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1 #!/usr/bin/env python
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2 """
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3 Converts SAM data to sorted BAM data.
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4 usage: sam_to_bam.py [options]
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5 --input1: SAM file to be converted
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6 --dbkey: dbkey value
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7 --ref_file: Reference file if choosing from history
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8 --output1: output dataset in bam format
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9 --index_dir: GALAXY_DATA_INDEX_DIR
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10 """
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11
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12 import optparse, os, sys, subprocess, tempfile, shutil, gzip
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13 from galaxy import eggs
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14 import pkg_resources; pkg_resources.require( "bx-python" )
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15 from bx.cookbook import doc_optparse
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16 from galaxy import util
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17
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18 def stop_err( msg ):
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19 sys.stderr.write( '%s\n' % msg )
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20 sys.exit()
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21
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22 def check_seq_file( dbkey, cached_seqs_pointer_file ):
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23 seq_path = ''
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24 for line in open( cached_seqs_pointer_file ):
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25 line = line.rstrip( '\r\n' )
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26 if line and not line.startswith( '#' ) and line.startswith( 'index' ):
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27 fields = line.split( '\t' )
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28 if len( fields ) < 3:
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29 continue
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30 if fields[1] == dbkey:
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31 seq_path = fields[2].strip()
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32 break
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33 return seq_path
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34
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35 def __main__():
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36 #Parse Command Line
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37 parser = optparse.OptionParser()
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38 parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' )
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39 parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' )
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40 parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
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41 parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' )
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42 parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' )
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43 ( options, args ) = parser.parse_args()
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44
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45 # output version # of tool
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46 try:
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47 tmp = tempfile.NamedTemporaryFile().name
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48 tmp_stdout = open( tmp, 'wb' )
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49 proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
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50 tmp_stdout.close()
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51 returncode = proc.wait()
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52 stdout = None
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53 for line in open( tmp_stdout.name, 'rb' ):
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54 if line.lower().find( 'version' ) >= 0:
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55 stdout = line.strip()
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56 break
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57 if stdout:
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58 sys.stdout.write( 'Samtools %s\n' % stdout )
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59 else:
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60 raise Exception
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61 except:
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62 sys.stdout.write( 'Could not determine Samtools version\n' )
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63
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64 cached_seqs_pointer_file = '%s/sam_fa_indices.loc' % options.index_dir
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65 if not os.path.exists( cached_seqs_pointer_file ):
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66 stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file )
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67 # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa,
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68 # and the equCab2.fa file will contain fasta sequences.
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69 seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file )
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70 tmp_dir = tempfile.mkdtemp()
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71 if not options.ref_file or options.ref_file == 'None':
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72 # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ).
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73 # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in
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74 # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai
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75 fai_index_file_base = seq_path
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76 fai_index_file_path = '%s.fai' % seq_path
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77 if not os.path.exists( fai_index_file_path ):
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78 #clean up temp files
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79 if os.path.exists( tmp_dir ):
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80 shutil.rmtree( tmp_dir )
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81 stop_err( 'No sequences are available for build (%s), request them by reporting this error.' % options.dbkey )
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82 else:
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83 try:
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84 # Create indexes for history reference ( e.g., ~/database/files/000/dataset_1.dat ) using samtools faidx, which will:
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85 # - index reference sequence in the FASTA format or extract subsequence from indexed reference sequence
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86 # - if no region is specified, faidx will index the file and create <ref.fasta>.fai on the disk
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87 # - if regions are specified, the subsequences will be retrieved and printed to stdout in the FASTA format
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88 # - the input file can be compressed in the RAZF format.
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89 # IMPORTANT NOTE: a real weakness here is that we are creating indexes for the history dataset
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90 # every time we run this tool. It would be nice if we could somehow keep track of user's specific
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91 # index files so they could be re-used.
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92 fai_index_file_base = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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93 # At this point, fai_index_file_path will look something like /tmp/dataset_13.dat
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94 os.symlink( options.ref_file, fai_index_file_base )
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95 fai_index_file_path = '%s.fai' % fai_index_file_base
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96 command = 'samtools faidx %s' % fai_index_file_base
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97 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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98 tmp_stderr = open( tmp, 'wb' )
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99 proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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100 returncode = proc.wait()
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101 tmp_stderr.close()
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102 # get stderr, allowing for case where it's very large
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103 tmp_stderr = open( tmp, 'rb' )
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104 stderr = ''
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105 buffsize = 1048576
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106 try:
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107 while True:
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108 stderr += tmp_stderr.read( buffsize )
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109 if not stderr or len( stderr ) % buffsize != 0:
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110 break
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111 except OverflowError:
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112 pass
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113 tmp_stderr.close()
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114 if returncode != 0:
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115 raise Exception, stderr
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116 if os.path.getsize( fai_index_file_path ) == 0:
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117 raise Exception, 'Index file empty, there may be an error with your reference file or settings.'
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118 except Exception, e:
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119 #clean up temp files
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120 if os.path.exists( tmp_dir ):
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121 shutil.rmtree( tmp_dir )
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122 stop_err( 'Error creating indexes from reference (%s), %s' % ( options.ref_file, str( e ) ) )
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123 try:
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124 # Extract all alignments from the input SAM file to BAM format ( since no region is specified, all the alignments will be extracted ).
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125 tmp_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
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126 tmp_aligns_file_name = tmp_aligns_file.name
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127 tmp_aligns_file.close()
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128 command = 'samtools view -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 )
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129 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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130 tmp_stderr = open( tmp, 'wb' )
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131 proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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132 returncode = proc.wait()
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133 tmp_stderr.close()
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134 # get stderr, allowing for case where it's very large
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135 tmp_stderr = open( tmp, 'rb' )
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136 stderr = ''
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137 buffsize = 1048576
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138 try:
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139 while True:
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140 stderr += tmp_stderr.read( buffsize )
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141 if not stderr or len( stderr ) % buffsize != 0:
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142 break
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143 except OverflowError:
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144 pass
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145 tmp_stderr.close()
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146 if returncode != 0:
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147 raise Exception, stderr
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148 except Exception, e:
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149 #clean up temp files
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150 if os.path.exists( tmp_dir ):
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151 shutil.rmtree( tmp_dir )
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152 stop_err( 'Error extracting alignments from (%s), %s' % ( options.input1, str( e ) ) )
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153 try:
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154 # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command
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155 # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted
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156 # into memory ( controlled by option -m ).
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157 tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
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158 tmp_sorted_aligns_file_name = tmp_sorted_aligns_file.name
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159 tmp_sorted_aligns_file.close()
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160 command = 'samtools sort %s %s' % ( tmp_aligns_file_name, tmp_sorted_aligns_file_name )
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161 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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162 tmp_stderr = open( tmp, 'wb' )
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163 proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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164 returncode = proc.wait()
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165 tmp_stderr.close()
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166 # get stderr, allowing for case where it's very large
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167 tmp_stderr = open( tmp, 'rb' )
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168 stderr = ''
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169 buffsize = 1048576
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170 try:
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171 while True:
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172 stderr += tmp_stderr.read( buffsize )
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173 if not stderr or len( stderr ) % buffsize != 0:
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174 break
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175 except OverflowError:
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176 pass
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177 tmp_stderr.close()
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178 if returncode != 0:
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179 raise Exception, stderr
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180 except Exception, e:
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181 #clean up temp files
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182 if os.path.exists( tmp_dir ):
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183 shutil.rmtree( tmp_dir )
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184 stop_err( 'Error sorting alignments from (%s), %s' % ( tmp_aligns_file_name, str( e ) ) )
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185 # Move tmp_aligns_file_name to our output dataset location
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186 sorted_bam_file = '%s.bam' % tmp_sorted_aligns_file_name
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187 shutil.move( sorted_bam_file, options.output1 )
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188 #clean up temp files
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189 if os.path.exists( tmp_dir ):
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190 shutil.rmtree( tmp_dir )
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191 # check that there are results in the output file
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192 if os.path.getsize( options.output1 ) > 0:
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193 sys.stdout.write( 'SAM file converted to BAM' )
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194 else:
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195 stop_err( 'Error creating sorted version of BAM file.' )
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196
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197 if __name__=="__main__": __main__()
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