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18
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1 #!/usr/bin/env python
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2 """
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3 Converts BAM data to sorted SAM data.
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4 usage: bam_to_sam.py [options]
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5 --input1: SAM file to be converted
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6 --output1: output dataset in bam format
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7 """
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8
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9 import optparse, os, sys, subprocess, tempfile, shutil, tarfile, random
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10 #from galaxy import eggs
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11 #import pkg_resources; pkg_resources.require( "bx-python" )
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12 #from bx.cookbook import doc_optparse
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13 #from galaxy import util
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14
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15 def stop_err( msg ):
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16 sys.stderr.write( '%s\n' % msg )
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17 sys.exit()
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18
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19 def toTar(tarFileName, samOutputNames):
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20 dir = os.path.dirname(tarFileName)
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21 tfile = tarfile.open(tarFileName + ".tmp.tar", "w")
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22 currentPath = os.getcwd()
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23 os.chdir(dir)
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24 for file in samOutputNames:
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25 relativeFileName = os.path.basename(file)
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26 tfile.add(relativeFileName)
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27 os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))
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28 tfile.close()
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29 os.chdir(currentPath)
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30
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31
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32 def __main__():
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33 #Parse Command Line
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34 parser = optparse.OptionParser()
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35 parser.add_option('-t', '--tar', dest='outputTar', default=None, help='output all SAM results in a tar file.' )
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36 parser.add_option( '', '--input1', dest='input1', help='The input list of BAM datasets on txt format.' )
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37 #parser.add_option( '', '--input1', dest='input1', help='The input BAM dataset' )
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38 parser.add_option( '', '--output1', dest='output1', help='The output list of SAM datasets on txt format.' )
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39 #parser.add_option( '', '--output1', dest='output1', help='The output SAM dataset' )
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40 parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' )
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41 ( options, args ) = parser.parse_args()
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42
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43
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44 #Parse the input txt file and read a list of BAM files.
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45 file = open(options.input1, "r")
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46 lines = file.readlines()
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47 inputFileNames = []
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48 samOutputNames = []
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49 outputName = options.output1
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50 resDirName = os.path.dirname(outputName) + '/'
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51 #Write output txt file and define all output sam file names.
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52 out = open(outputName, "w")
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53 for line in lines:
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54 tab = line.split()
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55 inputFileNames.append(tab[1])
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56 samOutName = resDirName + tab[0] + '_samOutput_%s.sam' % random.randrange(0, 10000)
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57 samOutputNames.append(samOutName)
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58 out.write(tab[0] + '\t' + samOutName + '\n')
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59 file.close()
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60 out.close()
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61
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62 # output version # of tool
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63 try:
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64 tmp_files = []
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65 tmp = tempfile.NamedTemporaryFile().name
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66 tmp_files.append(tmp)
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67 tmp_stdout = open( tmp, 'wb' )
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68 proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
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69 tmp_stdout.close()
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70 returncode = proc.wait()
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71 stdout = None
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72 for line in open( tmp_stdout.name, 'rb' ):
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73 if line.lower().find( 'version' ) >= 0:
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74 stdout = line.strip()
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75 break
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76 if stdout:
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77 sys.stdout.write( 'Samtools %s\n' % stdout )
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78 else:
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79 raise Exception
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80 except:
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81 sys.stdout.write( 'Could not determine Samtools version\n' )
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82
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83
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84
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85 tmp_dirs = []
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86 for i in range(len(inputFileNames)):
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87 try:
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88 # exit if input file empty
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89 if os.path.getsize( inputFileNames[i] ) == 0:
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90 raise Exception, 'Initial input txt file is empty.'
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91 # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command
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92 # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted
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93 # into memory ( controlled by option -m ).
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94 tmp_dir = tempfile.mkdtemp()
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95 tmp_dirs.append(tmp_dir)
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96 tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
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97 tmp_sorted_aligns_file_base = tmp_sorted_aligns_file.name
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98 tmp_sorted_aligns_file_name = '%s.bam' % tmp_sorted_aligns_file.name
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99 tmp_files.append(tmp_sorted_aligns_file_name)
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100 tmp_sorted_aligns_file.close()
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101
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102 command = 'samtools sort %s %s' % ( inputFileNames[i], tmp_sorted_aligns_file_base )
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103 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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104 tmp_stderr = open( tmp, 'wb' )
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105 proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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106 returncode = proc.wait()
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107 tmp_stderr.close()
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108 # get stderr, allowing for case where it's very large
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109 tmp_stderr = open( tmp, 'rb' )
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110 stderr = ''
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111 buffsize = 1048576
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112 try:
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113 while True:
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114 stderr += tmp_stderr.read( buffsize )
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115 if not stderr or len( stderr ) % buffsize != 0:
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116 break
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117 except OverflowError:
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118 pass
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119 tmp_stderr.close()
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120 if returncode != 0:
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121 raise Exception, stderr
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122 # exit if sorted BAM file empty
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123 if os.path.getsize( tmp_sorted_aligns_file_name) == 0:
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124 raise Exception, 'Intermediate sorted BAM file empty'
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125 except Exception, e:
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126 stop_err( 'Error sorting alignments from (%s), %s' % ( inputFileNames[i], str( e ) ) )
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127
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128 try:
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129 # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ).
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130 if options.header:
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131 view_options = "-h"
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132 else:
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133 view_options = ""
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134 command = 'samtools view %s -o %s %s' % ( view_options, samOutputNames[i], tmp_sorted_aligns_file_name )
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135 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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136 tmp_stderr = open( tmp, 'wb' )
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137 proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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138 returncode = proc.wait()
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139 tmp_stderr.close()
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140 # get stderr, allowing for case where it's very large
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141 tmp_stderr = open( tmp, 'rb' )
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142 stderr = ''
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143 buffsize = 1048576
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144 try:
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145 while True:
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146 stderr += tmp_stderr.read( buffsize )
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147 if not stderr or len( stderr ) % buffsize != 0:
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148 break
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149 except OverflowError:
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150 pass
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151 tmp_stderr.close()
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152 if returncode != 0:
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153 raise Exception, stderr
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154 except Exception, e:
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155 stop_err( 'Error extracting alignments from (%s), %s' % ( inputFileNames[i], str( e ) ) )
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156 if os.path.getsize( samOutputNames[i] ) > 0:
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157 sys.stdout.write( 'BAM file converted to SAM' )
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158 else:
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159 stop_err( 'The output file is empty, there may be an error with your input file.' )
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160
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161 if options.outputTar != None:
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162 toTar(options.outputTar, samOutputNames)
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163 #clean up temp files
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164 for tmp_dir in tmp_dirs:
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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 #print tmp_files
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168 #for tmp in tmp_files:
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169 # os.remove(tmp)
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170
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171
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172 if __name__=="__main__": __main__()
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