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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">You are correct, it was my mistake.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">The tutorial works fine and I’ve also launched the “python setup.py test” to see if the unittests are running fine.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Most of them do, there is only a failed test in
<i>test_Entrez_only.py</i> regarding an expected result.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">The problem with Bio.SeqIO and other related C modules disappear when I’m outside the source directory.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">What does it mean? I haven’t touched the code for those modules.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Francesco.<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"> Michiel de Hoon [mailto:mjldehoon@yahoo.com]
<br>
<b>Sent:</b> 27 June 2018 12:51<br>
<b>To:</b> p.j.a.cock@googlemail.com; Fulton, Ben <befulton@iu.edu>; Francesco Gastaldello (Staff) <f.gastaldello@dundee.ac.uk><br>
<b>Cc:</b> biopython@mailman.open-bio.org<br>
<b>Subject:</b> Re: [Biopython] problem with Bio.Align _aligns.c<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><i><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif">>>> from Bio import Seq</span></i><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif">This should be<o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif">>>> from Bio.Seq import Seq</span></i><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A">On Wednesday, June 27, 2018, 8:33:42 PM GMT+9, Francesco Gastaldello (Staff) <<a href="mailto:f.gastaldello@dundee.ac.uk">f.gastaldello@dundee.ac.uk</a>> wrote:
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:"Calibri",sans-serif;color:black">Peter:</span></b><span style="font-family:"Calibri",sans-serif;color:black">
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">After the upgrade to Ubuntu 18.04, my VM blow up and I had to re-build it from scratch. I'm not saying that I've made it exactly like the one that used the previous version, so
I might miss some dependencies. I do not use/contribute to Biopython on my local Wndows machine anymore (because some module gave problem when I was developing some tests).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:"Calibri",sans-serif;color:black">Ben:</span></b><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">I've followed your suggestion. Directly on terminal (not via PyCharm or other IDE) I've entered the virtual environment dedicated to biopython and build+installed it from the source
code. I get this in the console:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">--<o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">(biopython) gasta@gasta-VirtualBox:~/Documents/GitHub/biopython(master)$ python setup.py install</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">running install</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">running build</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">running build_py</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">running build_ext</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">running install_lib</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">copying build/lib.linux-x86_64-2.7/Bio/GenBank/__init__.py -> /home/gasta/venv/biopython/lib/python2.7/site-packages/Bio/GenBank</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">byte-compiling /home/gasta/venv/biopython/lib/python2.7/site-packages/Bio/GenBank/__init__.py to __init__.pyc</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">running install_egg_info</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">running egg_info</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">writing requirements to biopython.egg-info/requires.txt</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">writing biopython.egg-info/PKG-INFO</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">writing top-level names to biopython.egg-info/top_level.txt</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">writing dependency_links to biopython.egg-info/dependency_links.txt</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">reading manifest file 'biopython.egg-info/SOURCES.txt'</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">reading manifest template 'MANIFEST.in'</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">warning: no previously-included files matching '*.pyo' found anywhere in distribution</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">warning: no previously-included files matching '*.py{}' found anywhere in distribution</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">warning: no previously-included files matching '*.py-e' found anywhere in distribution</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">writing manifest file 'biopython.egg-info/SOURCES.txt'</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">removing '/home/gasta/venv/biopython/lib/python2.7/site-packages/biopython-1.72-py2.7.egg-info' (and everything under it)</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">Copying biopython.egg-info to /home/gasta/venv/biopython/lib/python2.7/site-packages/biopython-1.72-py2.7.egg-info</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">running install_scripts</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">--<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">If I run the python console from the source directory I'm not able to run the tests mentioned in the installation guidelines, but numpy is fine (linking to
<b>Michiel</b> comment):<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">--<o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">(biopython) gasta@gasta-VirtualBox:~/Documents/GitHub/biopython(master)$ python</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">Python 2.7.15rc1 (default, Apr 15 2018, 21:51:34) </span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">[GCC 7.3.0] on linux2</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">Type "help", "copyright", "credits" or "license" for more information.</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">>>> from Bio import Seq</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">>>> from Bio.Alphabet.IUPAC import unambiguous_dna</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">>>> new_seq = Seq('GATCAGAAG', unambiguous_dna)</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">Traceback (most recent call last):</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black"> File "<stdin>", line 1, in <module></span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">TypeError: 'module' object is not callable</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">>>> import numpy</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">>>> numpy.array([[1, 2], [3, 4]])</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">array([[1, 2],</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black"> [3, 4]])</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"> --<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">Same happen when I run the exact same test elsewhere but still inside the virtual environment<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">--<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">(biopython) gasta@gasta-VirtualBox:~$ python</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">Python 2.7.15rc1 (default, Apr 15 2018, 21:51:34) </span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">[GCC 7.3.0] on linux2</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">Type "help", "copyright", "credits" or "license" for more information.</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">>>> import numpy</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">>>> numpy.array([[1, 2], [3, 4]])</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">array([[1, 2],</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black"> [3, 4]]) </span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">>>> from Bio import Seq</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">>>> from Bio.Alphabet.IUPAC import unambiguous_dna</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">>>> new_seq = Seq('GATCAGAAG', unambiguous_dna)</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">Traceback (most recent call last):</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black"> File "<stdin>", line 1, in <module></span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Calibri",sans-serif;color:black">TypeError: 'module' object is not callable</span></i><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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</div>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">--<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">Francesco<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> Michiel de Hoon <<a href="mailto:mjldehoon@yahoo.com">mjldehoon@yahoo.com</a>><br>
<b>Sent:</b> 27 June 2018 04:11:05<br>
<b>To:</b> Francesco Gastaldello (Staff); <a href="mailto:p.j.a.cock@googlemail.com">
p.j.a.cock@googlemail.com</a>; Fulton, Ben<br>
<b>Cc:</b> <a href="mailto:biopython@mailman.open-bio.org">biopython@mailman.open-bio.org</a><br>
<b>Subject:</b> Re: [Biopython] problem with Bio.Align _aligns.c</span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A">
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif;color:#26282A">Francesco, in which directory are you running Python?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif;color:#26282A">I can replicate this error only if I try these commands in the biopython source directory. In that case, python imports from the current directory, not from
the installed directory.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif;color:#26282A">Importing Bio.Cluster will also fail for the same reason.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif;color:#26282A">Numpy has the same problem; there they show an informative error message if somebody tries to import numpy from the source tree:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif;color:#26282A">>>> from numpy import *<br>
Traceback (most recent call last):<br>
File "<stdin>", line 1, in <module><br>
File "numpy/__init__.py", line 131, in <module><br>
raise ImportError(msg)<br>
ImportError: Error importing numpy: you should not try to import numpy from<br>
its source directory; please exit the numpy source tree, and relaunch<br>
your python interpreter from there.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif;color:#26282A">-Michiel<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A">On Wednesday, June 27, 2018, 6:38:02 AM GMT+9, Fulton, Ben <<a href="mailto:befulton@iu.edu">befulton@iu.edu</a>> wrote:
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p> </o:p></span></p>
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<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A">Wouldn’t you have to run “python setup.py install” to get the libraries into the correct locations?<o:p></o:p></span></p>
<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"> <o:p></o:p></span></p>
<div>
<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#1F497D">--</span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p></o:p></span></p>
<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#1F497D">Ben Fulton</span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p></o:p></span></p>
<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#1F497D">Research Technologies</span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p></o:p></span></p>
<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#1F497D">Scientific Applications and Performance Tuning</span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p></o:p></span></p>
<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#1F497D">Indiana University</span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p></o:p></span></p>
<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#1F497D">E-Mail:
</span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><a href="mailto:befulton@iu.edu" target="_blank"><span style="color:#0563C1">befulton@iu.edu</span></a><o:p></o:p></span></p>
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<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"> <o:p></o:p></span></p>
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<p class="yiv2129460908xyiv8000510501msonormal"><b><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A">From:</span></b><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"> Biopython <<a href="mailto:biopython-bounces+befulton=iu.edu@mailman.open-bio.org">biopython-bounces+befulton=iu.edu@mailman.open-bio.org</a>>
<b>On Behalf Of </b>Francesco Gastaldello (Staff)<br>
<b>Sent:</b> Tuesday, June 26, 2018 10:36 AM<br>
<b>To:</b> <a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a><br>
<b>Cc:</b> <a href="mailto:biopython@mailman.open-bio.org">biopython@mailman.open-bio.org</a><br>
<b>Subject:</b> Re: [Biopython] problem with Bio.Align _aligns.c<o:p></o:p></span></p>
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<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"> <o:p></o:p></span></p>
<div id="yiv2129460908x_yiv8000510501divtagdefaultwrapper">
<p><span style="font-family:"Helvetica",sans-serif;color:black">I'm running the test via Pycharm and it is connected to my origin and upstream branches on GitHub.</span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p></o:p></span></p>
<p><span style="font-family:"Helvetica",sans-serif;color:black"> </span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p></o:p></span></p>
<p><span style="font-family:"Helvetica",sans-serif;color:black">I've done a quick test of the other modules that use C and I can confirm that the same problem is visible.<br>
<br>
I've run some tests even on the master branch, which I consider to be stable environment.</span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p></o:p></span></p>
<p><span style="font-family:"Helvetica",sans-serif;color:black"> </span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p></o:p></span></p>
<p><span style="font-family:"Helvetica",sans-serif;color:black">Francesco </span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p></o:p></span></p>
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<p class="yiv2129460908xyiv8000510501msonormal"><b><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:black">From:</span></b><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:black"> Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>><br>
<b>Sent:</b> 26 June 2018 15:29:39<br>
<b>To:</b> Francesco Gastaldello (Staff)<br>
<b>Cc:</b> <a href="mailto:biopython@mailman.open-bio.org" target="_blank">biopython@mailman.open-bio.org</a><br>
<b>Subject:</b> Re: [Biopython] problem with Bio.Align _aligns.c</span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A">
<o:p></o:p></span></p>
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<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"> <o:p></o:p></span></p>
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<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A">You must be running from Git, perhaps even the<br>
provisional tag for Biopython 1.72?<br>
<br>
The error is worryingly similar to what I am getting<br>
with the automated wheels for Linux and macOS<br>
under TravisCI - they seem to build fine, but when<br>
running the tests, the compiled code can't be found.<br>
<br>
This is holding up the Biopython 1.72 release, see also:<br>
<a href="http://mailman.open-bio.org/pipermail/biopython/2018-June/016474.html" target="_blank">http://mailman.open-bio.org/pipermail/biopython/2018-June/016474.html</a><br>
<br>
Do you see this with other C code as well, e.g.<br>
Bio.Cluster, or cpairwise2, or KDTree?<br>
<br>
Perhaps this is a problem with the current code in<br>
GitHub, not just something strange with the multi-<br>
wheel setup as I had been assuming?<br>
<br>
Peter<br>
<br>
On Tue, Jun 26, 2018 at 12:26 PM, Francesco Gastaldello (Staff)<br>
<<a href="mailto:f.gastaldello@dundee.ac.uk" target="_blank">f.gastaldello@dundee.ac.uk</a>> wrote:<br>
> Hi all,<br>
><br>
><br>
> I have a virtual environment with python 2.7.15rc1 and I get this error when<br>
> I run some commands:<br>
><br>
><br>
> ////<br>
><br>
> Python 2.7.15rc1 (default, Apr 15 2018, 21:51:34)<br>
> [GCC 7.3.0] on linux2<br>
> Type "help", "copyright", "credits" or "license" for more information.<br>
>>>> from Bio import SeqIO<br>
> Traceback (most recent call last):<br>
> File "<stdin>", line 1, in <module><br>
> File "Bio/SeqIO/__init__.py", line 375, in <module><br>
> from Bio.Align import MultipleSeqAlignment<br>
> File "Bio/Align/__init__.py", line 22, in <module><br>
> from Bio.Align import _aligners<br>
> ImportError: cannot import name _aligners<br>
><br>
> ////<br>
><br>
><br>
> I've made sure to run "python setup.py build" before trying anything but<br>
> that did not solve the problem.<br>
><br>
> I'm on Ububtu 18.04 on a virtual machine.<br>
><br>
><br>
> Thanks,<br>
><br>
> Francesco<br>
><br>
><br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
><br>
> _______________________________________________<br>
> Biopython mailing list - <a href="mailto:Biopython@mailman.open-bio.org" target="_blank">
Biopython@mailman.open-bio.org</a><br>
> <a href="http://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">
http://mailman.open-bio.org/mailman/listinfo/biopython</a><o:p></o:p></span></p>
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<p class="yiv2129460908xyiv8000510501msonormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><br>
The University of Dundee is a registered Scottish Charity, No: SC015096 <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A">_______________________________________________<br>
Biopython mailing list - <a href="mailto:Biopython@mailman.open-bio.org" target="_blank">
Biopython@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><br>
The University of Dundee is a registered Scottish Charity, No: SC015096 <o:p></o:p></span></p>
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<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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