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1 # -*- coding: utf-8 -*-
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2 """
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3 Edena (overlapping)
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4 version 0.2.1 (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 shutil
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9 import subprocess
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10 import sys
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11
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12 def __main__():
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13 # load arguments
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14 print 'Parsing Edena (overlapping) input options...'
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15 parser = optparse.OptionParser()
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1
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16 parser.add_option('--unpaired_input', action='append', dest='unpaired_input', help='')
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17 parser.add_option('--dr_pair_1', action='append', dest='dr_pair_1', help='')
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18 parser.add_option('--dr_pair_2', action='append', dest='dr_pair_2', help='')
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19 parser.add_option('--rd_pair_1', action='append', dest='rd_pair_1', help='')
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20 parser.add_option('--rd_pair_2', action='append', dest='rd_pair_2', help='')
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21 parser.add_option('--nThreads', dest='nThreads', type='int', help='')
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22 parser.add_option('--minOlap', dest='minOlap', type='int', help='')
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23 parser.add_option('--readsTruncation', dest='readsTruncation', type='int', help='')
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24 parser.add_option('--output', dest='output', help='')
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25 parser.add_option('--logfile', dest='logfile', help='')
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26 (options, args) = parser.parse_args()
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27 if len(args) > 0:
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28 parser.error('Wrong number of arguments')
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29
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30 # build Edena (overlapping) command to be executed
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31 # unpaired input(s)
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32 if options.unpaired_input:
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33 unpaired_input = '-r'
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34 for item in options.unpaired_input:
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35 unpaired_input += ' %s' % (item)
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36 else:
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37 unpaired_input = ''
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38 # direct-reverse paired-end files
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39 if options.dr_pair_1 and options.dr_pair_2:
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40 dr_pairs = '-DRpairs'
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41 for i in range(len(options.dr_pair_1)):
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42 dr_pairs += ' %s %s' % (options.dr_pair_1[i], options.dr_pair_2[i])
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43 else:
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44 dr_pairs = ''
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45 # reverse-direct paired-end files
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46 if options.rd_pair_1 and options.rd_pair_2:
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47 rd_pairs = '-RDpairs'
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48 for i in range(len(options.rd_pair_1)):
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49 rd_pairs += ' %s %s' % (options.rd_pair_1[i], options.rd_pair_2[i])
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50 else:
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51 rd_pairs = ''
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52 # nThreads
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53 nThreads = '-nThreads %d' % (options.nThreads) if options.nThreads is not None else ''
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54 # minimum overlap
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55 minOlap = '-M %d' % (options.minOlap) if options.minOlap is not None else ''
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56 # 3' end reads truncation
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57 readsTruncation = '-t %d' % (options.readsTruncation) if options.readsTruncation is not None else ''
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58 # output file(s)
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59 output = options.output
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60 logfile = options.logfile
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61
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62 # Build Edena (overlapping) command
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63 cmd = 'edena %s %s %s %s %s %s -p galaxy_output' % (unpaired_input, dr_pairs, rd_pairs, nThreads, minOlap, readsTruncation)
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64 print '\nEdena (overlapping) command to be executed:\n %s' % (cmd)
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65
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66 # Execution of Edena
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67 print 'Executing Edena (overlapping)...'
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68 log = open(logfile, 'w') if logfile else sys.stdout
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69 try:
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70 subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True) # need to redirect stderr because edena writes some logging info there (e.g. "Computing overlaps >=30...")
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71 finally:
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72 if log != sys.stdout:
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73 log.close()
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74 print 'Edena (overlapping) executed!'
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75
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76 shutil.move('galaxy_output.ovl', output)
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77
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78
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79 if __name__ == "__main__":
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80 __main__()
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