Analysis.py 文件源码

def parse_fasta(self):
        self.ref_id=dict()
        self.ref_inf=dict()
        i=1
        N = 0
        ref_inf=np.empty(shape=[0,3])
        for seqs in SeqIO.parse(self.ref,'fasta'):
            seq_id = seqs.id
            self.ref_id[i] = seq_id
            seq = str(seqs.seq.upper())
            seq_len = len(seq)
            self.ref_inf[seq_id]=seq_len
            N+=seq.count('N')
            ref_inf = np.append(ref_inf,[[i,seq_id,seq_len]],axis=0)
            i+=1
        self.ref_detail = pd.DataFrame(ref_inf,columns=['Index','Contig','Length(bp)'])
        self.N = N