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1 #!/usr/bin/env python
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2 """
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3 Yufei LUO
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4 """
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5 import optparse, os, sys, subprocess, tempfile, shutil, tarfile, random
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6 #from galaxy import eggs
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7 #import pkg_resources; pkg_resources.require( "bx-python" )
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8 #from bx.cookbook import doc_optparse
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9 #from galaxy import util
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10
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11 def stop_err( msg ):
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12 sys.stderr.write( '%s\n' % msg )
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13 sys.exit()
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14
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15 def toTar(tarFileName, samOutputNames):
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16 dir = os.path.dirname(tarFileName)
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17 tfile = tarfile.open(tarFileName + ".tmp.tar", "w")
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18 currentPath = os.getcwd()
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19 os.chdir(dir)
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20 for file in samOutputNames:
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21 relativeFileName = os.path.basename(file)
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22 tfile.add(relativeFileName)
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23 os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))
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24 tfile.close()
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25 os.chdir(currentPath)
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26
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27
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28 def __main__():
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29 #Parse Command Line
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30 parser = optparse.OptionParser()
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31 parser.add_option('-t', '--tar', dest='outputTar', default=None, help='output all SAM results in a tar file.' )
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32 parser.add_option( '', '--input1', dest='input1', help='The input list of BAM datasets on txt format.' )
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33 #parser.add_option( '', '--input1', dest='input1', help='The input BAM dataset' )
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34 parser.add_option( '', '--output1', dest='output1', help='The output list of SAM datasets on txt format.' )
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35 #parser.add_option( '', '--output1', dest='output1', help='The output SAM dataset' )
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36 parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' )
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37 ( options, args ) = parser.parse_args()
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38
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39
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40 #Parse the input txt file and read a list of BAM files.
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41 file = open(options.input1, "r")
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42 lines = file.readlines()
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43 inputFileNames = []
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44 samOutputNames = []
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45 outputName = options.output1
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46 resDirName = os.path.dirname(outputName) + '/'
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47 #Write output txt file and define all output sam file names.
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48 out = open(outputName, "w")
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49 for line in lines:
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50 tab = line.split()
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51 inputFileNames.append(tab[1])
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52 samOutName = resDirName + tab[0] + '_samOutput_%s.sam' % random.randrange(0, 10000)
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53 samOutputNames.append(samOutName)
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54 out.write(tab[0] + '\t' + samOutName + '\n')
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55 file.close()
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56 out.close()
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57
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58 # output version # of tool
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59 try:
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60 tmp_files = []
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61 tmp = tempfile.NamedTemporaryFile().name
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62 tmp_files.append(tmp)
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63 tmp_stdout = open( tmp, 'wb' )
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64 proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
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65 tmp_stdout.close()
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66 returncode = proc.wait()
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67 stdout = None
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68 for line in open( tmp_stdout.name, 'rb' ):
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69 if line.lower().find( 'version' ) >= 0:
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70 stdout = line.strip()
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71 break
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72 if stdout:
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73 sys.stdout.write( 'Samtools %s\n' % stdout )
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74 else:
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75 raise Exception
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76 except:
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77 sys.stdout.write( 'Could not determine Samtools version\n' )
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78
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79
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80
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81 tmp_dirs = []
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82 for i in range(len(inputFileNames)):
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83 try:
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84 # exit if input file empty
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85 if os.path.getsize( inputFileNames[i] ) == 0:
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86 raise Exception, 'Initial input txt file is empty.'
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87 # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command
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88 # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted
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89 # into memory ( controlled by option -m ).
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90 tmp_dir = tempfile.mkdtemp()
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91 tmp_dirs.append(tmp_dir)
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92 tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
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93 tmp_sorted_aligns_file_base = tmp_sorted_aligns_file.name
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94 tmp_sorted_aligns_file_name = '%s.bam' % tmp_sorted_aligns_file.name
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95 tmp_files.append(tmp_sorted_aligns_file_name)
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96 tmp_sorted_aligns_file.close()
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97
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98 command = 'samtools sort %s %s' % ( inputFileNames[i], tmp_sorted_aligns_file_base )
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99 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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100 tmp_stderr = open( tmp, 'wb' )
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101 proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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102 returncode = proc.wait()
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103 tmp_stderr.close()
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104 # get stderr, allowing for case where it's very large
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105 tmp_stderr = open( tmp, 'rb' )
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106 stderr = ''
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107 buffsize = 1048576
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108 try:
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109 while True:
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110 stderr += tmp_stderr.read( buffsize )
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111 if not stderr or len( stderr ) % buffsize != 0:
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112 break
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113 except OverflowError:
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114 pass
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115 tmp_stderr.close()
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116 if returncode != 0:
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117 raise Exception, stderr
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118 # exit if sorted BAM file empty
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119 if os.path.getsize( tmp_sorted_aligns_file_name) == 0:
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120 raise Exception, 'Intermediate sorted BAM file empty'
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121 except Exception, e:
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122 stop_err( 'Error sorting alignments from (%s), %s' % ( inputFileNames[i], str( e ) ) )
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123
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124 try:
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125 # 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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126 if options.header:
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127 view_options = "-h"
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128 else:
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129 view_options = ""
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130 command = 'samtools view %s -o %s %s' % ( view_options, samOutputNames[i], tmp_sorted_aligns_file_name )
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131 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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132 tmp_stderr = open( tmp, 'wb' )
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133 proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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134 returncode = proc.wait()
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135 tmp_stderr.close()
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136 # get stderr, allowing for case where it's very large
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137 tmp_stderr = open( tmp, 'rb' )
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138 stderr = ''
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139 buffsize = 1048576
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140 try:
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141 while True:
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142 stderr += tmp_stderr.read( buffsize )
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143 if not stderr or len( stderr ) % buffsize != 0:
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144 break
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145 except OverflowError:
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146 pass
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147 tmp_stderr.close()
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148 if returncode != 0:
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149 raise Exception, stderr
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150 except Exception, e:
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151 stop_err( 'Error extracting alignments from (%s), %s' % ( inputFileNames[i], str( e ) ) )
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152 if os.path.getsize( samOutputNames[i] ) > 0:
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153 sys.stdout.write( 'BAM file converted to SAM' )
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154 else:
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155 stop_err( 'The output file is empty, there may be an error with your input file.' )
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156
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157 if options.outputTar != None:
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158 toTar(options.outputTar, samOutputNames)
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159 #clean up temp files
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160 for tmp_dir in tmp_dirs:
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161 if os.path.exists( tmp_dir ):
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162 shutil.rmtree( tmp_dir )
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163 #print tmp_files
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164 #for tmp in tmp_files:
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165 # os.remove(tmp)
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166
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167
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168 if __name__=="__main__": __main__()
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