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comparison python/cluster.py @ 7:3ee329b129c6

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rename block properties, slightly revise result format
author Henry S. Thompson <ht@inf.ed.ac.uk>
date Wed, 26 May 2021 09:18:49 -0400
parents 672621ab4db4
children e411408d64ec
comparison
equal deleted inserted replaced
6:a01ff74f9fd7 7:3ee329b129c6
3 import sys 3 import sys
4 4
5 from util import * 5 from util import *
6 6
7 if len(sys.argv)==1 or sys.argv[1]=='-h': 7 if len(sys.argv)==1 or sys.argv[1]=='-h':
8 print("""Usage: cluster.py [-h] [-c n] infile.tsv [outfile.tsv] 8 print("""Usage: cluster.py [-h] [-c n] [-s] infile.tsv [outfile.tsv]
9 n is cluster diameter, default is 5 9 n is cluster diameter, default is 5
10 -s for strict circle distance, reduces number of candidates
10 default outfile is [infile]_c[n].tsv""") 11 default outfile is [infile]_c[n].tsv""")
11 exit(1) 12 exit(1)
12 if sys.argv[1]=='-c': 13 if sys.argv[1]=='-c':
13 sys.argv.pop(1) 14 sys.argv.pop(1)
14 n=float(sys.argv.pop(1)) 15 n=float(sys.argv.pop(1))
15 else: 16 else:
16 n=5.0 17 n=5.0
18
19 if sys.argv[1]=='-s':
20 sys.argv.pop(1)
21 strict=True
22 else:
23 strict=False
17 24
18 infile_name=sys.argv.pop(1) 25 infile_name=sys.argv.pop(1)
19 if len(sys.argv)>1: 26 if len(sys.argv)>1:
20 outfile_name=sys.argv.pop(1) 27 outfile_name=sys.argv.pop(1)
21 else: 28 else:
38 for l in infile: 45 for l in infile:
39 found=False 46 found=False
40 (_,td,qd)=l.rstrip().split('\t') 47 (_,td,qd)=l.rstrip().split('\t')
41 q=[float(i) for i in qd.split(',')] 48 q=[float(i) for i in qd.split(',')]
42 td=float(td) 49 td=float(td)
43 if td>orad: 50 if strict and td>orad:
44 # Enforce a circular region, not square 51 # Enforce a circular region, not square
52 print(td,orad,file=sys.stderr)
45 break 53 break
46 for c in cc: 54 for c in cc:
47 for p in c: 55 for p in c:
48 if d(p,q)<=n: 56 if d(p,q)<=n:
49 c.append(q) 57 c.append(q)