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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 import utils
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11
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12 class PrimerSequence( object ):
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13 """
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14 record sequence data, and store matched parts of the sequence
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15 """
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16
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17 def __init__( self, seqID, seqLength, sequence ):
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18 #an unmatched sub-sequence that starts at 0 goes until the end of the the sequence, to start out with.
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19
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20 self.seqID = seqID
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21 self.seqLength = seqLength
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22 self.matchedSubSequences = [ ]
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23 self.sequence = sequence
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24
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25 def addMatch( self, match ):
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26 """
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27 Input: a utils.Match object
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28 Removes the matched sequence from the list of valid sequence data
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29 """
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30
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31 self.matchedSubSequences.append( ( match.start, match.end ) )
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32
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33 def findNonMatchedIndices( self ):
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34
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35 utils.logMessage("PrimerSequence::findValidIndices( )", "getting unmatched sequence indices" )
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36
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37 sequence = set( range( self.seqLength ) )
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38
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39 #find the indices that are NOT excluded
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40 utils.logMessage( "PrimerSequence::findValidIndices( )", "there are {0} excluded sequences for {1}".format( len( self.matchedSubSequences ), self.seqID ) )
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41 for exclude in self.matchedSubSequences:
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42 excludedSequence = set( range( exclude[ 0 ], exclude[ 1 ] ) )
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43 utils.logMessage("PrimerSequence::findValidIndices( )", "removing exclude sequence {0} - {1}".format( exclude[ 0 ], exclude[ 1 ] ) )
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44 sequence = sequence - excludedSequence
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45
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46 utils.logMessage("PrimerSequence::findValidIndices( )", "{0} unique indices".format( len( sequence ) ) )
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47
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48 return list( sequence )
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49
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50 def findNonMatchedIndexSequences( self, indices ):
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51
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52 utils.logMessage("PrimerSequence::findValidIndexSequences( )", "getting sequences from unique indices" )
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53
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54 sequences = [ ]
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55 curSeq = [ ]
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56 for index in indices:
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57 if len( curSeq ) == 0:
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58 curSeq.append( index )
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59 elif index == curSeq[ -1 ] + 1:
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60 curSeq.append( index )
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61 else:
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62 sequences.append( curSeq )
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63 curSeq = [ ]
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64 sequences.append( curSeq )
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65 utils.logMessage("PrimerSequence::findValidIndexSequences( )", "{0} sequences found".format( len( sequences ) ) )
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66
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67 return sequences
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68
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69
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70 def getNonMatchedSubSequences( self, minLength = 100 ):
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71 """
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72 Get all valid sub sequences after removing matches
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73 """
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74
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75 utils.logMessage("PrimerSequence::getNonMatchedSubSequences( )", "finding valid sub sequences for {0}".format( self.seqID ) )
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76
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77 indices = self.findNonMatchedIndices( )
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78 indexSequences = self.findNonMatchedIndexSequences( indices )
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79
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80 subSequences = [ ]
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81
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82 for indexSequence in indexSequences:
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83 subSequence = [ self.sequence[ i ] for i in indexSequence ]
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84
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85 if len( subSequence ) >= minLength:
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86 subSequences.append( subSequence )
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87
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88 return subSequences
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89
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90 def getMatchedSubSequences( self, minLength = 100 ):
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91 utils.logMessage("PrimerSequence::getMatchedSubSequences( )", "finding valid sub sequences for {0}".format( self.seqID ) )
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92
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93 returnValue = [ ]
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94 for match in self.matchedSubSequences:
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95 subSequence = self.sequence[ match[ 0 ]:match[ 1 ] ]
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96
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97 if len( subSequence ) >= minLength :
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98 returnValue.append( subSequence )
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99
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100 return returnValue
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101
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102
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103
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104
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105
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106
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107
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108
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109
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110 |
