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annotate planemo-template/random_lines_two_pass.py @ 4:af383638de66 draft

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planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
author nick
date Mon, 23 Nov 2015 18:44:23 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4
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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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3 #Selects N random lines from a file and outputs to another file, maintaining original line order
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4 #allows specifying a seed
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5 #does two passes to determine line offsets/count, and then to output contents
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6
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7 import optparse, random
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8
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9 def get_random_by_subtraction( line_offsets, num_lines ):
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10 while len( line_offsets ) > num_lines:
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11 del line_offsets[ random.randint( 0, len( line_offsets ) - 1 ) ]
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12 return line_offsets
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13
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14 def get_random_by_sample( line_offsets, num_lines ):
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15 line_offsets = random.sample( line_offsets, num_lines )
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16 line_offsets.sort()
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17 return line_offsets
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18
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19 def get_random( line_offsets, num_lines ):
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20 if num_lines > ( len( line_offsets ) / 2 ):
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21 return get_random_by_subtraction( line_offsets, num_lines )
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22 else:
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23 return get_random_by_sample( line_offsets, num_lines )
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24
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25 def __main__():
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26 #Parse Command Line
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27 parser = optparse.OptionParser()
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28 parser.add_option( '-s', '--seed', dest='seed', action='store', type="string", default=None, help='Set the random seed.' )
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29 (options, args) = parser.parse_args()
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30
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31 assert len( args ) == 3, "Invalid command line specified."
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32
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33 input = open( args[0], 'rb' )
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34 output = open( args[1], 'wb' )
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35 num_lines = int( args[2] )
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36 assert num_lines > 0, "You must select at least one line."
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37
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38 if options.seed is not None:
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39 random.seed( options.seed )
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40
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41 #get line offsets
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42 line_offsets = []
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43 teller = input.tell
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44 readliner = input.readline
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45 appender = line_offsets.append
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46 while True:
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47 offset = teller()
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48 if readliner():
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49 appender( offset )
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50 else:
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51 break
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52
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53 total_lines = len( line_offsets )
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54 assert num_lines <= total_lines, "Error: asked to select more lines (%i) than there were in the file (%i)." % ( num_lines, total_lines )
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55
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56 #get random line offsets
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57 line_offsets = get_random( line_offsets, num_lines )
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58
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59 #write out random lines
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60 seeker = input.seek
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61 writer = output.write
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62 for line_offset in line_offsets:
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63 seeker( line_offset )
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64 writer( readliner() )
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65 input.close()
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66 output.close()
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67 print "Kept %i of %i total lines." % ( num_lines, total_lines )
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68 if options.seed is not None:
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69 print 'Used random seed of "%s".' % options.seed
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70
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71 if __name__=="__main__": __main__()