/lib/galaxy_utils/sequence/transform.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 73 lines · 62 code · 3 blank · 8 comment · 8 complexity · 6dadf556302e3f7a9a49da564e2adada MD5 · raw file
- #Dan Blankenberg
- #Contains methods to tranform sequence strings
- import string
- #Translation table for reverse Complement, with ambiguity codes
- DNA_COMPLEMENT = string.maketrans( "ACGTRYKMBDHVacgtrykmbdhv", "TGCAYRMKVHDBtgcayrmkvhdb" )
- RNA_COMPLEMENT = string.maketrans( "ACGURYKMBDHVacgurykmbdhv", "UGCAYRMKVHDBugcayrmkvhdb" )
- #Translation table for DNA <--> RNA
- DNA_TO_RNA = string.maketrans( "Tt", "Uu" )
- RNA_TO_DNA = string.maketrans( "Uu", "Tt" )
- #reverse sequence string
- def reverse( sequence ):
- return sequence[::-1]
- #complement DNA sequence string
- def DNA_complement( sequence ):
- return sequence.translate( DNA_COMPLEMENT )
- #complement RNA sequence string
- def RNA_complement( sequence ):
- return sequence.translate( RNA_COMPLEMENT )
- #returns the reverse complement of the sequence
- def DNA_reverse_complement( sequence ):
- sequence = reverse( sequence )
- return DNA_complement( sequence )
- def RNA_reverse_complement( sequence ):
- sequence = reverse( sequence )
- return RNA_complement( sequence )
- def to_DNA( sequence ):
- return sequence.translate( DNA_TO_RNA )
- def to_RNA( sequence ):
- return sequence.translate( RNA_TO_DNA )
- class ColorSpaceConverter( object ):
- unknown_base = 'N'
- unknown_color = '.'
- color_to_base_dict = {}
- color_to_base_dict[ 'A' ] = { '0':'A', '1':'C', '2':'G', '3':'T', '4':'N', '5':'N', '6':'N', '.':'N' }
- color_to_base_dict[ 'C' ] = { '0':'C', '1':'A', '2':'T', '3':'G', '4':'N', '5':'N', '6':'N', '.':'N' }
- color_to_base_dict[ 'G' ] = { '0':'G', '1':'T', '2':'A', '3':'C', '4':'N', '5':'N', '6':'N', '.':'N' }
- color_to_base_dict[ 'T' ] = { '0':'T', '1':'G', '2':'C', '3':'A', '4':'N', '5':'N', '6':'N', '.':'N' }
- color_to_base_dict[ 'N' ] = { '0':'N', '1':'N', '2':'N', '3':'N', '4':'N', '5':'N', '6':'N', '.':'N' }
- base_to_color_dict = {}
- for base, color_dict in color_to_base_dict.iteritems():
- base_to_color_dict[ base ] = {}
- for key, value in color_dict.iteritems():
- base_to_color_dict[ base ][ value ] = key
- 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
- base_to_color_dict[ 'N' ].update( { 'A':'5', 'C':'5', 'G':'5', 'T':'5', 'N':'6' } )
- def __init__( self, fake_adapter_base = 'G' ):
- assert fake_adapter_base in self.base_to_color_dict, 'A bad fake adapter base was provided: %s.' % fake_adapter_base
- self.fake_adapter_base = fake_adapter_base
- def to_color_space( self, sequence, adapter_base = None ):
- if adapter_base is None:
- adapter_base = self.fake_adapter_base
- last_base = adapter_base #we add a fake adapter base so that the sequence can be decoded properly again
- rval = last_base
- for base in sequence:
- rval += self.base_to_color_dict.get( last_base, self.base_to_color_dict[ self.unknown_base ] ).get( base, self.unknown_color )
- last_base = base
- return rval
- def to_base_space( self, sequence ):
- if not isinstance( sequence, list ):
- sequence = list( sequence )
- if sequence:
- last_base = sequence.pop( 0 )
- else:
- last_base = None
- 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
- rval = ''
- for color_val in sequence:
- last_base = self.color_to_base_dict[ last_base ].get( color_val, self.unknown_base )
- rval += last_base
- return rval