Mercurial > repos > miller-lab > genome_diversity
view reorder.py @ 25:cba0d7a63b82
workaround for gd_genotype datatype
admix shift int -> float
author | Richard Burhans <burhans@bx.psu.edu> |
---|---|
date | Wed, 29 May 2013 13:49:19 -0400 |
parents | 248b06e86022 |
children |
line wrap: on
line source
#!/usr/bin/env python import sys def parse_rangelist(string): rv = [] tokens = strip_split(string, ',') for token in tokens: int_list = parse_token(token) for int_val in int_list: int_val -= 1 if int_val not in rv: rv.append(int_val) return rv def parse_token(token): values = strip_split(token, '-') num_values = len(values) if num_values not in [1, 2]: print >> sys.stderr, 'Error: "%s" is not a valid range' % token sys.exit(1) int_list = [] for value in values: if value: int_val = as_int(value) if int_val < 1: print >> sys.stderr, 'Error: "%s" is not >= 1' % value sys.exit(1) int_list.append(int_val) else: print >> sys.stderr, 'Error: "%s" is not a valid range' % token sys.exit(1) if num_values == 1: return int_list a, b = int_list if a <= b: return range(a, b+1) else: return range(a, b-1, -1) def strip_split(string, delim): return [elem.strip() for elem in string.split(delim)] def as_int(string): try: val = int(string) except: print >> sys.stderr, 'Error: "%s" does not appear to be an integer' % string sys.exit(1) return val def get_lines(filename): rv = [] fh = open(filename) for line in fh: line = line.rstrip('\r\n') rv.append(line) fh.close() return rv def reorder(old_lines, new_order, filename): max_index = len(old_lines) - 1 fh = open(filename, 'w') for index in new_order: if index <= max_index: print >> fh, old_lines[index] old_lines[index] = None for line in old_lines: if line is not None: print >> fh, line fh.close() if len(sys.argv) != 4: print >> sys.stderr, "Usage" sys.exit(1) input, output, order_string = sys.argv[1:] new_order = parse_rangelist(order_string) old_lines = get_lines(input) reorder(old_lines, new_order, output) sys.exit(0)