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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 exceptions
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12 import time
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13 import os.path
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14 from os import pathsep
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15 from string import split
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16 import tempfile
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17 import shutil
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18
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19 def getTimeStamp( ):
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20 return time.strftime('%d%m%Y-%H%M%S')
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21
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22
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23 class Match( object ):
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24 '''
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25 record where two genomes line up. stores only alignments for one part of the genome
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26 '''
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27 def __init__( self, start, end, seqID ):
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28 self.seqID = seqID
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29 self.start = start
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30 self.end = end
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31
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32 def __repr__( self ):
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33 return "Start: {0}, End:{1}, SeqID:{2}".format( self.start, self.end, self.seqID )
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34
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35 class PrimerSet( object ):
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36
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37 def __init__( self, id ):
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38 self.id = id
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39 self.productSize = 0
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40 self.forwardPrimer = ""
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41 self.forwardMeltTemp = ""
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42 self.reversePrimer = ""
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43 self.reverseMeltTemp = ""
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44
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45
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46 def setProductSize( self, productSize):
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47 self.productSize = productSize
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48
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49 def setForwardPrimerData( self, sequence, temp ):
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50 self.forwardPrimer = sequence
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51 self.forwardMeltTemp = temp
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52
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53 def setReversePrimerData( self, sequence, temp):
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54 self.reversePrimer = sequence
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55 self.reverseMeltTemp = temp
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56
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57
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58 #search function from http://code.activestate.com/recipes/52224-find-a-file-given-a-search-path/
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59 def search_file( filename ):
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60 """ find file
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61 """
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62 search_path = os.getenv( 'PATH' )
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63 logMessage( "utils::search_file", "Path: {0}".format( search_path ) )
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64 file_found = 0
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65 paths = split( search_path, pathsep )
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66 for path in paths:
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67 if os.path.exists( os.path.join( path, filename ) ):
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68 file_found = 1
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69 break
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70 if file_found:
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71 return os.path.abspath( os.path.join( path, filename ) )
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72 else:
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73 return None
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74
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75 tempDir = ""
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76 removeTemp = True
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77
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78 verbose = False
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79
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80
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81 def initialize( isVerbose, cleanup, lf): ##Mau: added lf
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82 global removeTemp
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83 global tempDir
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84 global verbose
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85 global logFile ##Mau: added logFile variable
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86
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87 logFile = lf #:Mau add line
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88
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89 verbose = isVerbose
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90 tempDir = tempfile.mkdtemp( dir="" )
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91 initializeLogging()
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92 removeTemp = cleanup
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93 logMessage( "utils::Initialize( )", "Initialization complete. Temporary directory: {0}".format( tempDir ) )
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94
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95 logFile = None
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96
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97
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98 def printProgressMessage( message ):
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99 global verbose
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100 if verbose == True:
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101 print message
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102
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103 def getTemporaryDirectory( ):
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104 global tempDir
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105 return tempDir
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106
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107 def initializeLogging():
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108 global logFile
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109 #logFileName = "uniqprimer_{0}.log".format( getTimeStamp( ) )
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110 #logFileName = "log_uniqprimer.txt" ##Mau: commented out
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111 logFileName = logFile ##Mau: changed
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112 logFile = open( logFileName, 'w' )
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113
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114 def shutdown( ):
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115 global removeTemp
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116 global tempDir
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117 shutdownLogging( )
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118 if removeTemp == True:
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119 print "*** Removing temporary directory ***"
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120 shutil.rmtree( tempDir )
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121
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122 def shutdownLogging( ):
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123 global logFile
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124 if logFile != None:
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125 logFile.close( )
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126
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127 def logList( method, list ):
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128
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129 message = reduce( lambda x,y: str( x ) + " " + str( y ) , list )
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130 logMessage(method, message)
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131
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132
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133 def logMessage( method, message ):
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134 global logFile
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135 if logFile == None:
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136 return
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137 log = "{0} - {1}".format( method, message )
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138
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139 logFile.write( log + "\n" )
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140 logFile.flush( )
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141
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142 class EPrimerOptions( object ):
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143
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144 def __init__( self ):
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145
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146 self.minPrimerSize = 18
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147 self.maxPrimerSize = 27
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148 self.primerSize = 20
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149 self.productRange = "200-250"
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150
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151 def setPrimerSize( self, size ):
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152
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153 size = int( size )
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154 if size > 35:
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155 size = 35
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156
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157 self.primerSize = size
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158 if self.primerSize < self.minPrimerSize:
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159 self.maxPrimerSize = self.primerSize
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160 elif self.primerSize > self.maxPrimerSize:
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161 self.maxPrimerSize = self.primerSize
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162
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163 def getPrimerSize( self ):
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164 return self.primerSize
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165
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166 def setMinPrimerSize( self, minSize):
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167 self.minPrimerSize = minSize
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168
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169 def getMinPrimerSize( self ):
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170 return self.minPrimerSize
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171
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172 def setMaxPrimerSize( self, size ):
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173 self.maxPrimerSize = size
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174
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175 def getMaxPrimerSize( self ):
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176 return self.maxPrimerSize
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177
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178 def setProductRange( self, range ):
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179 self.productRange = range
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180
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181 def getProductRange( self ):
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182 return self.productRange
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183
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184 class NoPrimersExistException( exceptions.BaseException ):
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185
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186 def __init__( self ):
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187 exceptions.BaseException( self )
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188
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189 class ProgramNotFoundException( exceptions.BaseException ):
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190
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191 def __init__( self, programName, details ):
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192 exceptions.BaseException.__init__(self)
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193 self.programName = programName
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194 self.details = details
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195
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196 class NoFileFoundException( exceptions.BaseException ):
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197
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198 def __init__( self, filename ):
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199 exceptions.BaseException.__init__(self)
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200 self.filename = filename
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201
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202
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203 class ModuleNotInitializedException( exceptions.BaseException ):
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204
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205 def __init__( self, moduleName, reason ):
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206 self.moduleName = moduleName
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207 self.reason = reason
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