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10
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1 #!/usr/bin/python
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2
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3 import argparse, optparse, os, shutil, subprocess, sys, tempfile, shlex, time
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4
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5
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6 parser = argparse.ArgumentParser(description='')
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7
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8 parser.add_argument ( '-i1', dest='input_bam', help='the bam input file' )
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9 parser.add_argument ( '-o1', dest='output_raw', help='the output file' )
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10 parser.add_argument ( '-o2', dest='output_vcf', help='the output file' )
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11
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12
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13 tmp_dir = tempfile.mkdtemp()
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14 errorFile = tmp_dir+"/errorLog"
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15
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16
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16 currentDir = os.path.dirname(os.path.abspath(__file__))
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19
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17 bam2cfg = "./bam2cfg.pl"
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18 # breakdancer = "/usr/bin/breakdancer-max"
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19 breakdancer = "breakdancer-max"
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20 breakdancer2vcf = "./breakdancer2vcf.py"
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10
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21
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22
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23 def bam2cfg(args):
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24 config = tmp_dir+"/breakdancer_config"
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19
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25 cmd = 'perl %s %s' % (bam2cfg, args.input_bam)
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10
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26 execute(cmd, output=config)
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27 print ("\ncmd = %s \n" ) %(cmd)
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28 return config
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29
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30
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31 def breakdancer(args, config):
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19
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32 cmd = '%s %s' % (breakdancer, config)
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33 execute(cmd, output=args.output_raw)
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34
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35
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36 def breakdancer2vcf(args):
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19
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37 cmd = "python %s -i %s -o %s" % ( breakdancer2vcf, args.output_raw, args.output_vcf )
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10
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38 execute(cmd)
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39
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40
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41 def execute( cmd, output="" ):
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42 try:
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43 err = open(tmp_dir+"/errorLog", 'a')
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44 if output != "":
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45 out = open(output, 'w')
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46 else:
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47 out = subprocess.PIPE
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48 process = subprocess.Popen( args=shlex.split(cmd), stdout=out, stderr=err )
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49 process.wait()
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50 err.close()
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51 if out != subprocess.PIPE:
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52 out.close()
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53 except Exception, e:
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54 sys.stderr.write("problem doing : %s\n" %(cmd))
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55 sys.stderr.write( '%s\n\n' % str(e) )
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56
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57
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58 def check( output ):
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59 if (os.path.getsize(output)>0):
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60 return True
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61 else:
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62 sys.stderr.write('The output file is empty : %s\n' % (output))
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63
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64
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65 def getLine(file):
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66 try:
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67 f = open(file, 'r')
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68 lignes = f.readlines()
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69 n=0
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70 for ligne in lignes:
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71 if ligne.strip()[0]!="#":
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72 n+=1
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73 # n = len(lignes)
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74 f.close()
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75 except Exception, e:
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76 sys.stderr.write( '%s\n' % str(e) )
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77 return n
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78
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79
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80 def compare( output1, output2 ):
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81 # compare le nombre de ligne entre 2 fichiers
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82 # pour verifier qu'aucune ligne n'a ete saute
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83 num_raw = getLine(output1)
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84 num_vcf = getLine(output2)
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85 if (num_raw==num_vcf):
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86 return True
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87 else:
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88 sys.stderr.write('Not the same number of variant between the raw file and the vcf file : %d vs %d\n' % (num_raw, num_vcf))
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89
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90
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91 def __main__():
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92
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93 time0 = time.time()
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94 args = parser.parse_args()
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95
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96 try:
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97 config = bam2cfg(args)
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98 breakdancer(args, config)
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99 breakdancer2vcf(args)
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100
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101 # quelques tests
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102 # verifier que les fichiers de sorties ne sont pas vides
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103 check(args.output_raw)
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104 check(args.output_vcf)
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105 # comparer le nombre de ligne entre les 2 fichiers
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106 # pour etre sur que toute les variations ont ete prises en compte
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107 compare(args.output_raw, args.output_vcf)
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108
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109 sys.stdout.write( '\nDone in %d seconds\n' %(int(time.time()-time0)))
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110
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111 if ( os.path.getsize(errorFile)>0 ):
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112 sys.stdout.write( 'At least one non fatal error was send, check the file : %s\n' %(errorFile) )
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113 try:
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114 err = open(errorFile, 'r')
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115 errors = err.read()
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116 err.close()
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117 sys.stdout.write( "Errors :\n%s" %(errors))
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118 except Exception, e:
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119 sys.stderr.write( '%s\n' % str(e) )
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120 else:
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121 sys.stdout.write( 'BreakDancer successful' )
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122
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123 except Exception, e:
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124 sys.stdout.write( 'BreakDancer fail\n' )
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125 sys.stderr.write( '%s\n' % str(e) )
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126 sys.exit()
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127
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128 finally:
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129 if os.path.exists( tmp_dir ):
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130 shutil.rmtree( tmp_dir )
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131
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132 if __name__=="__main__":
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133 __main__()
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