python怎么实现CDS序列

本篇内容主要讲解"python怎么实现CDS序列"，感兴趣的朋友不妨来看看。本文介绍的方法操作简单快捷，实用性强。下面就让小编来带大家学习"python怎么实现CDS序列"吧!

筛选编码蛋白的CDS序列

#!python# coding:utf-8'''##############################################################################################北京组学生物科技有限公司#author huangls#date 2021.01.26#version 1.2#学习python课程推荐：#python 入门到精通(生物信息):#https://study.163.com/course/introduction/1209531837.htm?share=1&shareId=1030291076###############################################################################################'''from Bio.Seq import Seqfrom Bio import SeqIO#from Bio.Alphabet import IUPACfrom Bio.SeqRecord import SeqRecordimport os, argparse, os.path,reparser = argparse.ArgumentParser(description='This script is used to get coding sequence from fasta file.')parser.add_argument('-f','--fasta',help='Please input fasta file. [REQUIRED]',required=True)parser.add_argument('-l','--len',type=int,default=300,help='seq length filter, default 300.  [OPTIONAL]',required=False)parser.add_argument('-p','--prefix',default ='demo_seq',required=False,help='Please specify the output file prefix, default demo_seq. [OPTIONAL]')parser.add_argument('-o','--out_dir',help='Please input  output directory path default cwd.  [OPTIONAL]',default = os.getcwd(),required=False)################################################################################args = parser.parse_args()dout=''if os.path.exists(args.out_dir):    dout=os.path.abspath(args.out_dir)else:    os.mkdir(args.out_dir)    dout=os.path.abspath(args.out_dir)count=0total=0output_handle = open(dout+'/'+args.prefix+'.fa', "w")for rec in SeqIO.parse(args.fasta, "fasta"):    seq=str(rec.seq)    #seq=seq.upper()    total+=1    if(len(seq)>=args.len and re.search("^ATG",seq,re.I) and len(seq)%3==0):        if re.search('TAG$',seq,re.I) or re.search('TGA$',seq,re.I) or re.search('TAA$',seq,re.I):            seq = seq[:-3]            f=re.finditer('TAG|TGA|TAA',seq,re.I)            if not f:                SeqIO.write(rec, output_handle, "fasta")                count+=1            else:                isstop=False                for i in f:                    index=i.start()                    if index%3 ==0:                        isstop=True                        break                if not isstop:                    SeqIO.write(rec, output_handle, "fasta")                    count+=1print("Total input seqs: %s"%total)print("Coding seqs: %s"%count)print("Output file: %s"%dout+'/'+args.prefix+'.fa')output_handle.close()

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