Пример #1
0
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
Пример #2
0
    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)