# HG changeset patch
# User greg
# Date 1511293163 18000
# Node ID 7a5b618675a63856d15e56ff8fdc556ce89144e8
# Parent  e2995f2f127f6464bcc16db3b9008a0ea131c3ca
Uploaded

diff -r e2995f2f127f -r 7a5b618675a6 create_window_positions_by_chrom.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_window_positions_by_chrom.py	Tue Nov 21 14:39:23 2017 -0500
@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+import argparse
+import collections
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--input', dest='input', help='Input bed dataset')
+parser.add_argument('--output', dest='output', help='Output window positions by chromosome dataset')
+
+args = parser.parse_args()
+
+chroms = collections.OrderedDict()
+
+with open(args.input, 'r') as fh:
+    for count, line in enumerate(fh):
+        line = line.strip()
+        if not line or line.startswith('#'):
+            # Skip blank lines and comments.
+            continue
+        items = line.split('\t')
+        chrom = items[0]
+        if count == 0:
+            # First window.
+            chroms[chrom] = [0, count+1]
+        elif chrom in chroms:
+            # Get the start / end tuple.
+            tup = chroms[chrom]
+            # Increment end by 1.
+            tup[1] += 1
+            chroms[chrom] = tup
+        else:
+            # chrom not in chroms.
+            chroms[chrom] = [count, count+1]
+
+with open(args.output, 'w') as fh:
+    for k, v in chroms.items():
+        fh.write('%s %d %d\n' % (k, v[0], v[1]))