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Dear Sean,<br>
<br>
remove the quotes from the restriction enzyme's name, its not a
string.<br>
<br>
This should work:<br>
>>> from Bio import Restriction as res<br>
>>> from Bio.Restriction import RestrictionBatch as rb<br>
>>> from Bio.Seq import Seq<br>
>>> my_batch = rb([res.EcoRI, res.HindIII])<br>
>>> my_seq = Seq('GAATTC')<br>
>>> my_analysis = res.Analysis(my_batch, my_seq)<br>
>>> result = my_analysis.full()<br>
>>> print(result)<br>
{EcoRI: [2], HindIII: []}<br>
>>> result[res.EcoRI]<br>
[2]<br>
<br>
Best,<br>
Markus<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">Am 22.08.2017 um 23:15 schrieb Sean
Brimer:<br>
</div>
<blockquote
cite="mid:CACbeMhRyULuofaXfrhWKgAxsp2qt2t+jdFRu_z5R4E-epqFv6w@mail.gmail.com"
type="cite">
<div dir="ltr">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.
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>
<pre style="box-sizing:border-box;overflow:auto;font-size:14px;padding:0px;margin-top:0px;margin-bottom:0px;line-height:inherit;word-break:break-all;word-wrap:break-word;border:0px;border-radius:0px;white-space:pre-wrap;vertical-align:baseline"><span class="inbox-inbox-ansicyan" style="box-sizing:border-box;color:steelblue"><span class="inbox-inbox-ansigreen" style="box-sizing:border-box;color:darkgreen">----> 1<span class="inbox-inbox-ansiyellow" style="box-sizing:border-box;color:rgb(196,160,0)"> </span>ana<span class="inbox-inbox-ansiyellow" style="box-sizing:border-box;color:rgb(196,160,0)">[</span><span class="inbox-inbox-ansiblue" style="box-sizing:border-box;color:darkblue">'MluI'</span><span class="inbox-inbox-ansiyellow" style="box-sizing:border-box;color:rgb(196,160,0)">]</span><span class="inbox-inbox-ansiyellow" style="box-sizing:border-box;color:rgb(196,160,0)"></span>
<span class="inbox-inbox-ansired" style="box-sizing:border-box;color:darkred">TypeError</span>: 'Analysis' object is not subscriptable</span></span></pre>
<pre style="box-sizing:border-box;overflow:auto;font-size:14px;padding:0px;margin-top:0px;margin-bottom:0px;line-height:inherit;word-break:break-all;word-wrap:break-word;border:0px;border-radius:0px;white-space:pre-wrap;vertical-align:baseline">
</pre>
<pre style="box-sizing:border-box;overflow:auto;font-size:14px;padding:0px;margin-top:0px;margin-bottom:0px;line-height:inherit;word-break:break-all;word-wrap:break-word;border:0px;border-radius:0px;white-space:pre-wrap;vertical-align:baseline">Am I wrong about this class? </pre>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Tue, Aug 22, 2017 at 3:11 PM Sean Brimer <<a
moz-do-not-send="true" href="mailto:skbrimer@gmail.com">skbrimer@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi All,
<div><br>
</div>
<div>I'm having issue with the RestrictionBatch class, when
I tried to create it I get the following error</div>
<div><br>
</div>
<div>
<div>rb = RestrictionBatch([MluI,HincII,SacII])</div>
<div>---------------------------------------------------------------------------</div>
<div>NameError Traceback
(most recent call last)</div>
<div><ipython-input-11-90ba40b69f00> in
<module>()</div>
<div> 1 # rb stands for restriction batch</div>
<div>----> 2 rb = RestrictionBatch([MluI,HincII,SacII])</div>
<div><br>
</div>
<div>NameError: name 'RestrictionBatch' is not defined</div>
</div>
<div><br>
</div>
<div>I'm not sure how you would define this class, I am
following the cookbook but not having much luck. </div>
<div><br>
</div>
<div>Any advice is welcomed and thank you, </div>
</div>
<div dir="ltr">
<div><br>
</div>
<div>Sean</div>
<div><br>
</div>
</div>
</blockquote>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
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Dr. Markus Piotrowski
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