diff cofold.py @ 0:65fff071414e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cofold.py	Wed Jan 14 08:56:58 2015 -0500
@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+
+import sys, os
+import argparse
+import shlex
+import subprocess
+
+parser = argparse.ArgumentParser()
+parser.add_argument('-i', '--input', help='Input file name')
+parser.add_argument('-o1','--output1', help='tabular output file')
+parser.add_argument('-s', '--parameters', help='arguments')
+args=parser.parse_args()
+
+myinput = open(args.input)
+
+parameters = args.parameters
+
+# we assume that the param files are located next to the python dir
+script_dir = os.path.dirname(os.path.realpath(__file__))
+parameters = args.parameters.replace('-P ', '-P %s/' % script_dir)
+p = subprocess.check_output(shlex.split('CoFold '+ parameters), stdin=myinput)
+
+lines=p.split('\n')
+# FASTA header
+o=lines[0].replace('\t',' ')
+
+for x in range(1, len(lines)):
+    if x % 3 == 2:
+        [seq,st]=lines[x].split(' ',1)
+        st=st.strip().lstrip('(').rstrip(')')
+        o+='\t' + seq + '\t' + st
+    if x % 3 == 1:
+        o+='\t'+lines[x]
+    if x % 3 == 0:
+        o+='\n'+lines[x].replace('\t',' ')
+out=open(args.output1,'w')
+out.write(o)
+out.close()
+
+
+
+
+