def get_pepseq(dnaseq): pepseq = '' rf = 0 for i in [-3,-2,-1,1,2,3]: tmpseq = utils.translate_nucleotides(dnaseq, reading_frame=i) if len(tmpseq) > len(pepseq): pepseq = tmpseq rf = i return pepseq, rf
def __init__(self, sequence, known=None, id='', revcom=False): self.nt_seq = sequence self.aa_seq = utils.translate_nucleotides(sequence) self.qseq = '' self.refseq = '' self.backwards = {} self.positions = [] self.code = [] self.specificity = 'unknown' self.library = {} self.oligos = {} self.id = id self.revcom = revcom self._muscle_align() self._get_positions() self._get_backwards() self._get_code() if known: self.get_specificity(known)