python设计宠物系统_Biopython:为生物信息而设计的python

biopython安装

pip3 install biopython

引入Bio模块

import Bio

from Bio.Seq import Seq

新建序列

seq1 = Seq("ATTCCGTTTGACTGCGTGTTGAAAAACCTGGGGCCCATGCTGCATGGC")

GC含量

from Bio.SeqUtils import GC

GC(seq1)

序列处理

注意：下表是从0开始，区间是左闭右开。

seq1[0:10:1] #获取第1到10个序列，step是1.

反向

seq1.complement()

反向互补

seq1.reverse_complement()

转录DNA成mRNA

mRNA_seq1 = seq1.reverse_complement().transcribe()

转录翻译DNA成蛋白序列

protein_seq1 = seq1.translate() #默认是常用table id 1

biopython的翻译表是基于NCBI.可以根据实际设定table

protein_seq1 = seq1.translate(table=2,to_stop=True) #设置为线粒体模式，遇到终止密码子则停止

protein_seq1 = seq1.translate(to_stop=True) #遇到终止密码子则停止

protein_seq1 = seq1.translate(cds=True) #说明你输入的是完整的cds序列，不含中止密码子，如果出现终止密码子则会抛出异常

翻译表

from Bio.Data import CodonTable

standard_table = CodonTable.unambiguous_dna_by_name["Standard"]

print(standard_table)

MutableSeq对象

Seq对象的序列是只读的。使用MutableSeq可以转换成可变的序列

from Bio.Seq import MutableSeq

mutable_seq = MutableSeq("GCCATTGTAATGGGCCGCTGGCCATTTGCCCGACCATTGTAATGGGCCGCTGAAAGGGTGCCCGAGAAAGGGTGCCCGA")

mutable_seq[5] = "G"

mutable_seq.remove("T")

当编辑完成时，可以用toseq()转变为Seq序列。

new_Seq = mutable_seq.toseq()

UnknownSeq对象 使用UnknownSeq可以节省内存

from Bio.Seq import UnknownSeq

unk1 = UnknownSeq(20) #20个未知序列，默认是用？

unk2 = UnknownSeq(30,character="N") #指定字符为N

第4章 序列注释对象

from Bio.SeqRecord import SeqRecord

第5章 序列输入和输出

读取单条序列

from Bio import SeqIO

single_seq_record = Bio.SeqIO.read("single.fa","fasta")

读取多条序列

from Bio import SeqIO

for seq_record in SeqIO.parse("Sua.5LTR3.fa","fasta"):

print(seq_record.id)

print(repr(seq_record.seq))

print(len(seq_record))

把结果读取到list

records = list(SeqIO.parse("unknown.lib.fa","fasta"))

使用文件句柄

with open("test.fa") as handle:

print(sum(len(r) for r in SeqIO.parse(handle,"fasta")))

打开gzip压缩文件

import gzip

from Bio import SeqIO

with gzip.open("chr.fa.gz","rt") as handle:

print(sum(len(r) for r in SeqIO.Parse(handle,"fasta")))

打开bzip2压缩文件

import bz2

from Bio import SeqIO

with bz2.open("cha.fa.bz2","rt") as handle:

print(sum(len(r) for r in SeqIO.Parse(handle,"fasta")))

写入序列文件

from Bio.Seq import Seq

from Bio.SeqRecord import SeqRecord

from Bio import SeqIO

SeqIO.write(proteins,"translations.fasta","fasta")

模块化1：把DNA序列转换为蛋白质序列

修改最后一行的输入文件和输出文件即可运行

#转换DNA序列为protein序列

def dna2protein(in_fasta,out_fasta,table=1):

##定义转换函数

from Bio.SeqRecord import SeqRecord

def make_protein_record(dna_record):

"""return a new SeqRecord with the translate sequence"""

return SeqRecord(seq = dna_record.seq.translate(table=table),id = dna_record.id,description = "translation of protein ")

##读取fasta序列

from Bio import SeqIO

proteins = (make_protein_record(dna_record) for dna_record in SeqIO.parse(in_fasta,"fasta"))

SeqIO.write(proteins,out_fasta,"fasta")

dna2protein("unknown.fa","unknown.protein.fa")