[2] | 1 | #Dan Blankenberg |
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| 2 | #Contains methods to tranform sequence strings |
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| 3 | import string |
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| 4 | |
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| 5 | #Translation table for reverse Complement, with ambiguity codes |
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| 6 | DNA_COMPLEMENT = string.maketrans( "ACGTRYKMBDHVacgtrykmbdhv", "TGCAYRMKVHDBtgcayrmkvhdb" ) |
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| 7 | RNA_COMPLEMENT = string.maketrans( "ACGURYKMBDHVacgurykmbdhv", "UGCAYRMKVHDBugcayrmkvhdb" ) |
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| 8 | #Translation table for DNA <--> RNA |
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| 9 | DNA_TO_RNA = string.maketrans( "Tt", "Uu" ) |
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| 10 | RNA_TO_DNA = string.maketrans( "Uu", "Tt" ) |
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| 11 | |
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| 12 | #reverse sequence string |
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| 13 | def reverse( sequence ): |
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| 14 | return sequence[::-1] |
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| 15 | #complement DNA sequence string |
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| 16 | def DNA_complement( sequence ): |
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| 17 | return sequence.translate( DNA_COMPLEMENT ) |
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| 18 | #complement RNA sequence string |
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| 19 | def RNA_complement( sequence ): |
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| 20 | return sequence.translate( RNA_COMPLEMENT ) |
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| 21 | #returns the reverse complement of the sequence |
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| 22 | def DNA_reverse_complement( sequence ): |
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| 23 | sequence = reverse( sequence ) |
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| 24 | return DNA_complement( sequence ) |
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| 25 | def RNA_reverse_complement( sequence ): |
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| 26 | sequence = reverse( sequence ) |
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| 27 | return RNA_complement( sequence ) |
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| 28 | def to_DNA( sequence ): |
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| 29 | return sequence.translate( DNA_TO_RNA ) |
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| 30 | def to_RNA( sequence ): |
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| 31 | return sequence.translate( RNA_TO_DNA ) |
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| 32 | |
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| 33 | class ColorSpaceConverter( object ): |
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| 34 | unknown_base = 'N' |
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| 35 | unknown_color = '.' |
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| 36 | color_to_base_dict = {} |
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| 37 | color_to_base_dict[ 'A' ] = { '0':'A', '1':'C', '2':'G', '3':'T', '4':'N', '5':'N', '6':'N', '.':'N' } |
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| 38 | color_to_base_dict[ 'C' ] = { '0':'C', '1':'A', '2':'T', '3':'G', '4':'N', '5':'N', '6':'N', '.':'N' } |
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| 39 | color_to_base_dict[ 'G' ] = { '0':'G', '1':'T', '2':'A', '3':'C', '4':'N', '5':'N', '6':'N', '.':'N' } |
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| 40 | color_to_base_dict[ 'T' ] = { '0':'T', '1':'G', '2':'C', '3':'A', '4':'N', '5':'N', '6':'N', '.':'N' } |
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| 41 | color_to_base_dict[ 'N' ] = { '0':'N', '1':'N', '2':'N', '3':'N', '4':'N', '5':'N', '6':'N', '.':'N' } |
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| 42 | base_to_color_dict = {} |
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| 43 | for base, color_dict in color_to_base_dict.iteritems(): |
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| 44 | base_to_color_dict[ base ] = {} |
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| 45 | for key, value in color_dict.iteritems(): |
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| 46 | base_to_color_dict[ base ][ value ] = key |
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| 47 | base_to_color_dict[ base ][ 'N' ] = '4' #force ACGT followed by N to be '4', because this is now 'processed' data; we could force to '.' (non-processed data) also |
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| 48 | base_to_color_dict[ 'N' ].update( { 'A':'5', 'C':'5', 'G':'5', 'T':'5', 'N':'6' } ) |
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| 49 | def __init__( self, fake_adapter_base = 'G' ): |
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| 50 | assert fake_adapter_base in self.base_to_color_dict, 'A bad fake adapter base was provided: %s.' % fake_adapter_base |
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| 51 | self.fake_adapter_base = fake_adapter_base |
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| 52 | def to_color_space( self, sequence, adapter_base = None ): |
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| 53 | if adapter_base is None: |
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| 54 | adapter_base = self.fake_adapter_base |
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| 55 | last_base = adapter_base #we add a fake adapter base so that the sequence can be decoded properly again |
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| 56 | rval = last_base |
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| 57 | for base in sequence: |
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| 58 | rval += self.base_to_color_dict.get( last_base, self.base_to_color_dict[ self.unknown_base ] ).get( base, self.unknown_color ) |
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| 59 | last_base = base |
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| 60 | return rval |
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| 61 | def to_base_space( self, sequence ): |
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| 62 | if not isinstance( sequence, list ): |
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| 63 | sequence = list( sequence ) |
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| 64 | if sequence: |
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| 65 | last_base = sequence.pop( 0 ) |
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| 66 | else: |
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| 67 | last_base = None |
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| 68 | assert last_base in self.color_to_base_dict, 'A valid adapter base must be included when converting to base space from color space. Found: %s' % last_base |
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| 69 | rval = '' |
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| 70 | for color_val in sequence: |
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| 71 | last_base = self.color_to_base_dict[ last_base ].get( color_val, self.unknown_base ) |
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| 72 | rval += last_base |
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| 73 | return rval |
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