Merge branch 'develop'

.bumpversion.cfg

@@ -0,0 +1,12 @@
+[bumpversion]
+current_version = 0.2.0
+
+[bumpversion:file:setup.py]
+
+[bumpversion:file:conda/meta.yaml]
+search = version: {current_version}
+replace = version: {new_version}
+
+[bumpversion:file:src/pyim/__init__.py]
+search = __version__ = '{current_version}'
+replace = __version__ = '{new_version}'

.gitattributes

@@ -0,0 +1 @@
+src/pyim/_version.py export-subst

.gitignore

@@ -7,3 +7,6 @@ htmlcov
 .coverage
 _legacy
 docs/_build
+RELEASE-VERSION
+/.vscode
+/.cache

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "external/cimpl"]
+	path = external/cimpl
+	url = https://github.com/jrderuiter/cimpl.git

.travis.yml

@@ -0,0 +1,34 @@
+language: python
+
+python:
+    # We don't actually use the Travis Python, but this keeps it organized.
+    - '3.4'
+    - '3.5'
+
+install:
+    - sudo apt-get update
+
+    # Install conda.
+    - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    - bash miniconda.sh -b -p $HOME/miniconda
+    - export PATH="$HOME/miniconda/bin:$PATH"
+    - hash -r
+    - conda config --set always_yes yes --set changeps1 no
+    - conda update -q conda
+
+    # Useful for debugging any issues with conda.
+    - conda info -a
+
+    # Create conda environment.
+    - conda create -q -n test python=$TRAVIS_PYTHON_VERSION
+    - source activate test
+
+    # Install dependencies.
+    - conda install -c r -c bioconda r r-cimpl
+    - pip install .[dev]
+
+script:
+    py.test tests --cov pyim --cov-report term-missing
+
+#after_success:
+#    - coveralls

AUTHORS.rst

@@ -0,0 +1,13 @@
+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Julian de Ruiter <[email protected]>
+
+Contributors
+------------
+
+None yet. Why not be the first?

CONTRIBUTING.rst

@@ -0,0 +1,102 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/jrderuiter/pyim/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+and "help wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+PyIM could always use more documentation, whether as part of the
+official PyIM docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/jrderuiter/pyim/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `pyim` for local development.
+
+1. Fork the `pyim` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone [email protected]:your_name_here/pyim.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv pyim
+    $ cd pyim/
+    $ pip install .[dev]
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass the tests::
+
+    $ make test
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 3.4 and 3.5. Check
+   https://travis-ci.org/jrderuiter/pyim/pull_requests
+   and make sure that the tests pass for all supported Python versions.

HISTORY.rst

@@ -0,0 +1,14 @@
+=======
+History
+=======
+
+0.2.0 (2017-05-10)
+------------------
+
+* Refactored pipeline structure.
+* Added ShearSplink and Nextera pipelines.
+
+0.1.0 (2016-09-01)
+------------------
+
+* Initial release.

LICENSE

@@ -0,0 +1,11 @@
+
+MIT License
+
+Copyright (c) 2016, Julian de Ruiter
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+

MANIFEST.IN

@@ -0,0 +1,13 @@
+
+include AUTHORS.rst
+
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

Makefile

@@ -0,0 +1,76 @@
+.PHONY: clean clean-test clean-pyc clean-build docs help
+.DEFAULT_GOAL := help
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+try:
+	from urllib import pathname2url
+except:
+	from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-test: ## remove test and coverage artifacts
+	rm -fr .tox/
+	rm -f .coverage
+	rm -fr htmlcov/
+
+lint: ## check style with flake8
+	flake8 pyim tests
+
+test: ## run tests quickly with the default Python
+	py.test
+
+coverage: ## check code coverage quickly with the default Python
+	coverage run --source pyim py.test
+
+		coverage report -m
+		coverage html
+		$(BROWSER) htmlcov/index.html
+
+docs: ## generate Sphinx HTML documentation, including API docs
+	rm -rf docs/_build
+	sphinx-autobuild docs docs/_build
+
+release: clean ## package and upload a release
+	python setup.py sdist upload
+	python setup.py bdist_wheel upload
+
+dist: clean ## builds source and wheel package
+	python setup.py sdist
+	python setup.py bdist_wheel
+	ls -l dist
+
+install: clean ## install the package to the active Python's site-packages
+	python setup.py install

README.rst

@@ -0,0 +1,71 @@
+===============================
+PyIM
+===============================
+
+.. image:: https://img.shields.io/travis/jrderuiter/pyim.svg
+        :target: https://travis-ci.org/jrderuiter/pyim
+
+PyIM (Python Insertional Mutagenesis) is a python package for analyzing
+insertional mutagenesis data from targeted sequencing of transposon insertion
+sites. The package provides several command line tools for identifying
+insertions, calling common insertion sites (CISs) and annotating
+insertions/CISs directly from the command line. It also aims to provides
+the basic building blocks for implementing new pipelines, CIS callers, etc.
+
+Documentation
+-------------
+
+PyIM's documentation is available at
+`jrderuiter.github.io/pyim <http://jrderuiter.github.io/pyim/>`_.
+
+
+Requirements
+------------
+
+PyIM is written for Python 3 and requires Python 3.3 or newer to be installed.
+Depending on the used functionality, PyIM also has the following external
+dependencies:
+
+- cutadapt/bowtie2 (Needed for identifying insertions from sequencing data)
+- cimpl (R package, needed for calling CIS sites using CIMPL)
+
+Installation
+------------
+
+Using conda
+~~~~~~~~~~~
+
+The recommended way to install PyIM is using conda, as with conda you can
+install PyIM together with its external dependencies (cutadapt and bowtie2)
+into an isolated environment using a single command:
+
+.. code:: bash
+
+    conda create -n pyim -c jrderuiter -c bioconda -c r pyim
+
+Alternatively, PyIM can be installed in an existing environent using:
+
+.. code:: bash
+
+    conda install -c jrderuiter -c bioconda -c r pyim
+
+Conda packages are available for both OSX and Linux (64-bit).
+
+Using pip
+~~~~~~~~~
+
+PyIM can be installed from Github using pip as follows:
+
+.. code:: bash
+
+    pip install git+git://github.com/jrderuiter/pyim.git#egg=pyim
+
+Note that in this case, external dependencies must be installed manually.
+
+Unfortunately, PyIM is not yet available on PyPI, though this may
+change when the package is further developed.
+
+License
+-------
+
+This software is released under the MIT license.

conda/build.sh

@@ -0,0 +1 @@
+$PYTHON setup.py install     # Python command to install the script.