问题描述
我正在尝试使用 Bio.Restrictions
方法的一些问题,我不知道是由于python,biopython还是我对python的了解不足。
当我尝试在,我想从字典中使用酶I(从文件中读取),它说:
在python for dict.keys
说:
所以我试过这个:
code> rb = RestrictionBatch(Enzymes.keys())
但是我收到一个错误: ValueError:< type'list'>不是RestrictionType
测试可能是我创建此代码的错误,以确定它是否真的是一个列表
从Bio.Seq import Seq
Enzymes = {'XhoI':Seq('CTCGAG' BsmBI':Seq('CGTCTC'),'SceI':Seq('AGTTACGCTAGGGATAACAGGGTAATATAG'),'BamHI':Seq('GGATCC')''BsaI':Seq('GGTCTC')''SacI' GAGCTC'),'BbsI':Seq('GAAGAC'),'AarI':Seq('CACCTGC'),'EcoRI':Seq('GAATTC')''SpeI':Seq('ACTAGT')''CeuI ':Seq('TTCGCTACCTTAGGACCGTTATAGTTACG')}
print Enzymes.keys()是list #prints False
print isinstance(Enzymes.keys(),list)#prints True
打印类型(Enzymes.keys())#prints< type'list'>
为什么会这样的行为?如何使用字典来运行 RestrictionBatch
?
我正在使用:
Python 2.7.3 | EPD 7.3 -2(64位)| (默认,2012年4月11日17:52:16)
[GCC 4.1.2 20080704(Red Hat 4.1.2-44)] on linux2
import Bio
打印(Bio .__ version__)
1.59
次要问题:
我如何检查如果是否限制在数据库?有没有办法在这个数据库中添加一个酶(假设我有需要的信息)?
食谱松散地使用单词表。他们谈论一个列出了有效酶的名称,这些列表已经在 import Bio.Restriction
中定义。您可以列出所有(以及其他实用程序):
从生物进口限制作为rst
dir(rst)
但是RestrictionType比名字和序列的dict有点复杂。这是EcoRI的完整定义:
rest_dict [EcoRI] = {
'compsite': '(ΔP GAATTC)|(ΔP GAATTC)',
'results':None,
'site':'GAATTC',
'substrat' 'DNA',
'fst3':-1,
'fst5':1,
'freq':4096,
'size':6,
' opt_temp':37,
'dna':无,
'inact_temp':65,
'ovhg':-4,
'scd3':无,
'''('B','C','F','H','I','J','K','M','N','O' R'
'scd5':None,
'charac':(1,-1,None,None,'GAATTC'),
'ovhgseq':'AATT',
}
加上供应商的一套,例如
pre>
供应商[B] =(
'Invitrogen Corporation',
['MluI','HpaII','SalI','NcoI ,'ClaI','DraI','SstII','AvaI',...)
并且打字:
typedict [212] =(
('NonPalindromic','OneCut' Ov5','Defined','Meth_Dep',...),
['BssHII','BsrFI','DpnII','MluI','NgoMIV','HpaII','TspMI' ...],
)
这些定义在 Bio。 Restriction.Restriction_Dictionary
使用我之前放在另一个:
from Bio.Restriction import限制作为rst
来自Bio.Restriction.Restriction_Dictionary import rest_dict,typedict
def create_enzyme(name):
e_types = [x for t,(x,y )in typedict.items()if name in y] [0]
enzyme_types = tuple(getattr(rst,x)for e in e_types)
return rst.RestrictionType(name,enzyme_types,rest_dict [name])
enzyme_list = [EcoRI,MstI]
rb = reduce(lambda x,y: x + y,map(create_enzyme,enzyme_list))
当菜谱说通过传递一个列表的酶或酶名称,他们正在简化的事情。在源代码中可以看到 /Bio/Restriction/Restriction.py
,当对象RestrictionBatch初始化时, __ init __
调用 self.format
和 self.format
检查列表中的每个项目是否为 RestrictionType
。
次要问题的次要答案是:
>>>从生物进口限制作为rst
>>>> rst.hasattr(rst,EcoRI)
True
>>> rst.hasattr(rst,FakeEnzyme)
False
或
>>>来自Bio.Restriction.Restriction_Dictionary import rest_dict
>>> rest_dict.keys()中的EcoRI
True
>>> rest_dict.keys()中的FakeEnzyme
False
I am experimenting some problems using the Bio.Restrictions
methods, I am not sure if it is due to python, biopython or my poor understanding of python.
When I try to crate a RestrictionBatch
following the cookbook, I want to use enzymes I from a dictionary (read from files), and it says:
In the python documentation for dict.keys
says:
So I tried this:
rb = RestrictionBatch(Enzymes.keys())
But I get an error: ValueError: <type 'list'> is not a RestrictionType
Testing where could be the error I created this code, to know if it is really a list or not
from Bio.Seq import Seq
Enzymes = {'XhoI': Seq('CTCGAG'), 'BsmBI': Seq('CGTCTC'), 'SceI': Seq('AGTTACGCTAGGGATAACAGGGTAATATAG'), 'BamHI': Seq('GGATCC'), 'BsaI': Seq('GGTCTC'), 'SacI': Seq('GAGCTC'), 'BbsI': Seq('GAAGAC'), 'AarI': Seq('CACCTGC'), 'EcoRI': Seq('GAATTC'), 'SpeI': Seq('ACTAGT'), 'CeuI': Seq('TTCGCTACCTTAGGACCGTTATAGTTACG')}
print Enzymes.keys() is list #prints False
print isinstance(Enzymes.keys(), list) #prints True
print type(Enzymes.keys()) #prints <type 'list'>
Why this behaviour? And how can I use the dictionary to run the RestrictionBatch
?
I am using:
Python 2.7.3 |EPD 7.3-2 (64-bit)| (default, Apr 11 2012, 17:52:16)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2
import Bio
print(Bio.__version__)
1.59
Minor question:How can I check if it is or not in the database of Restriction? Is there any way to add one enzyme to this database (assuming I have the information needed)?
The cookbook uses loosely the word "list". They talk about a list with the names of valid enzymes, that are already defined in the import Bio.Restriction
. You can list all of them (along with other utilities) with:
from Bio import Restriction as rst
dir(rst)
But the RestrictionType is a bit more complex than a dict with names and seqs. This is the full definition for "EcoRI":
rest_dict["EcoRI"] = {
'compsite' : '(?P<EcoRI>GAATTC)|(?P<EcoRI_as>GAATTC)',
'results' : None,
'site' : 'GAATTC',
'substrat' : 'DNA',
'fst3' : -1,
'fst5' : 1,
'freq' : 4096,
'size' : 6,
'opt_temp' : 37,
'dna' : None,
'inact_temp' : 65,
'ovhg' : -4,
'scd3' : None,
'suppl' : ('B', 'C', 'F', 'H', 'I', 'J', 'K', 'M', 'N', 'O', 'Q', 'R'
'scd5' : None,
'charac' : (1, -1, None, None, 'GAATTC'),
'ovhgseq' : 'AATT',
}
Plus a set with the suppliers, e.g.
suppliers["B"] = (
'Invitrogen Corporation',
['MluI', 'HpaII', 'SalI', 'NcoI', 'ClaI', 'DraI', 'SstII', 'AvaI', ...)
And the typedict:
typedict["212"] = (
('NonPalindromic', 'OneCut', 'Ov5', 'Defined', 'Meth_Dep', ...),
['BssHII', 'BsrFI', 'DpnII', 'MluI', 'NgoMIV', 'HpaII', 'TspMI', ...],
)
These definitions are in Bio.Restriction.Restriction_Dictionary
Using the code I previously put in another anwer:
from Bio.Restriction import Restriction as rst
from Bio.Restriction.Restriction_Dictionary import rest_dict, typedict
def create_enzyme(name):
e_types = [x for t, (x, y) in typedict.items() if name in y][0]
enzyme_types = tuple(getattr(rst, x) for x in e_types)
return rst.RestrictionType(name, enzyme_types, rest_dict[name])
enzyme_list = ["EcoRI", "MstI"]
rb = reduce(lambda x, y: x + y, map(create_enzyme, enzyme_list))
When the cookbook says "by passing it a list of enzymes or enzymes name", they are simplifying the things. As you can see in the source, /Bio/Restriction/Restriction.py
, when the object RestrictionBatch is initialized, __init__
calls self.format
, and self.format
checks that every item in the "list" is an instance of RestrictionType
.
The minor answer for the minor question is:
>>> from Bio import Restriction as rst
>>> rst.hasattr(rst, "EcoRI")
True
>>> rst.hasattr(rst, "FakeEnzyme")
False
Or
>>> from Bio.Restriction.Restriction_Dictionary import rest_dict
>>> "EcoRI" in rest_dict.keys()
True
>>> "FakeEnzyme" in rest_dict.keys()
False
这篇关于列表和限制类型从Biopython的文章就介绍到这了,希望我们推荐的答案对大家有所帮助,也希望大家多多支持!