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1 # -*- coding: utf-8 -*-
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2 """
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3 Glimmer --> extract
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4 version 0.2 (andrea.pinna@crs4.it)
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5 """
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6
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7 import optparse
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8 import subprocess
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9 import sys
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10
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11 def __main__():
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12 # load arguments
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13 print 'Parsing Extract input options...'
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14 parser = optparse.OptionParser()
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15 parser.add_option('--exSequence', dest='sequence', help='')
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16 parser.add_option('--exCoords', dest='coords', help='')
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17 parser.add_option('--ex2Fields', action='store_true', dest='twofields', help='')
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18 parser.add_option('--exDir', action='store_true', dest='dir', help='')
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19 parser.add_option('--exMinLen', dest='minlen', type='int', help='')
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20 parser.add_option('--exNoStart', action='store_true', dest='nostart', help='')
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21 parser.add_option('--exNoStop', action='store_true', dest='nostop', help='')
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22 parser.add_option('--exNoWrap', action='store_true', dest='nowrap', help='')
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23 parser.add_option('--exOutput', dest='output', help='')
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24 parser.add_option('--logfile', dest='logfile', help='')
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25 (options, args) = parser.parse_args()
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26 if len(args) > 0:
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27 parser.error('Wrong number of arguments')
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28
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29 # build Extract command to be executed
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30 sequence = options.sequence
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31 coords = options.coords
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32 if options.twofields:
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33 twofields = '--2_fields'
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34 else:
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35 twofields = ''
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36 if options.dir:
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37 direct = '--dir'
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38 else:
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39 direct = ''
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40 if options.minlen is not None:
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41 minlen = '--minlen %d' % (options.minlen)
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42 else:
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43 minlen = ''
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44 if options.nostart:
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45 nostart = '--nostart'
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46 else:
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47 nostart = ''
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48 if options.nostop:
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49 nostop = '--nostop'
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50 else:
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51 nostop = ''
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52 if options.nowrap:
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53 nowrap = '--nowrap'
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54 else:
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55 nowrap = ''
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56 output = options.output
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57 logfile = options.logfile
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58
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59 # Build Extract command
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60 cmd = 'extract %s %s %s %s %s %s %s %s > %s' % (twofields, direct, minlen, nostart, nostop, nowrap, sequence, coords, output)
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61 print '\nExtract command to be executed: \n %s' % (cmd)
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62
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63 print 'Executing Extract...'
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64 if logfile:
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65 log = open(logfile, 'w')
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66 else:
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67 log = sys.stdout
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68 try:
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69 subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True)
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70 finally:
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71 if log != sys.stdout:
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72 log.close()
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73 print 'Extract executed!'
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74
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75
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76 if __name__ == "__main__":
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77 __main__()
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