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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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3
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4 """
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5 A wrapper script for running SAMTools commands.
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6 """
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7
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8 import sys, optparse, os, tempfile, subprocess, shutil
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9 from string import Template
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10
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11 GALAXY_EXT_TO_SAMTOOLS_EXT = { 'bam_index':'bam.bai', } #items not listed here will use the galaxy extension as-is
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12 GALAXY_EXT_TO_SAMTOOLS_FILE_TYPE = GALAXY_EXT_TO_SAMTOOLS_EXT #for now, these are the same, but could be different if needed
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13 DEFAULT_SAMTOOLS_PREFIX = "SAMTools_file"
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14 CHUNK_SIZE = 2**20 #1mb
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15
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16
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17 def cleanup_before_exit( tmp_dir ):
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18 if tmp_dir and os.path.exists( tmp_dir ):
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19 shutil.rmtree( tmp_dir )
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20
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21 def SAMTOOLS_filename_from_galaxy( galaxy_filename, galaxy_ext, target_dir = None, prefix = None ):
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22 suffix = GALAXY_EXT_TO_SAMTOOLS_EXT.get( galaxy_ext, galaxy_ext )
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23 if prefix is None:
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24 prefix = DEFAULT_SAMTOOLS_PREFIX
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25 if target_dir is None:
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26 target_dir = os.getcwd()
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27 SAMTools_filename = os.path.join( target_dir, "%s.%s" % ( prefix, suffix ) )
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28 os.symlink( galaxy_filename, SAMTools_filename )
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29 return SAMTools_filename
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30
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31 def SAMTOOLS_filetype_argument_substitution( argument, galaxy_ext ):
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32 return argument % dict( file_type = GALAXY_EXT_TO_SAMTOOLS_FILE_TYPE.get( galaxy_ext, galaxy_ext ) )
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33
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34 def open_file_from_option( filename, mode = 'rb' ):
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35 if filename:
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36 return open( filename, mode = mode )
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37 return None
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38
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39 def html_report_from_directory( html_out, dir ):
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40 html_out.write( '<html>\n<head>\n<title>Galaxy - SAMTOOLS Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' )
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41 for fname in sorted( os.listdir( dir ) ):
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42 html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
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43 html_out.write( '</ul>\n</body>\n</html>\n' )
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44
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45 def __main__():
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46 #Parse Command Line
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47 parser = optparse.OptionParser()
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48 parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to SAMTOOLS, without any modification.' )
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49 parser.add_option( '-d', '--dataset', dest='datasets', action='append', type="string", nargs=4, help='"-argument" "original_filename" "galaxy_filetype" "name_prefix"' )
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50 parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' )
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51 parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' )
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52 parser.add_option( '', '--html_report_from_directory', dest='html_report_from_directory', action='append', type="string", nargs=2, help='"Target HTML File" "Directory"')
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53 (options, args) = parser.parse_args()
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54
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55 tmp_dir = tempfile.mkdtemp( prefix='tmp-SAMTOOLS-' )
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56
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57 #set up stdout and stderr output options
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58 stdout = open_file_from_option( options.stdout, mode = 'wb' )
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59 stderr = open_file_from_option( options.stderr, mode = 'wb' )
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60 #if no stderr file is specified, we'll use our own
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61 if stderr is None:
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62 stderr = tempfile.NamedTemporaryFile( prefix="SAMTOOLS-stderr-", dir=tmp_dir )
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63
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64 if options.pass_through_options:
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65 cmd = ' '.join( options.pass_through_options )
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66 else:
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67 cmd = ''
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68 return_code = None
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69 if options.datasets:
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70 for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets:
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71 SAMTools_filename = SAMTOOLS_filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix )
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72 if dataset_arg:
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73 if '>' in cmd:
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74 cmd = cmd.replace( '>', ' %s "%s" >' % ( SAMTOOLS_filetype_argument_substitution( dataset_arg, galaxy_ext ), SAMTools_filename ), 1 )
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75 else:
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76 cmd = '%s %s "%s"' % ( cmd, SAMTOOLS_filetype_argument_substitution( dataset_arg, galaxy_ext ), SAMTools_filename )
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77 #auto index fasta files:
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78 if galaxy_ext == 'fa':
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79 index_cmd = 'samtools faidx %s' % ( SAMTools_filename )
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80 proc = subprocess.Popen( args=index_cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
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81 return_code = proc.wait()
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82 if return_code:
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83 break
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84 if return_code is None or not return_code:
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85 proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
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86 return_code = proc.wait()
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87 if return_code:
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88 stderr_target = sys.stderr
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89 else:
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90 if stdout:
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91 stderr_target = stdout
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92 else:
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93 stderr_target = sys.stdout
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94 stderr.flush()
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95 stderr.seek(0)
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96 while True:
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97 chunk = stderr.read( CHUNK_SIZE )
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98 if chunk:
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99 stderr_target.write( chunk )
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100 else:
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101 break
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102 stderr.close()
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103 #generate html reports
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104 if options.html_report_from_directory:
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105 for ( html_filename, html_dir ) in options.html_report_from_directory:
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106 html_report_from_directory( open( html_filename, 'wb' ), html_dir )
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107
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108 cleanup_before_exit( tmp_dir )
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109
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110 if __name__=="__main__": __main__()
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