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comparison create_window_positions_by_chrom.py @ 124:7a5b618675a6 draft

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author greg
date Tue, 21 Nov 2017 14:39:23 -0500
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123:e2995f2f127f 124:7a5b618675a6
1 #!/usr/bin/env python
2 import argparse
3 import collections
4
5 parser = argparse.ArgumentParser()
6 parser.add_argument('--input', dest='input', help='Input bed dataset')
7 parser.add_argument('--output', dest='output', help='Output window positions by chromosome dataset')
8
9 args = parser.parse_args()
10
11 chroms = collections.OrderedDict()
12
13 with open(args.input, 'r') as fh:
14 for count, line in enumerate(fh):
15 line = line.strip()
16 if not line or line.startswith('#'):
17 # Skip blank lines and comments.
18 continue
19 items = line.split('\t')
20 chrom = items[0]
21 if count == 0:
22 # First window.
23 chroms[chrom] = [0, count+1]
24 elif chrom in chroms:
25 # Get the start / end tuple.
26 tup = chroms[chrom]
27 # Increment end by 1.
28 tup[1] += 1
29 chroms[chrom] = tup
30 else:
31 # chrom not in chroms.
32 chroms[chrom] = [count, count+1]
33
34 with open(args.output, 'w') as fh:
35 for k, v in chroms.items():
36 fh.write('%s %d %d\n' % (k, v[0], v[1]))