annotate reorder.py @ 31:a631c2f6d913

Update to Miller Lab devshed revision 3c4110ffacc3
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:25:27 -0400
parents 248b06e86022
children
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1 #!/usr/bin/env python
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2
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3 import sys
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4
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5 def parse_rangelist(string):
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6 rv = []
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7
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8 tokens = strip_split(string, ',')
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9 for token in tokens:
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10 int_list = parse_token(token)
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11 for int_val in int_list:
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12 int_val -= 1
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13 if int_val not in rv:
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14 rv.append(int_val)
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15
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16 return rv
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17
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18 def parse_token(token):
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19 values = strip_split(token, '-')
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20 num_values = len(values)
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21
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22 if num_values not in [1, 2]:
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23 print >> sys.stderr, 'Error: "%s" is not a valid range' % token
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24 sys.exit(1)
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25
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26 int_list = []
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27 for value in values:
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28 if value:
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29 int_val = as_int(value)
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30
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31 if int_val < 1:
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32 print >> sys.stderr, 'Error: "%s" is not >= 1' % value
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33 sys.exit(1)
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34
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35 int_list.append(int_val)
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36 else:
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37 print >> sys.stderr, 'Error: "%s" is not a valid range' % token
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38 sys.exit(1)
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39
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40 if num_values == 1:
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41 return int_list
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42
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43 a, b = int_list
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44
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45 if a <= b:
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46 return range(a, b+1)
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47 else:
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48 return range(a, b-1, -1)
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49
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50 def strip_split(string, delim):
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51 return [elem.strip() for elem in string.split(delim)]
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52
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53 def as_int(string):
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54 try:
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55 val = int(string)
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56 except:
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57 print >> sys.stderr, 'Error: "%s" does not appear to be an integer' % string
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58 sys.exit(1)
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59 return val
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60
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61 def get_lines(filename):
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62 rv = []
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63
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64 fh = open(filename)
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65 for line in fh:
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66 line = line.rstrip('\r\n')
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67 rv.append(line)
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68 fh.close()
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69
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70 return rv
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71
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72 def reorder(old_lines, new_order, filename):
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73 max_index = len(old_lines) - 1
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74
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75 fh = open(filename, 'w')
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76
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77 for index in new_order:
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78 if index <= max_index:
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79 print >> fh, old_lines[index]
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80 old_lines[index] = None
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81
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82 for line in old_lines:
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83 if line is not None:
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84 print >> fh, line
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85
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86 fh.close()
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87
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88 if len(sys.argv) != 4:
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89 print >> sys.stderr, "Usage"
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90 sys.exit(1)
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91
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92 input, output, order_string = sys.argv[1:]
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93
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94 new_order = parse_rangelist(order_string)
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95 old_lines = get_lines(input)
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96 reorder(old_lines, new_order, output)
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97
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98 sys.exit(0)