Initial commit

.flake8

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+#########################
+# Flake8 Configuration  #
+# (.flake8)             #
+# (formerly in tox.ini) #
+#########################
+
+[flake8]
+ignore = E501
+exclude =
+    .tox,
+    .git,
+    __pycache__,
+    docs/source/conf.py,
+    build,
+    dist,
+    tests/fixtures/*,
+    *.pyc,
+    *.egg-info,
+    .cache,
+    .eggs
+max-complexity = 10
+import-order-style = google
+application-import-names = flake8
+format = ${cyan}%(path)s${reset}:${yellow_bold}%(row)d${reset}:${green_bold}%(col)d${reset}: ${red_bold}%(code)s${reset} %(text)s

.gitignore

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+.Rproj.user
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+
+# PyCharm project settings
+.idea/*
+
+*.pickle
+*.gpickle
+
+scratch
+scratch/*
+
+.pytest_cache
+.DS_Store
+
+.idea

.travis.yml

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+sudo: false
+cache: pip
+language: python
+python:
+- 3.6
+stages:
+  - lint
+  - docs
+jobs:
+  include:
+    # lint stage
+    - stage: lint
+      env: TOXENV=manifest
+    - env: TOXENV=flake8
+    - env: TOXENV=pylint
+    # docs stage
+    - stage: docs
+      env: TOXENV=doc8
+    - env: TOXENV=readme
+    - env: TOXENV=docs
+matrix:
+  allow_failures:
+      - env: TOXENV=flake8
+      - env: TOXENV=pylint
+install:
+  - pip install tox
+script:
+  - tox

LICENSE

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+MIT License
+
+Copyright (c) 2018 LifeScienceDataAnalytics
+
+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

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+graft src
+graft tests
+prune data
+prune hooks
+
+recursive-include docs/source *.py
+recursive-include docs/source *.rst
+include docs/Makefile
+
+global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
+
+exclude .bumpversion.cfg
+include *.rst *.txt *.yml LICENSE tox.ini .coveragerc .R

requirements.txt

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+-e git+https://github.com/GuiltyTargets/ppi-network-annotation#egg=ppi-network-annotation
+-e git+https://github.com/ozlemmuslu/guiltytargets#egg=guiltytargets
+-e git+https://github.com/ozlemmuslu/GAT2VEC#egg=GAT2VEC
+flask[web]
+flask-bootstrap[web]
+wtforms[web]
+flask-wtf[web]
+celery[web]
+sqlalchemy[web]

setup.py

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+# -*- coding: utf-8 -*-
+
+"""Setup module for the gene_prioritization package."""
+
+import codecs  # To use a consistent encoding
+import os
+import re
+
+import setuptools
+
+#################################################################
+
+PACKAGES = setuptools.find_packages(where='src')
+META_PATH = os.path.join('src', 'gene_prioritization', '__init__.py')
+KEYWORDS = ['Gene Prioritization', 'Networks Biology',
+            'Drug Target Prioritization']
+CLASSIFIERS = [
+    'Development Status :: 4 - Beta',
+    'Environment :: Console',
+    'Intended Audience :: Developers',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: MIT Software License',
+    'Operating System :: OS Independent',
+    'Programming Language :: Python',
+    'Programming Language :: Python :: 3.4',
+    'Programming Language :: Python :: 3.5',
+    'Programming Language :: Python :: 3.6',
+    'Topic :: Scientific/Engineering :: Bio-Informatics'
+]
+INSTALL_REQUIRES = [
+]
+
+EXTRAS_REQUIRE = {
+
+}
+TESTS_REQUIRE = [
+
+]
+ENTRY_POINTS = {
+    'console_scripts': [
+        'guiltytargets-web = guiltytargets-web.cli:main',
+    ]
+}
+DEPENDENCY_LINKS = [
+
+]
+
+PACKAGE_DATA = {
+    '': []
+}
+
+#################################################################
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+
+
+def read(*parts):
+    """Build an absolute path from *parts* and return the contents of the resulting file. Assume UTF-8 encoding."""
+    with codecs.open(os.path.join(HERE, *parts), 'rb', 'utf-8') as f:
+        return f.read()
+
+
+META_FILE = read(META_PATH)
+
+
+def find_meta(meta):
+    """Extract __*meta*__ from META_FILE"""
+    meta_match = re.search(
+        r'^__{meta}__ = ["\']([^"\']*)["\']'.format(meta=meta),
+        META_FILE, re.M
+    )
+    if meta_match:
+        return meta_match.group(1)
+    raise RuntimeError('Unable to find __{meta}__ string'.format(meta=meta))
+
+
+def get_long_description():
+    """Get the long_description from the README.rst file. Assume UTF-8 encoding."""
+    with codecs.open(os.path.join(HERE, 'README.rst'), encoding='utf-8') as f:
+        long_description = f.read()
+    return long_description
+
+
+if __name__ == '__main__':
+    setuptools.setup(
+        name=find_meta('title'),
+        version=find_meta('version'),
+        description=find_meta('description'),
+        long_description=get_long_description(),
+        url=find_meta('url'),
+        author=find_meta('author'),
+        author_email=find_meta('email'),
+        maintainer=find_meta('author'),
+        maintainer_email=find_meta('email'),
+        license=find_meta('license'),
+        classifiers=CLASSIFIERS,
+        keywords=KEYWORDS,
+        packages=PACKAGES,
+        package_dir={'': 'src'},
+        install_requires=INSTALL_REQUIRES,
+        extras_require=EXTRAS_REQUIRE,
+        tests_require=TESTS_REQUIRE,
+        entry_points=ENTRY_POINTS,
+        dependency_links=DEPENDENCY_LINKS,
+        package_data=PACKAGE_DATA,
+        include_package_data=True,
+    )

src/guiltytargets_web/__init__.py

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+# -*- coding: utf-8 -*-
+
+"""Web module for Gene-Prioritization"""

src/guiltytargets_web/forms.py

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+# -*- coding: utf-8 -*-
+
+from flask_wtf import FlaskForm
+from flask_wtf.file import FileField
+from wtforms.fields import RadioField, StringField, SubmitField, TextAreaField
+
+PPI_PATH = '/Users/cthoyt/ownCloud/Gene-Prioritization-Data/MayoRNASeq-TCX/hippie_current.edgelist'
+
+ppi_graph = RadioField(
+    'PPI Graph',
+    choices=[
+        ('string', 'STRING'),  # TODO add link
+        (PPI_PATH, 'HIPPIE'),
+    ],
+    default=PPI_PATH
+)
+
+class GuiltyTargetsForm(FlaskForm):
+    """The form for using the GAT2VEC pipeline."""
+    entrez_gene_identifiers = TextAreaField('Entrez Gene Identifiers')
+    ppi_graph = ppi_graph
+    file = FileField(
+        'Differential Gene Expression File',
+        # validators=[DataRequired()],
+    )
+    gene_symbol_column = StringField(
+        'Gene Symbol Column Name',
+        default='Gene.symbol',
+    )
+    log_fold_change_column = StringField(
+        'Log Fold Change Column Name',
+        default='logFC',
+    )
+    separator = RadioField(
+        'Separator',
+        choices=[
+            ('\t', 'My document is a TSV file'),
+            (',', 'My document is a CSV file'),
+        ],
+        default='\t')
+
+    # Submit
+    submit = SubmitField('Upload')