--- a/splitSHAPE.py	Wed May 24 09:56:11 2017 -0400
+++ b/splitSHAPE.py	Mon Nov 20 05:01:21 2017 -0500
@@ -3,7 +3,6 @@
 import sys
 
 shape_file = sys.argv[1]
-win_size = int(sys.argv[2])
 
 pattern = re.compile("^>.*$")
 toWrite = ""
@@ -18,9 +17,9 @@
 name_file = "FASTA/data.names"
 array_all_chunks = []
 with open(name_file, 'r') as f:
-    content = f.read()
-    lines = content.split('\n')[:-1]
-    for line in lines:
+    for line in f:
+        if len(line.strip()) == 0:
+            continue
         seq_id.append(int(line.split()[0]))
         seq_string.append(line.split()[1])
         orig_id_srt = line.split()[3]
@@ -36,7 +35,7 @@
     lines = content.split('\n')
     for line in lines:
         if pattern.match(line):
-            line = line.replace('>','').strip()
+            line = line.replace('>','').split()[0]
             react_arr=[]
             react_dict[line] = react_arr
             continue
@@ -47,7 +46,7 @@
 chunks = []
 for i in range(len(orig_id)):
     if not orig_id[i] in react_dict:
-        raise RuntimeError('Error key {} not found'.format(orig_id))
+        raise RuntimeError('Error key {} {} not found'.format(i, orig_id[i]))
 
     react_val = react_dict[orig_id[i]]
     toWrite += '>' + str(seq_id[i]) + " " + seq_string[i] + "\n"