/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

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