#Dan Blankenberg
import transform
import string
from copy import deepcopy
[docs]class SequencingRead( object ):
color_space_converter = transform.ColorSpaceConverter()
valid_sequence_list = string.letters
def __init__( self ):
self.identifier = None
self.sequence = '' #holds raw sequence string: no whitespace
self.description = None
self.quality = '' #holds raw quality string: no whitespace, unless this contains decimal scores
def __len__( self ):
return len( self.sequence )
def __str__( self ):
return "%s\n%s\n%s\n%s\n" % ( self.identifier, self.sequence, self.description, self.quality )
[docs] def append_sequence( self, sequence ):
self.sequence += sequence.rstrip( '\n\r' )
[docs] def append_quality( self, quality ):
self.quality += quality.rstrip( '\n\r' )
[docs] def is_DNA( self ):
return 'u' not in self.sequence.lower()
[docs] def clone( self ):
return deepcopy( self )
[docs] def reverse( self, clone = True ):
if clone:
rval = self.clone()
else:
rval = self
rval.sequence = transform.reverse( self.sequence )
rval.quality = rval.quality[::-1]
return rval
[docs] def complement( self, clone = True ):
if clone:
rval = self.clone()
else:
rval = self
if rval.is_DNA():
rval.sequence = transform.DNA_complement( rval.sequence )
else:
rval.sequence = transform.RNA_complement( rval.sequence )
return rval
[docs] def reverse_complement( self, clone = True ):
#need to reverse first, then complement
rval = self.reverse( clone = clone )
return rval.complement( clone = False ) #already working with a clone if requested
[docs] def sequence_as_DNA( self, clone = True ):
if clone:
rval = self.clone()
else:
rval = self
rval.sequence = transform.to_DNA( rval.sequence )
return rval
[docs] def sequence_as_RNA( self, clone = True ):
if clone:
rval = self.clone()
else:
rval = self
rval.sequence = transform.to_RNA( rval.sequence )
return rval