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1 #!/usr/bin/python
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2 #
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3 # Copyright (c) 2011, Pacific Biosciences of California, Inc.
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4 #
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5 # All rights reserved.
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6 #
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7 #Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
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8 # * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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9 # * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
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10 # * Neither the name of Pacific Biosciences nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
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11 #
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12 #THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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13 #WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY
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14 #DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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15 #LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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16 #(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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17 #
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18 import sys
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19 import os
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20 import subprocess
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21
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22 QUAKE_EXE = os.path.join( os.path.dirname(os.path.abspath(sys.argv[0])), 'quake.py' )
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23 cmdLine = sys.argv
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24 cmdLine.pop(0)
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25
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26 #
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27 # horribly not robust, but it was a pain to rewrite everything with
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28 # optparse
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29 #
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30 j = -1
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31 cut = 0
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32 for i,arg in enumerate(cmdLine):
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33 if '--default_cutoff' in arg:
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34 j = i
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35 cut = int(arg.split('=')[1])
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36 if j>=0:
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37 cmdLine = cmdLine[:j] + cmdLine[j+1:]
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38
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39 j = -1
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40 output=''
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41 for i,arg in enumerate(cmdLine):
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42 if '--output' in arg:
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43 j = i
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44 output = arg.split('=')[1]
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45 if j>=0:
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46 cmdLine = cmdLine[:j] + cmdLine[j+1:]
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47
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48 def backticks( cmd, merge_stderr=True ):
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49 """
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50 Simulates the perl backticks (``) command with error-handling support
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51 Returns ( command output as sequence of strings, error code, error message )
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52 """
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53 if merge_stderr:
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54 _stderr = subprocess.STDOUT
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55 else:
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56 _stderr = subprocess.PIPE
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57
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58 p = subprocess.Popen( cmd, shell=True, stdin=subprocess.PIPE,
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59 stdout=subprocess.PIPE, stderr=_stderr,
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60 close_fds=True )
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61
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62 out = [ l[:-1] for l in p.stdout.readlines() ]
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63
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64 p.stdout.close()
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65 if not merge_stderr:
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66 p.stderr.close()
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67
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68 # need to allow process to terminate
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69 p.wait()
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70
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71 errCode = p.returncode and p.returncode or 0
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72 if p.returncode>0:
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73 errorMessage = os.linesep.join(out)
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74 output = []
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75 else:
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76 errorMessage = ''
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77 output = out
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78
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79 return output, errCode, errorMessage
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80
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81 def to_stdout():
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82 def toCorFastq(f):
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83 stem, ext = os.path.splitext( os.path.basename(f) )
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84 dir = os.path.dirname(f)
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85 corFastq = os.path.join(dir,'%s.cor%s' % (stem,ext) )
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86 if not os.path.exists(corFastq):
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87 print >>sys.stderr, "Can't find path %s" % corFastq
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88 sys.exit(1)
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89 return corFastq
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90 if '-r' in cmdLine:
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91 fastqFile = cmdLine[ cmdLine.index('-r')+1 ]
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92 corFastq = toCorFastq(fastqFile)
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93 infile = open( corFastq, 'r' )
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94 for line in infile:
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95 sys.stdout.write( line )
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96 infile.close()
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97 else:
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98 fofnFile = cmdLine[ cmdLine.index('-f')+1 ]
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99 infile = open(fofnFile,'r')
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100 for line in infile:
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101 line = line.strip()
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102 if len(line)>0:
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103 fastqFiles = line.split()
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104 break
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105 infile.close()
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106 outs = output.split(',')
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107 for o,f in zip(outs,fastqFiles):
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108 cf = toCorFastq(f)
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109 os.system( 'cp %s %s' % ( cf, o ) )
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110
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111 def run():
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112 cmd = '%s %s' % ( QUAKE_EXE, " ".join(cmdLine) )
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113 output, errCode, errMsg = backticks( cmd )
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114
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115 if errCode==0:
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116 to_stdout()
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117 else:
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118 # if Quake exits with an error in cutoff determination we
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119 # can force correction if requested
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120 if 'cutoff.txt' in errMsg and cut>0:
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121 outfile = open( 'cutoff.txt', 'w' )
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122 print >>outfile, str(cut)
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123 outfile.close()
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124 cmd = '%s --no_count --no_cut %s' % ( QUAKE_EXE, " ".join(cmdLine) )
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125 output, errCode, errMsg = backticks( cmd )
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126 if errCode==0:
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127 to_stdout()
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128 else:
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129 print >>sys.stderr, errMsg
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130 sys.exit(1)
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131
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132 if __name__=='__main__': run()
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