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Merge pull request #18 from CGATOxford/TS-RefactorTools
Ts refactor tools
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language: python | ||
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python: | ||
- "2.7" | ||
# - "3.4" | ||
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script: | ||
- cd $TRAVIS_BUILD_DIR ; pip install cython; python setup.py install | ||
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after_script: | ||
- umi_tools --help | ||
- umi_tools extract --help | ||
- umi_tools dedup --help | ||
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# to do | ||
#deploy: | ||
# provider: pypi | ||
# user: toms | ||
# password: | ||
# secure: my_secure_password | ||
# on: | ||
# tags: true | ||
# branch: master | ||
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notifications: | ||
email: | ||
- thomas.smith2@dpag.ox.ac.uk | ||
- i.sudbery@sheffield.ac.uk |
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# extensions | ||
include umi_tools/*.pyx |
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Tools for dealing with Unique Molecular Identifiers | ||
==================================================== | ||
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This repository contains a number of tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs). Currently there are two tools:: | ||
This repository contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs). Currently there are two tools: | ||
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extract_umi.py: Flexible removal of UMI sequences from fastq reads. | ||
UMIs are removed and appended to the read name. Any other barcode, for example a | ||
library barcode, is left on the read. | ||
* extract: Flexible removal of UMI sequences from fastq reads. | ||
UMIs are removed and appended to the read name. Any other barcode, for example a library barcode, is left on the read. | ||
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dedup_umi.py: Implements a number of different UMI deduplication schemes. | ||
The recommended methods are `directional_adjecency` and `adjecency`. In general | ||
`directional_adjecency` seems to be less sensitive to starting conditions, but there | ||
are situations where `adjecency` might out perform. | ||
* dedup: Implements a number of different UMI deduplication schemes. | ||
The recommended method is `directional_adjecency`. | ||
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See simulation results at the `CGAT blog <https://cgatoxford.wordpress.com/2015/08/14/unique-molecular-identifiers-the-problem-the-solution-and-the-proof/>`_. | ||
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`Genome Science 2015 poster <http://f1000research.com/posters/4-728>`_. | ||
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Preprint on the way shortly... | ||
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Installation | ||
------------ | ||
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Both tools are just python scripts. Type | ||
If you're using Conda, you can use: | ||
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.. code:: bash | ||
conda install -c https://conda.anaconda.org/toms umi_tools | ||
Or pip: | ||
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.. code:: bash | ||
pip install umi_tools | ||
Or if you'd like to work directly from the git repository: | ||
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.. code:: bash | ||
git clone git@github.com:CGATOxford/UMI-tools.git | ||
Enter repository and run: | ||
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``` | ||
python dedup_umi.py --help | ||
``` | ||
.. code:: bash | ||
or | ||
python setup.py install | ||
``` | ||
python extract_umi.py --help | ||
``` | ||
Help | ||
----- | ||
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for help. `dedup_umi.py` is dependent on `numpy`, `pandas` and both are dependent, at the moment, on `CGAT <https://www.cgat.org/downloads/public/cgat/documentation/cgat.html#cgat>`_. | ||
To get help on umi_tools run | ||
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.. code:: bash | ||
`umi_tools --help` | ||
To get help on umi_tools extract run | ||
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.. code:: bash | ||
`umi_tools extract --help` | ||
To get help on umi_tools dedup run | ||
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.. code:: bash | ||
`umi_tools dedup --help` | ||
Dependencies | ||
------------ | ||
umi_tools is dependent on `numpy`, `pandas`, `cython`, `pysam` and `future` |
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setuptools>=1.1 | ||
cython>=0.19 | ||
numpy>=1.7 | ||
pandas>=0.12.0 | ||
pysam>=0.8.4 | ||
future |
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[metadata] | ||
description-file = README.rst |
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import sys | ||
import os | ||
import glob | ||
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try: | ||
import Cython | ||
except ImportError: | ||
raise ImportError( | ||
"UMI-tools requires cython to " | ||
"be installed before running setup.py (pip install cython)") | ||
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try: | ||
import pysam | ||
except ImportError: | ||
raise ImportError( | ||
"UMI-tools requires pysam to " | ||
"be installed before running setup.py (pip install pysam)") | ||
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######################################################################## | ||
######################################################################## | ||
# Import setuptools | ||
# Use existing setuptools, otherwise try ez_setup. | ||
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try: | ||
import setuptools | ||
except ImportError: | ||
raise ImportError( | ||
"UMI-tools requires setuptools" | ||
"be installed before running setup.py (pip install setuptools)") | ||
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from setuptools import setup, find_packages, Extension | ||
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from distutils.version import LooseVersion | ||
if LooseVersion(setuptools.__version__) < LooseVersion('1.1'): | ||
print ("Version detected:", LooseVersion(setuptools.__version__)) | ||
raise ImportError( | ||
"UMI-tools requires setuptools 1.1 higher") | ||
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from Cython.Build import cythonize | ||
######################################################################## | ||
######################################################################## | ||
# collect umi_tools version | ||
sys.path.insert(0, "umi_tools") | ||
import version | ||
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version = version.__version__ | ||
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############################################################### | ||
############################################################### | ||
# Define dependencies | ||
# Perform a umi_tools Installation | ||
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major, minor1, minor2, s, tmp = sys.version_info | ||
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if (major == 2 and minor1 < 7) or major < 2: | ||
raise SystemExit("""UMI-tools requires Python 2.7 or later.""") | ||
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umi_tools_packages = ["umi_tools"] | ||
umi_tools_package_dirs = {'umi_tools': 'umi_tools'} | ||
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install_requires = [] | ||
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for requirement in ( | ||
l.strip() for l in open('requirements.txt') if not l.startswith("#")): | ||
install_requires.append(requirement) | ||
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########################################################## | ||
########################################################## | ||
# Classifiers | ||
classifiers = """ | ||
Development Status :: 3 - Alpha | ||
Intended Audience :: Science/Research | ||
Intended Audience :: Developers | ||
License :: OSI Approved | ||
Programming Language :: Python | ||
Topic :: Software Development | ||
Topic :: Scientific/Engineering | ||
Operating System :: POSIX | ||
Operating System :: Unix | ||
Operating System :: MacOS | ||
""" | ||
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setup( | ||
# package information | ||
name='umi_tools', | ||
version=version, | ||
description='umi-tools: Tools for UMI analyses', | ||
author='Ian Sudbery', | ||
author_email='i.sudbery@sheffield.ac.uk', | ||
license="MIT", | ||
platforms=["any"], | ||
keywords="computational genomics", | ||
long_description='umi-tools: Tools for UMI analyses', | ||
classifiers=list(filter(None, classifiers.split("\n"))), | ||
url="https://github.com/CGATOxford/UMI-tools", | ||
download_url="https://github.com/CGATOxford/UMI-tools/tarball/%s" % version, | ||
# package contents | ||
packages=umi_tools_packages, | ||
package_dir=umi_tools_package_dirs, | ||
include_package_data=True, | ||
# dependencies | ||
install_requires=install_requires, | ||
# extension modules | ||
ext_modules=cythonize("umi_tools/_dedup_umi.pyx"), | ||
entry_points={ | ||
'console_scripts': ['umi_tools = umi_tools.umi_tools:main'] | ||
}, | ||
# other options | ||
zip_safe=False, | ||
) |
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