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1 #!/usr/bin/env python
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2
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3 """
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4 Runs DWGSIM
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5
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6 usage: dwgsim_wrapper.py [options]
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7 -e,--errorOne=e: base/color error rate of the first read [0.020]
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8 -E,--errorTwo=E: base/color error rate of the second read [0.020]
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9 -d,--innertDist=d: inner distance between the two ends [500]
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10 -s,--stdev=s: standard deviation [50]
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11 -N,--numReads=N: number of read pairs [1000000]
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12 -1,--lengthOne=1: length of the first read [70]
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13 -2,--lengthTwo=2: length of the second read [70]
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14 -r,--mutRate=r: rate of mutations [0.0010]
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15 -R,--fracIndels=R: fraction of indels [0.10]
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16 -X,--indelExt=X: probability an indel is extended [0.30]
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17 -y,--randProb=y: probability of a random DNA read [0.10]
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18 -n,--maxN=n: maximum number of Ns allowed in a given read [0]
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19 -c,--colorSpace=c: generate reads in color space (SOLiD reads)
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20 -S,--strand=S: strand 0: default, 1: same strand, 2: opposite strand
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21 -H,--haploid=H: haploid mode
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22 -f,--fasta=f: the reference genome FASTA
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23 -3,--outputBFAST=3: the BFAST output FASTQ
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24 -4,--outputBWA1=4: the first BWA output FASTQ
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25 -5,--outputBWA2=5: the second BWA output FASTQ
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26 -6,--outputMutations=6: the output mutations TXT
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27 """
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28
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29 import optparse, os, shutil, subprocess, sys, tempfile
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30
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31 def stop_err( msg ):
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32 sys.stderr.write( '%s\n' % msg )
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33 sys.exit()
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34
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35 def run_process ( cmd, name, tmp_dir, buffsize ):
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36 try:
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37 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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38 tmp_stderr = open( tmp, 'wb' )
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39 proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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40 returncode = proc.wait()
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41 tmp_stderr.close()
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42 # get stderr, allowing for case where it's very large
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43 tmp_stderr = open( tmp, 'rb' )
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44 stderr = ''
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45 try:
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46 while True:
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47 stderr += tmp_stderr.read( buffsize )
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48 if not stderr or len( stderr ) % buffsize != 0:
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49 break
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50 except OverflowError:
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51 pass
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52 tmp_stderr.close()
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53 if returncode != 0:
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54 raise Exception, stderr
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55 except Exception, e:
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56 raise Exception, 'Error in \'' + name + '\'. \n' + str( e )
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57
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58 def check_output ( output, canBeEmpty ):
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59 if 0 < os.path.getsize( output ):
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60 return True
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61 elif False == canBeEmpty:
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62 raise Exception, 'The output file is empty:' + output
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63
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64 def __main__():
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65 #Parse Command Line
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66 parser = optparse.OptionParser()
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67 parser.add_option( '-e', '--errorOne', dest='errorOne', type='float', help='base/color error rate of the first read' )
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68 parser.add_option( '-E', '--errorTwo', dest='errorTwo', type='float', help='base/color error rate of the second read' )
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69 parser.add_option( '-d', '--innertDist', dest='innertDist', type='int', help='inner distance between the two ends' )
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70 parser.add_option( '-s', '--stdev', dest='stdev', type='float', help='standard deviation' )
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71 parser.add_option( '-N', '--numReads', dest='numReads', type='int', help='number of read pairs' )
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72 parser.add_option( '-1', '--lengthOne', dest='lengthOne', type='int', help='length of the first read' )
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73 parser.add_option( '-2', '--lengthTwo', dest='lengthTwo', type='int', help='length of the second read' )
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74 parser.add_option( '-r', '--mutRate', dest='mutRate', type='float', help='rate of mutations' )
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75 parser.add_option( '-R', '--fracIndels', dest='fracIndels', type='float', help='fraction of indels' )
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76 parser.add_option( '-X', '--indelExt', dest='indelExt', type='float', help='probability an indel is extended' )
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77 parser.add_option( '-y', '--randProb', dest='randProb', type='float', help='probability of a random DNA read' )
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78 parser.add_option( '-n', '--maxN', dest='maxN', type='int', help='maximum number of Ns allowed in a given read' )
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79 parser.add_option( '-c', '--colorSpace', action='store_true', dest='colorSpace', default=False, help='generate reads in color space (SOLiD reads)' )
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80 parser.add_option( '-S', '--strand', dest='strand', type='choice', default='0', choices=('0', '1', '2'), help='strand 0: default, 1: same strand, 2: opposite strand' )
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81 parser.add_option( '-H', '--haploid', action='store_true', dest='haploid', default=False, help='haploid mode' )
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82 parser.add_option( '-f', '--fasta', dest='fasta', help='The reference genome fasta' )
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83 parser.add_option( '-3', '--outputBFAST', dest='outputBFAST', help='the BFAST output FASTQ' )
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84 parser.add_option( '-4', '--outputBWA1', dest='outputBWA1', help='the first BWA output FASTQ' )
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85 parser.add_option( '-5', '--outputBWA2', dest='outputBWA2', help='the second BWA output FASTQ' )
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86 parser.add_option( '-6', '--outputMutations', dest='outputMutations', help='the output mutations TXT' )
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87
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88 (options, args) = parser.parse_args()
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89
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90 # output version # of tool
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91 try:
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92 tmp = tempfile.NamedTemporaryFile().name
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93 tmp_stdout = open( tmp, 'wb' )
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94 proc = subprocess.Popen( args='dwgsim 2>&1', shell=True, stdout=tmp_stdout )
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95 tmp_stdout.close()
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96 returncode = proc.wait()
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97 stdout = None
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98 for line in open( tmp_stdout.name, 'rb' ):
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99 if line.lower().find( 'version' ) >= 0:
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100 stdout = line.strip()
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101 break
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102 if stdout:
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103 sys.stdout.write( '%s\n' % stdout )
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104 else:
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105 raise Exception
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106 except:
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107 sys.stdout.write( 'Could not determine DWGSIM version\n' )
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108
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109 buffsize = 1048576
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110
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111 # make temp directory for dwgsim, requires trailing slash
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112 tmp_dir = '%s/' % tempfile.mkdtemp()
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113
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114 #'generic' options used in all dwgsim commands here
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115
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116 try:
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117 reference_filepath = tempfile.NamedTemporaryFile( dir=tmp_dir, suffix='.fa' ).name
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118 os.symlink( options.fasta, reference_filepath )
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119 assert reference_filepath and os.path.exists( reference_filepath ), 'A valid genome reference was not provided.'
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120 tmp_dir = '%s/' % tempfile.mkdtemp()
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121 dwgsim_output_prefix = "dwgsim_output_prefix"
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122 dwgsim_cmd = 'dwgsim -e %s -E %s -d %s -s %s -N %s -1 %s -2 %s -r %s -R %s -X %s -y %s -n %s' % \
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123 (options.errorOne, \
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124 options.errorTwo, \
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125 options.innertDist, \
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126 options.stdev, \
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127 options.numReads, \
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128 options.lengthOne, \
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129 options.lengthTwo, \
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130 options.mutRate, \
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131 options.fracIndels, \
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132 options.indelExt, \
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133 options.randProb, \
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134 options.maxN)
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135 if options.colorSpace:
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136 dwgsim_cmd = dwgsim_cmd + ' -c'
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137 if options.haploid:
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138 dwgsim_cmd = dwgsim_cmd + ' -H'
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139 dwgsim_cmd = dwgsim_cmd + ' ' + options.fasta
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140 dwgsim_cmd = dwgsim_cmd + ' ' + tmp_dir + '/' + dwgsim_output_prefix
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141
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142 # need to nest try-except in try-finally to handle 2.4
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143 try:
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144 # dwgsim
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145 run_process ( dwgsim_cmd, 'dwgsim', tmp_dir, buffsize )
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146 # Move files
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147 cmd = 'mv ' + tmp_dir + '/' + dwgsim_output_prefix + '.mutations.txt' + ' ' + options.outputMutations
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148 run_process ( cmd, 'mv #1', tmp_dir, buffsize )
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149 cmd = 'mv ' + tmp_dir + '/' + dwgsim_output_prefix + '.bfast.fastq' + ' ' + options.outputBFAST
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150 run_process ( cmd, 'mv #2', tmp_dir, buffsize )
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151 cmd = 'mv ' + tmp_dir + '/' + dwgsim_output_prefix + '.bwa.read1.fastq' + ' ' + options.outputBWA1
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152 run_process ( cmd, 'mv #3', tmp_dir, buffsize )
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153 cmd = 'mv ' + tmp_dir + '/' + dwgsim_output_prefix + '.bwa.read2.fastq' + ' ' + options.outputBWA2
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154 run_process ( cmd, 'mv #4', tmp_dir, buffsize )
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155 # check that there are results in the output file
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156 check_output ( options.outputMutations, True )
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157 check_output ( options.outputBFAST, False )
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158 check_output ( options.outputBWA1, False )
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159 check_output ( options.outputBWA2, False )
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160 sys.stdout.write( 'DWGSIM successful' )
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161 except Exception, e:
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162 stop_err( 'DWGSIM failed.\n' + str( e ) )
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163 finally:
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164 # clean up temp dir
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165 if os.path.exists( tmp_dir ):
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166 shutil.rmtree( tmp_dir )
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167
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168 if __name__=="__main__": __main__()
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