From 0dde7a1ae613ac3e9b555d1ba83956cf320f0ba9 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 9 May 2018 11:15:39 -0500
Subject: [PATCH] Add in setup for python packages.

---
 .gitignore                             | 100 +++++++++++++++++++++++++
 alignment/convert_reads.py             |   4 +-
 alignment/map_qc.py                    |   4 +-
 alignment/map_reads.py                 |   4 +-
 call_peaks/call_peaks_macs.py          |   7 +-
 call_peaks/overlap_peaks.py            |   3 +-
 call_peaks/pool_and_psuedoreplicate.py |   3 +-
 quality_metrics/xcor.py                |   4 +-
 setup.py                               |   7 ++
 9 files changed, 115 insertions(+), 21 deletions(-)
 create mode 100644 .gitignore
 create mode 100644 setup.py

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..db1f598
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,100 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+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
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
diff --git a/alignment/convert_reads.py b/alignment/convert_reads.py
index 7d57c88..72e5d98 100644
--- a/alignment/convert_reads.py
+++ b/alignment/convert_reads.py
@@ -9,9 +9,7 @@ import subprocess
 import shlex
 import logging
 from multiprocessing import cpu_count
-import sys
-sys.path.append(os.path.abspath('../python_utils'))
-import utils
+from python_utils import utils
 
 EPILOG = '''
 For more details:
diff --git a/alignment/map_qc.py b/alignment/map_qc.py
index 7959973..5bb74f0 100644
--- a/alignment/map_qc.py
+++ b/alignment/map_qc.py
@@ -9,10 +9,8 @@ import shutil
 import shlex
 import logging
 from multiprocessing import cpu_count
-import sys
 import pandas as pd
-sys.path.append(os.path.abspath('../python_utils'))
-import utils
+from python_utils import utils
 
 
 EPILOG = '''
diff --git a/alignment/map_reads.py b/alignment/map_reads.py
index 80f4708..877c7c7 100644
--- a/alignment/map_reads.py
+++ b/alignment/map_reads.py
@@ -9,9 +9,7 @@ import shutil
 import shlex
 import logging
 from multiprocessing import cpu_count
-import sys
-sys.path.append(os.path.abspath('../python_utils'))
-import utils
+from python_utils import utils
 
 EPILOG = '''
 For more details:
diff --git a/call_peaks/call_peaks_macs.py b/call_peaks/call_peaks_macs.py
index 154bdc6..8b13b3b 100644
--- a/call_peaks/call_peaks_macs.py
+++ b/call_peaks/call_peaks_macs.py
@@ -7,11 +7,8 @@ import argparse
 import shutil
 import logging
 from multiprocessing import cpu_count
-import sys
-sys.path.append(os.path.abspath('../python_utils'))
-import utils
-sys.path.append(os.path.abspath('../cross_correlation'))
-from xcor import xcor as calculate_xcor
+from python_utils import utils
+from quality_metrics.xcor import xcor as calculate_xcor
 
 EPILOG = '''
 For more details:
diff --git a/call_peaks/overlap_peaks.py b/call_peaks/overlap_peaks.py
index 9bfd19c..3687eb7 100644
--- a/call_peaks/overlap_peaks.py
+++ b/call_peaks/overlap_peaks.py
@@ -8,8 +8,7 @@ import logging
 import shutil
 import pandas as pd
 import sys
-sys.path.append(os.path.abspath('../python_utils'))
-import utils
+from python_utils import utils
 
 EPILOG = '''
 For more details:
diff --git a/call_peaks/pool_and_psuedoreplicate.py b/call_peaks/pool_and_psuedoreplicate.py
index 6c2d0cc..f5078e7 100644
--- a/call_peaks/pool_and_psuedoreplicate.py
+++ b/call_peaks/pool_and_psuedoreplicate.py
@@ -8,8 +8,7 @@ import pandas as pd
 import numpy as np
 import os
 import sys
-sys.path.append(os.path.abspath('../python_utils'))
-import utils
+from python_utils import utils
 
 EPILOG = '''
 For more details:
diff --git a/quality_metrics/xcor.py b/quality_metrics/xcor.py
index 672fdbb..5047469 100644
--- a/quality_metrics/xcor.py
+++ b/quality_metrics/xcor.py
@@ -7,9 +7,7 @@ import argparse
 import shutil
 import logging
 from multiprocessing import cpu_count
-import sys
-sys.path.append(os.path.abspath('../python_utils'))
-import utils
+from python_utils import utils
 
 EPILOG = '''
 For more details:
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..d188725
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,7 @@
+from distutils.core import setup
+from setuptools import find_packages
+
+setup(
+    name = 'ProcessScripts',
+    packages = find_packages('.'),
+)
-- 
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