Version 0.0.1 initial commit

.gitignore

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+# package-specific output
+*_mf_output.tsv
+
+# 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/
+wheels/
+*.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/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# pytest
+.pytest_cache/
+
+.DS_Store

README.md

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 # motif-finder
 A novel approach to motif identification in proteins
+
+### Important
+
+This code is in BETA and features may change without notice.
+
+### Usage
+
+Provide a text query file, which is required. If not using manual motifs, also provide one more motif files using the `-m` flag to generate motifs dynamically.
+
+```
+pip install motiffinder
+# main program
+motiffinder <query file> -m <optional motif file>
+
+# for help
+motiffind -h
+
+# for version
+motiffinder -v
+```
+
+Or, clone this repository and set up with:
+
+```
+pip install -r requirements.text
+python -m motiffinder <query file> -m <optional motif file>
+
+# alternately, use setup.py to get the motiffinder package
+python setup.py install
+```
+
+### Contributors
+
+Written by Carl Vitzthum and Prof. Andrea Tilden

motiffinder/__init__.py

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+from __future__ import absolute_import
+from .mf_main import mf_main
+from ._version import __version__

motiffinder/__main__.py

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+from __future__ import absolute_import
+from . import (
+    mf_main,
+    __version__
+)
+import argparse
+import sys
+
+
+def main():
+    """
+    Execute the program from the command line
+    """
+    main_help = ("Main program for motif finding. Provide a query file and "
+                 "optional motif file(s) with the -m argument")
+    parser = argparse.ArgumentParser(prog='motiffinder', description=main_help)
+    parser.add_argument('queries', help="File containing settings and queries")
+    motifs_help = ("File containing proteins used to generate motifs."
+                   "Can specify multiple")
+    parser.add_argument('-m', '--motifs', action='append', help=motifs_help)
+    parser.add_argument('-v', '--version', action='version',
+                        version='%(prog)s ' + __version__)
+    args = parser.parse_args()
+    mf_main(args.queries, args.motifs)
+
+
+if __name__ == '__main__':
+    main()

motiffinder/_version.py

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+__version__ = "0.0.1"