diff reformat.py @ 0:db0f5c1cb227 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reformat.py	Fri May 02 06:15:38 2014 -0400
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+
+"""
+    Extract importent information from the standard output file and put it in some standard format, like BED and tabular.
+"""
+
+import sys
+
+bed = open(sys.argv[2], 'w+')
+tabular = open(sys.argv[3], 'w+')
+
+for line in open(sys.argv[1]):
+    # ORGANISM:  gi|21226102|ref|NC_003901.1| Methanosarcina mazei Go1 chromosome, complete genome
+    if line.startswith('ORGANISM:'):
+        organism = line.lstrip('ORGANISM:').strip()
+    # CRISPR 1   Range: 679197 - 682529
+    if line.startswith('CRISPR '):
+        start,end = line.split('Range:')[1].strip().split('-')
+        start = start.strip()
+        end = end.strip()
+        bed.write('%s\t%s\t%s\n' % (organism, start, end))
+    if line.rstrip().endswith(']'):
+        cols = line.split()
+        tabular.write("%s\t%s\t%s\t%s\t%s\t%s\n" % (organism, cols[0], cols[1], cols[2], cols[4].rstrip(','), cols[5]))