Add license, more docstrings

remove hard-coded test paths

diff --git a/find_meme_letter_probabilities.py b/find_meme_letter_probabilities.py
index fa34bab0307183c496a624136c7343c16a20b51d..50ab65049ae3fa6f27197a496402f2b48c9c0428 100644 (file)
--- a/find_meme_letter_probabilities.py
+++ b/find_meme_letter_probabilities.py
@@ -1,12 +1,27 @@
 #!/usr/bin/python 3
+"""Program to search through MEME report to find letter-probabilties matrix
+"""
+
+# Copyright (2015) Diane Trout & California Institute of Technology
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 import argparse
 import re
 import os
 
 def main(cmdline=None):
-    #filename = '/woldlab/castor/home/kfisher/ChIA/AliNodes/DNase4/Wellington/PP_DE_analysis/Consolidated_Wellington_promoters_3xUp_10FPKM.cyteConnected_myocyteFootprints.20rad.MEME2_maxw25/meme.txt'
-    #output_dir = '.'
-
     parser = make_parser()
     args = parser.parse_args(cmdline)