[Biopython] Restriction Batch Error, Python3.5 Biopython 1.7 Jupyter notebook

[Sean Brimer]

Wonderful! Thank you Markus! I will try this right away!

On Thu, Aug 24, 2017 at 10:09 AM Markus Piotrowski <
Markus.Piotrowski at ruhr-uni-bochum.de> wrote:

> Dear Sean,
>
> remove the quotes from the restriction enzyme's name, its not a string.
>
> This should work:
> >>> from Bio import Restriction as res
> >>> from Bio.Restriction import RestrictionBatch as rb
> >>> from Bio.Seq import Seq
> >>> my_batch = rb([res.EcoRI, res.HindIII])
> >>> my_seq = Seq('GAATTC')
> >>> my_analysis = res.Analysis(my_batch, my_seq)
> >>> result = my_analysis.full()
> >>> print(result)
> {EcoRI: [2], HindIII: []}
> >>> result[res.EcoRI]
> [2]
>
> Best,
> Markus
>
>
>
>
>
>
>
>
> Am 22.08.2017 um 23:15 schrieb Sean Brimer:
>
> Alright, So I have gotten it to work, I had to do 'from Bio.Restriction
> import *' I know its not the best way to import a module but it worked. So
> now I have a follow up question.
>
> I would like to capture the output of the restriction batch result and use
> it to look for a match from another table. The result looks like a
> dictionary however when I do the following I'm denied.
>
> ----> 1 ana['MluI']
> TypeError: 'Analysis' object is not subscriptable
>
>  Am I wrong about this class?
>
>
> On Tue, Aug 22, 2017 at 3:11 PM Sean Brimer <skbrimer at gmail.com> wrote:
>
>> Hi All,
>>
>> I'm having issue with the RestrictionBatch class, when I tried to create
>> it I get the following error
>>
>> rb = RestrictionBatch([MluI,HincII,SacII])
>>
>> ---------------------------------------------------------------------------
>> NameError                                 Traceback (most recent call
>> last)
>> <ipython-input-11-90ba40b69f00> in <module>()
>>       1 # rb stands for restriction batch
>> ----> 2 rb = RestrictionBatch([MluI,HincII,SacII])
>>
>> NameError: name 'RestrictionBatch' is not defined
>>
>> I'm not sure how you would define this class, I am following the cookbook
>> but not having much luck.
>>
>> Any advice is welcomed and thank you,
>>
>> Sean
>>
>>
>
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>
> --
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