Exemplo n.º 1
0
	def seq(self, coding=True):
		"""Returns the sequence of the fragment in the 'sense' sense """
		if coding:
			if self.is_rev(): return complement(self.__seq)
			else: return self.__seq
		else:
			return self.__seq
Exemplo n.º 2
0
	def __seq_from_codons(self):
		t_seq=''
		for one in sorted(self.coding_codon.keys()): 
			t_seq+=self.coding_codon[one]
		t_seq = t_seq.replace(' ','')
		if self.is_rev():
			t_seq = complement( t_seq )
		self.__seq = t_seq
		self.updated=True
Exemplo n.º 3
0
	def insert(self, pos, AAseq):
		new_dna_seq, new_frag_seq = '',''
		for aa in AAseq: new_dna_seq+= self.CodonData.codon(aa, False)
		for frag in self.frags:
			if not frag.contains(pos): continue
			if ' ' == frag.coding_codon[int(pos)][:-1]: continue
			
			for cod in sorted(frag.coding_codon.keys()):
				new_frag_seq += frag.coding_codon[cod]
				if cod == int(pos): new_frag_seq += new_dna_seq
			if frag.is_rev(): new_frag_seq  = complement(new_frag_seq.replace(' ','') )
			frag._Fragment__seq = new_frag_seq 
		self.assemble(self.min_overlap )