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1 '''
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2 Created on Jan 1, 2011
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3
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4 @author: John L. Herndon
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5 @contact: herndon@cs.colostate.edu
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6 @organization: Colorado State University
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7 @group: Computer Science Department, Asa Ben-Hur's laboratory
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8 '''
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9
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10
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11 import utils
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12 import os
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13 import subprocess
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14
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15
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16 class ProgramBase( object ):
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17
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18 def __init__( self ):
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19
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20 self.programName = None
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21 self.proc = None
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22
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23 def getProcessArgs( self, args ):
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24 crash #abstract
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25
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26 def execute( self, args, async = False ):
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27 '''
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28 run the nucmer program with a given compare file and an exclude file
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29 '''
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30
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31 utils.logMessage( "ProgramBase::Execute( )", "Running the {0} program.".format( self.programName ) )
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32
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33 args, outputFile = self.getProcessArgs( args )
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34
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35 print "*** Running {0} ***".format( self.programName )
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36
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37 utils.logList( "ProgramBase::Execute( )", args )
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38
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39 proc = subprocess.Popen( args )
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40
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41 if async == False:
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42 #wait for the nucmer instance to finish
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43 proc.wait( )
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44 print "*** Running {0} Complete ***".format( self.programName )
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45
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46 #return the name of the coords file
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47 return outputFile
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48
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49 def isFinished( self ):
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50 ifIsFinished
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51
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52 class Nucmer( ProgramBase ):
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53
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54 def __init__( self ):
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55 #if we can't find the nucemer binary, throw
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56 nucmerPath = utils.search_file( 'nucmer' )
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57 ProgramBase.__init__( self )
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58 if nucmerPath is None:
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59 raise utils.ProgramNotFoundException( 'nucmer', "Please ensure that the MUMmer package is installed and configured on your system." )
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60
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61 self.nucmer = nucmerPath
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62
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63 self.programName = "nucmer"
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64 self.outputExtension = ".coords"
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65
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66
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67 def getProcessArgs( self, inputArgs ):
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68
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69
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70 time = utils.getTimeStamp( )
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71
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72 identifier = "nucmer_alignments"
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73 args = [ self.nucmer, '-p', identifier, '-o', '--minmatch', '300', '--maxgap', '1' ]
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74
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75 args.extend( inputArgs )
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76
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77 outputFile = "{0}.coords".format( identifier )
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78
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79 return args, outputFile
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80
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81 class Eprimer( ProgramBase ):
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82
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83 def __init__( self, eprimerOptions ):
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84
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85 self.programName = "EPrimer3"
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86 self.options = eprimerOptions
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87
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88 primer3corePath = utils.search_file( "primer3_core" )
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89 if primer3corePath is None:
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90 raise utils.ProgramNotFoundException( "primer3_core", "Please ensure that the primer3 package is installed on your system. It can be obtained from http://primer3.sourceforge.net/" )
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91
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92 eprimerPath = utils.search_file( "eprimer3" )
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93 if eprimerPath is None:
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94 raise utils.ProgramNotFoundException( 'eprimer3', "Please ensure that the EMBOSS package is installed and configured on your system." )
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95
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96 self.primer3core = primer3corePath
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97 self.eprimer3 = eprimerPath
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98
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99 def getProcessArgs( self, inputArgs ):
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100
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101 #todo - allow user to determine output file location/name
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102
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103 inputFasta = inputArgs[ 0 ]
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104 outputFile = inputArgs[ 1 ]
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105 args = [ self.eprimer3, inputFasta, outputFile, '-numreturn', '2', '-prange', self.options.getProductRange( ), '-osize', str( self.options.getPrimerSize( ) ),
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106 '-minsize', str( self.options.getMinPrimerSize( ) ), '-maxsize', str( self.options.getMaxPrimerSize( ) )]
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107
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108 return args, outputFile
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109
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110 class PrimerSearch( ProgramBase ):
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111 def __init__( self ):
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112
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113 self.programName = "PrimerSearch"
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114 primerSearchPath = utils.search_file( "primersearch" )
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115 if primerSearchPath is None:
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116 raise utils.ProgramNotFoundException( "primersearch", "Please ensure that the EMBOSS package is installed on your system." )
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117
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118 self.primerSearch = primerSearchPath
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119
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120 def getProcessArgs( self, inputArgs ):
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121 '''
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122 usage for this program: inputArgs is an array length 4
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123 inputArgs[0] = sequence file
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124 inputArgs[1] = primer pairs file
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125 inputArgs[2] = output file name
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126 inputArgs[3] = percent mismatch
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127 '''
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128
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129 args = [ self.primerSearch ]
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130 args.extend( [ '-seqall', inputArgs[ 0 ] ] )
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131 args.extend( [ '-infile', inputArgs[ 1 ] ] )
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132 args.extend( [ '-mismatchpercent', inputArgs[ 3 ] ] )
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133 args.extend( [ '-outfile', inputArgs[ 2 ] ] )
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134
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135
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136 return args, inputArgs[ 2 ]
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137
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138
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139
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140
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141
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