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)