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1 # -*- coding: utf-8 -*-
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2 """
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3 Wrapper for EDGE - Gene expression in Prokaryotes
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4 Author: Paolo Uva paolo dot uva at crs4 dot it
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5 Date: March 18, 2013
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6 """
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7
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8 import glob
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9 import optparse
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10 import os
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11 import shutil
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12 import subprocess
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13 import tempfile
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14 import sys
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15
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16 def __main__():
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17 # Parse Command Line
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18 parser = optparse.OptionParser()
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19 # Input
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20 parser.add_option('-g', '--genome', dest="genome")
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21 parser.add_option('-p', '--ptt', dest="ptt")
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22 parser.add_option('-r', '--rnt', dest="rnt")
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23 parser.add_option('-u', '--input1', dest="input1")
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24 parser.add_option('-v', '--input2', dest="input2")
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25 parser.add_option('-t', '--num-threads', dest="num_threads", type='int')
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26 parser.add_option('-m', '--minInsertSize', dest="minInsertSize", type='int')
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27 parser.add_option('-M', '--maxInsertSize', dest="maxInsertSize", type='int')
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28 parser.add_option('-w', '--window', dest="window", type='int')
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29 parser.add_option('-i', '--utrSize', dest="utrSize", type='int')
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30 parser.add_option('-x', '--similarity', dest="similarity", type='float')
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31 parser.add_option('-c', '--minCoverage', dest="minCoverage", type='int')
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32 parser.add_option('-l', '--readLength', dest="readLength", type='int')
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33 # Output
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34 parser.add_option('--out-aln', dest="out_aln")
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35 parser.add_option('--out-rpkm', dest="out_rpkm")
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36 parser.add_option('--out-log', dest="out_log")
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37 (options, args) = parser.parse_args()
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38 if len(args) > 0:
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39 parser.error('Wrong number of arguments')
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40
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41 # Build command
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42 if options.input2:
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43 input2_flag = '-v %s' % (options.input2)
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44 else:
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45 input2_flag = ''
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46 if options.num_threads is not None:
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47 num_threads_flag = '-t %d' % options.num_threads
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48 else:
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49 num_threads_flag = ''
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50 if options.minInsertSize is not None:
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51 minInsertSize_flag = '-m %d' % options.minInsertSize
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52 else:
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53 minInsertSize_flag = ''
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54 if options.maxInsertSize is not None:
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55 maxInsertSize_flag = '-M %d' % options.maxInsertSize
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56 else:
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57 maxInsertSize_flag = ''
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58 if options.window is not None:
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59 window_flag = '-w %d' % options.window
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60 else:
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61 window_flag = ''
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62 if options.utrSize is not None:
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63 utrSize_flag = '-i %d' % options.utrSize
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64 else:
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65 utrSize_flag = ''
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66 if options.similarity is not None:
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67 similarity_flag = '-x %s' % options.similarity
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68 else:
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69 similarity_flag = ''
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70 if options.readLength is not None:
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71 readLength_flag = '-l %d' % (options.readLength)
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72 else:
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73 readLength_flag = ''
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74 if options.minCoverage is not None:
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75 minCoverage_flag = '-c %d' % options.minCoverage
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76 else:
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77 minCoverage_flag = ''
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78
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79 wd = tempfile.mkdtemp()
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80 try:
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81 prefix = os.path.join(wd, 'out')
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82 cl = 'edge.pl -g %s -p %s -r %s -u %s -o %s %s %s %s %s %s %s %s %s %s' % (options.genome, options.ptt, options.rnt, options.input1, prefix, input2_flag, num_threads_flag, minInsertSize_flag, maxInsertSize_flag, window_flag, utrSize_flag, similarity_flag, readLength_flag, minCoverage_flag)
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83 print cl
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84
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85 if options.out_log:
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86 sout = open(options.out_log, 'w')
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87 else:
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88 sout = sys.stdout
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89 try:
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90 subprocess.check_call(cl, stdout=sout, stderr=subprocess.STDOUT, shell=True) # need to redirect stderr because edge.pl calls bowtie2 and count which write some logging info there
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91 finally:
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92 if sout != sys.stdout:
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93 sout.close()
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94
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95 # Move alignment file
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96 shutil.move(prefix + '.alignments', options.out_aln)
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97 # Concatenate multiple RPKM files together
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98 with open(options.out_rpkm, 'wb') as destination:
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99 for filename in glob.iglob(prefix + '.rpkm_*'):
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100 with open(filename, 'rb') as source:
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101 shutil.copyfileobj(source, destination)
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102 finally:
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103 shutil.rmtree(wd)
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104
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105
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106 if __name__ == "__main__":
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107 __main__()
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