clermontpcr', '__init__.py'), 'r') as fh:
-#     for line in fh:
-#         m = re.search(r"^__version__ = '(?P<version>[^']+)'$", line)
-#         if m:
-#             init_version = m.group('version')
-#             break
-# from http://stackoverflow.com/questions/458550/
-#         standard-way-to-embed-version-into-python-package
 VERSIONFILE = "clermontpcr/_version.py"
 verstrline = open(VERSIONFILE, "rt").read()
 VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
@@ -46,16 +33,8 @@
                      "or above...exiting.\n")
     sys.exit(1)
 
-## parse requirements file
-# install_reqs = parse_requirements(path.join(here, "requirements.txt"),
-#                                  session=False)
-# requirements = [str(ir.req) for ir in install_reqs]
 setup(
     name='clermontpcr',
-    # dependency_links=['https://github.com/WarrenWeckesser/heatmapcluster.git#egg=heatmapcluster'],
-    # Versions should comply with PEP440.  For a discussion on single-sourcing
-    # the version across setup.py and the project code, see
-    # https://packaging.python.org/en/latest/single_source_version.html
     version=verstr,
 
     description='clermontpcr: phylotype your strains, in silico',
@@ -65,94 +44,30 @@
     repo for the real README.md file
     """,
 
-    # The project's main homepage.
     url='https://github.com/nickp60/clermontpcr',
 
     # Author details
     author='Nick Waters',
     author_email='nickp60@gmail.com',
-
-    # Choose your license
     license='MIT',
 
     # See https://pypi.python.org/pypi?%3Aaction=list_classifiers
     classifiers=[
-        # How mature is this project? Common values are
-        #   3 - Alpha
-        #   4 - Beta
-        #   5 - Production/Stable
         'Development Status :: 3 - Alpha',
-
-        # Indicate who your project is intended for
         'Intended Audience :: Developers',
         'Topic :: Software Development :: Build Tools',
-
-        # Pick your license as you wish (should match "license" above)
         'License :: OSI Approved :: MIT License',
-
-        # Specify the Python versions you support here. In particular, ensure
-        # that you indicate whether you support Python 2, Python 3 or both.
-        #'Programming Language :: Python :: 2',
-        #'Programming Language :: Python :: 2.6',
-        #'Programming Language :: Python :: 2.7',
-        #'Programming Language :: Python :: 3',
-        #'Programming Language :: Python :: 3.3',
-        #'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
     ],
-
-    # What does your project relate to?
     keywords='bioinformatics evolution genomics development',
-
-    # You can just specify the packages manually here if your project is
-    # simple. Or you can use find_packages().
-    # packages=['clermontpcr'],
     packages=find_packages(),
-
-    # Alternatively, if you want to distribute just a my_module.py, uncomment
-    # this:
-    #   py_modules=["my_module"],
-
-    # List run-time dependencies here.  These will be installed by pip when
-    # your project is installed. For an analysis of "install_requires" vs pip's
-    # requirements files see:
-    # https://packaging.python.org/en/latest/requirements.html
-    # install_requires=requirements,
     install_requires=[
         'Biopython==1.68'
     ],
-    # List additional groups of dependencies here (e.g. development
-    # dependencies). You can install these using the following syntax,
-    # for example:
-    # $ pip install -e .[dev,test]
-    #extras_require={
-    #    'dev': ['check-manifest'],
-    #    'test': ['coverage'],
-    #},
     include_package_data=True,
-    # If there are data files included in your packages that need to be
-    # installed, specify them here.  If using Python 2.6 or less, then these
-    # have to be included in MANIFEST.in as well.
     package_data={
        '': [path.join(__name__, "tests", "refs/*")],
     },
-
-    # Although 'package_data' is the preferred approach, in some case you may
-    # need to place data files outside of your packages. See:
-    # http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files # noqa
-    # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
-    #data_files=[('my_data', ['data/data_file'])],
-
-    # To provide executable scripts, use entry points in preference to the
-    # "scripts" keyword. Entry points provide cross-platform support and allow
-    # pip to create the appropriate form of executable for the target platform.
-    #entry_points={
-    #    'console_scripts': [
-    #        'sample=sample:main',
-    #    ],
-    #},
-    # Using the scripts keyword here for speed, as the entry points are not
-    # yet defined
     scripts=['clermontpcr/clermontpcr.py'],
 )

tests/context.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python3
+#-*- coding: utf-8 -*-
+import os
+import sys
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
+
+import clermontpcr