--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnafold_SHAPE.py	Tue May 16 16:30:23 2017 -0400
@@ -0,0 +1,45 @@
+### overcoming the problem of SHAPE data working with a single line.
+### creating multiple multiple files containg SHAPE data for a single sequence and running RNAfold for every
+### single sequence.
+
+import os
+import sys
+from os import system
+from Bio import SeqIO
+import re
+from subprocess import Popen, PIPE
+
+params_list = sys.argv[1:]
+param_list_no_shape = [s for s in params_list if not "--shape=" in s ]
+shape_file = [s for s in params_list if "--shape=" in s ]
+assert (len(shape_file) == 1)
+
+shape_file = shape_file[0]
+shape_file = shape_file.replace('--shape=', '')
+
+params_no_shape  =  " ".join(str(x) for x in param_list_no_shape)
+
+pattern = re.compile("^>.*$")
+id_line = ""
+with open(shape_file, 'r') as f:
+    content = f.read()
+    lines = content.split('\n')
+    for line in lines:
+        if pattern.match(line):
+            id_line = line.split()[0]
+            id_line = id_line[1:]
+            continue
+        else:
+            with open(id_line +'.tmp', "a") as clFile:
+                clFile.write(line + "\n")
+                
+input_file = sys.stdin
+
+for record in SeqIO.parse(input_file, "fasta"):
+    seq = ">{}\n{}".format(record.id,record.seq)
+    cmd =  " RNAfold  --shape=" + record.id + '.tmp ' + params_no_shape
+    p = Popen(cmd , stdin=PIPE, shell=True, stdout=PIPE, stderr=PIPE)
+    out,err = p.communicate(seq.encode())
+    if err:
+        raise RuntimeError("Error in calling RNAfold\n{}\n{}\n".format(out, err))
+    print (out.decode('utf-8').strip())