Added initial setup script. Added utils module. Updated import script.

.gitignore

+build/
+*.swp
+*.pyc

Readme.md

 New project for Chip-seq stuff.
+
+meta/ contains the initial metadata setup.
+
+doc/ contains documentation for the project.
+
+chipathlon/ contains workflow code.

chipathlon/utils.py

+import sys
+
+def progress(current, end):
+    percent = float(current) / end
+    hashes = "#" * int(round(percent * 20))
+    spaces = " " * (20 - len(hashes))
+    sys.stdout.write("\rProcessed %s / %s entries. [%s] %s%%" % (current, end, hashes + spaces, int(round(percent * 100))))
+
+

test_data/import.py → meta/import.py

@@ -2,13 +2,7 @@ from pymongo import MongoClient
 import argparse
 import json
 import sys
-
-def progress(current, end):
-	percent = float(current) / end
-	hashes = "#" * int(round(percent * 20))
-	spaces = " " * (20 - len(hashes))
-	sys.stdout.write("\rProcessed %s / %s entries. [%s] %s%%" % (current, end, hashes + spaces, int(round(percent * 100))))
-	sys.stdout.flush()
+from chipathlon.utils import progress
 
 parser = argparse.ArgumentParser(description = "Import all test data into the database.")
 parser.add_argument("--password", dest="password", required=True, help="Database user password.")
@@ -29,7 +23,7 @@ if args.drop:
 	db.samples.drop()
 
 # Insert all experiment metadata, expected in meta/meta_clean.json
-with open("meta/meta_clean.json", "r") as rh:
+with open("data/meta_clean.json", "r") as rh:
 	data = json.load(rh)
 	exp_ids = db.experiments.insert_many(data)
 

setup.py

+from distutils.core import setup
+
+setup(
+    name="chipathlon",
+    version="1.0",
+    packages=["chipathlon"],
+    license="???",
+    scripts = []
+)