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
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
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 )