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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thank you, that worked like a charm. I left a comment on the BioStars page for the following generations to learn from it :-)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> Bastien<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Calibri",sans-serif;color:#008FD5">--
<br>
DSM Nutritional Products Microbia Inc | Bioinformatics<br>
60 Westview Street | Lexington, MA 02421 | United States<br>
Phone +1 781 259 7613 | Fax +1 781 259 0615</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Kevin Bonham [mailto:kevbonham@gmail.com]
<br>
<b>Sent:</b> Tuesday, November 22, 2016 12:50 AM<br>
<b>To:</b> Chevreux, Bastien <bastien.chevreux@dsm.com>; biopython@biopython.org<br>
<b>Subject:</b> Re: [Biopython] Problems with SeqFeature<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">--- This mail has been sent from an external source ---
<o:p></o:p></p>
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<p>Hi Bastien,<o:p></o:p></p>
<p>Yeah, it looks like you're pulling from two different snippets and they're not using the same conventions. When you're doing `from Bio.SeqFeature import SeqFeature...`, you're overwriting what Python thinks `SeqFeature` means from when you did `from Bio
import SeqFeature`. And, as you say, you're importing a bunch of stuff twice, which doesn't make much sense.<o:p></o:p></p>
<p>My recommendation would be to do:<br>
<br>
from Bio import SeqFeature as sf<br>
<br>
def myfun():<br>
spos = sf.BeforePosition(50);<o:p></o:p></p>
<p> epos = sf.ExactPosition(100);<o:p></o:p></p>
<p> l1 = sf.FeatureLocation(spos, epos, strand=+1)<o:p></o:p></p>
<p> f1 = sf.SeqFeature(l1, strand=1, type="CDS", qualifiers={});<o:p></o:p></p>
<p>This way everything is nice and tidy, and you can see where those functions came from in your code. Plus you have access to everything in Bio.SeqFeature if you need it.<o:p></o:p></p>
<p>If you really only need those four things, and you want to reduce the overhead a bit, you could do<o:p></o:p></p>
<p> from Bio.SeqFeature import BeforePosition, ExactPosition, FeatureLocation, SeqFeature<o:p></o:p></p>
<p> ...<o:p></o:p></p>
<p>And then just use these unqualified. Hope this helps!<o:p></o:p></p>
<p>Kevin<o:p></o:p></p>
<p>PS I didn't actually try to run any of the above code and im typing on my phone, so don't be mad if there's a syntax error somewhere :-)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, Nov 21, 2016, 1:03 PM Chevreux, Bastien <<a href="mailto:bastien.chevreux@dsm.com">bastien.chevreux@dsm.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi all,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I am basing my question on
<a href="https://www.biostars.org/p/57549/" target="_blank">https://www.biostars.org/p/57549/</a> which gives a code snipped which shows on how to add SeqFeatures.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Adapted, that code looks like this:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">---<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">from Bio import SeqFeature;<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">spos = SeqFeature.BeforePosition(50);<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">epos = SeqFeature.ExactPosition(100);<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span class="gmailmsg"><span lang="FR">l1 = FeatureLocation(spos, epos, strand=+1)</span></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">f1 = SeqFeature(l1, strand=1, type="CDS", qualifiers={});<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">---<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">And it does work, no problem.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">However, I have some terrible issues with the above code: it imports SeqFeature twice. And I cannot write:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">---<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">from Bio import SeqFeature;<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">…<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">---<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">as this will bomb.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">And therefore I cannot easily stick the above into a function without re-importing in the function every time I use the functionality. Like this:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">---<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">def myfun():<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> from Bio import SeqFeature;<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> spos = SeqFeature.BeforePosition(50);<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> epos = SeqFeature.ExactPosition(100);<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span class="gmailmsg"><span lang="FR"> l 1 = FeatureLocation(spos, epos, strand=+1)</span></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> f1 = SeqFeature(l1, strand=1, type="CDS", qualifiers={});<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">---<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">This seems so infinitely wrong to me. What’s the correct way to write a function like this:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">---<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">from … import …<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">from … import …<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">def myfun(x,y):<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> spos = SeqFeature.BeforePosition(x);<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span class="gmailmsg"><span lang="FR"> epos = SeqFeature.ExactPosition(y);</span></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span class="gmailmsg"><span lang="FR"> l 1 = FeatureLocation(spos, epos, strand=+1)</span></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span class="gmailmsg"><span lang="FR">
</span></span>f1 = SeqFeature(l1, strand=1, type="CDS", qualifiers={});<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> return f1;<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">---<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Best,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Bastien<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span class="gmailmsg"><span style="font-size:8.5pt;color:#008FD5">--
</span></span><span style="font-size:8.5pt;color:#008FD5"><br>
<span class="gmailmsg">DSM Nutritional Products Microbia Inc | Bioinformatics</span><br>
<span class="gmailmsg">60 Westview Street | Lexington, MA 02421 | United States</span><br>
<span class="gmailmsg">Phone +1 781 259 7613 | Fax +1 781 259 0615</span></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal">Lecturer, Harvard Medical School<o:p></o:p></p>
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