From 3c4f733eb627dce9c2e8566f617dbe7dbf58a1fd Mon Sep 17 00:00:00 2001
From: renewiegandt <rene.wiegandt@mpi-bn.mpg.de>
Date: Wed, 19 Dec 2018 14:40:59 +0100
Subject: [PATCH] get_best_motif.py: fixed bug which caused to print motif
 header as last line + improved documentation

---
 bin/get_best_motif.py | 54 ++++++++++++++++++++++++++++++++++++-------
 1 file changed, 46 insertions(+), 8 deletions(-)

diff --git a/bin/get_best_motif.py b/bin/get_best_motif.py
index cc24949..37eccc5 100644
--- a/bin/get_best_motif.py
+++ b/bin/get_best_motif.py
@@ -1,26 +1,64 @@
-# parses arguments using argparse
-# @return args list of all parameters
+'''
+parses arguments using argparse
+@return args list of all parameters
+'''
 def parse_arguments():
-    parser = argparse.ArgumentParser()
-    parser.add_argument("meme", help="Path to meme file")
+    parser = argparse.ArgumentParser(description='A script to convert from GLAM2 output to MEME-format and parsing only the [num] first motifs from file to the output.')
+    parser.add_argument("meme", help="Path to 'meme' file generated by GLAM2")
     parser.add_argument("output", help="Output file")
     parser.add_argument("num", help="Number of motifs parsed from file")
     args = parser.parse_args()
     return args
 
-# write lines of file till certain line (MOTIF + [num])
+'''
+The script has to functions:
+    1. Writing lines of file till certain line (MOTIF + [num])
+    2. Converting GLAM2 output to minimal meme-format
+@params meme STING Path to 'meme' file generated from Meme suite
+@parmas output STING Output file
+@params num INT Number of motifs parsed from file
+
+@author René Wiegandt
+@contact rene.wiegandt(at)mpi-bn.mpg.de
+'''
 def main():
+
     args = parse_arguments()
     out = open(args.output, "w+")
+    
+    '''
+    Create pattern where script should stop writing
+    For Example:
+    If num == 3, which means that you want the first/best 3 Motifs, the script
+    should stop writing lines to output if loop reaches line 'MOTIF  4'
+    '''
     number = int(args.num) + 1
-    motif = "MOTIF " + str(number)
+    break_header = "MOTIF  " + str(number)
+
+    # Pattern for motif header
+    pattern = re.compile("^MOTIF\s{2}(\d)+")
+    # Init count
+    count = 0
+
     with open(args.meme) as f:
         for line in f:
-            if motif in line:
+            ## do not write [count] lines after each header -> needed for meme-format
+            if count > 0:
+                count-=1
+                continue
+            if pattern.match(line):
+                # if line is a motif header
+                count = 2
+            ##
+
+            if break_header in line:
+                # line matches breaking_header, e.g. 'MOTIF  4'
                 break
-            out.write(line)
+            else:
+                out.write(line)
 
 
 if __name__ == "__main__":
     import argparse
+    import re
     main()