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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 fastaparser
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12 import utils
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13 import os
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14 import programs
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15 import nucmerparser
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16 import copy
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17
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18 class IncludeFileManager( object ):
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19 """
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20 A class to manage include files
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21 """
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22 #This class needs some work. Need to come up with a way to find unique sequences between all include files....
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23
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24 def __init__( self ):
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25 """
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26 Constructor
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27 """
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28 self.includeFiles = [ ]
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29 self.nucmer = programs.Nucmer( )
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30 self.isExcludeFileInitialized = False
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31 self.isReferenceFileInitialized = False
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32 self.referenceFile = None
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33 self.referenceSequence = None
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34 self.uniqueSequences = None
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35
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36 def setExcludeFile( self, excludeFileName ):
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37 """
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38 A function to set the exclude file that will be used when nucmer is called
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39 """
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40
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41 utils.logMessage( "IncludeFileManager::setExcludeFile( )", "fileName {0}".format( excludeFileName ) )
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42 self.excludeFileName = excludeFileName
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43 self.isExcludeFileInitialized = True
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44
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45
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46 def findUniqueSequencesInFile(self, doWantFile, doNotWantFile ):
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47 utils.logMessage( "IncludeFileManager::findUniqueSequence( )", "running nucmer for reference file: {0}".format( doWantFile ) )
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48 coordFile = self.nucmer.execute( [ doWantFile, doNotWantFile ] )
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49
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50 matches = nucmerparser.parseCoordMatchFile( coordFile )
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51 sequences = fastaparser.parseFastaFileAsPrimerSequence( doWantFile )
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52
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53 for match in matches:
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54 if sequences.has_key( match.seqID ):
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55 primerData = sequences[ match.seqID ]
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56 primerData.addMatch( match )
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57 else:
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58 print "Warning: id from .coords file not found in sequence data..."
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59 utils.logMessage( "IncludeFileManager::processMatches( )", "WARNING - an ID was read in a Match that does not correspond to a sequence read from the fasta file!" )
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60
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61 returnValue = [ ]
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62
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63 for key in sequences.keys( ):
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64 sequence = sequences[ key ]
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65 subSequences = sequence.getNonMatchedSubSequences( )
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66 returnValue.extend( subSequences )
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67
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68 return returnValue
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69
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70
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71 def findCommonSequencesInFile(self, want, alsoWant ):
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72 utils.logMessage( "IncludeFileManager::findUniqueSequence( )", "running nucmer for reference file: {0}".format( want ) )
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73
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74 print want, alsoWant
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75 coordFile = self.nucmer.execute( [ want, alsoWant ] )
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76
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77 matches = nucmerparser.parseCoordMatchFile( coordFile )
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78 sequences = fastaparser.parseFastaFileAsPrimerSequence( want )
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79
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80 for match in matches:
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81 if sequences.has_key( match.seqID ):
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82 primerData = sequences[ match.seqID ]
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83 primerData.addMatch( match )
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84
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85 returnValue = [ ]
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86 for key in sequences:
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87 sequence = sequences[ key ]
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88 subSequences = sequence.getMatchedSubSequences( )
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89 returnValue.extend( subSequences )
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90
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91
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92 return returnValue
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93
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94
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95 def processIncludeFile( self, includeFileName ):
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96 """
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97 A function that adds and processes and include file.
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98 An exclude file must be set for this function to be called.
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99 """
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100
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101 utils.logMessage( "IncludeFileManager::processIncludeFile( )", "processing {0}".format( includeFileName ) )
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102
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103 if self.isExcludeFileInitialized == False:
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104 utils.logMessage( "IncludeFileManager::processIncludeFile( )", "no exclude file set".format( includeFileName ) )
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105 raise utils.ModuleNotInitializedException( "includefilemanager", "no exclude file set" )
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106
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107 if self.isReferenceFileInitialized == False:
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108
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109 utils.logMessage( "IncludeFileManager::processIncludeFile( )", "running nucmer for reference file: {0}".format( includeFileName ) )
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110 self.uniqueSequences = self.findUniqueSequencesInFile( includeFileName, self.excludeFileName )
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111
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112 self.referenceFile = includeFileName
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113 self.isReferenceFileInitialized = True
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114
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115 else:
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116 #write the unique sequences to a temp file
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117 tempSequences = utils.getTemporaryDirectory( ) + "/tempSequences.fasta"
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118 fastaparser.writeFastaFile( self.uniqueSequences, tempSequences )
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119 self.findCommonSequencesInFile( includeFileName, tempSequences )
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120 self.includeFiles.append( includeFileName )
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121
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122
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123 def getUniqueSequences( self ):
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124 """
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125 getUniqueSequences - return a dictionary of all sequences that are found in include fasta files, but not the
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126 combined exclude fasta files. The dictionary is indexed by the file ID
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127 """
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128
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129 return self.uniqueSequences
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130
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131
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132 |
