[Biopython] problem with Bio.Align _aligns.c
Robert Campbell
robert.campbell at queensu.ca
Wed Jun 27 14:36:55 UTC 2018
Francesco:
You need to use change "Seq" to "Seq.Seq" here:
>>> new_seq = Seq.Seq('GATCAGAAG', unambiguous_dna)
>>> new_seq
Seq('GATCAGAAG', IUPACUnambiguousDNA())
Cheers,
Rob
On Wed, 2018-06-27 11:33 +0000, "Francesco Gastaldello (Staff)" <f.gastaldello at dundee.ac.uk> wrote:
> Peter:
>
> 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).
>
> Ben:
> 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:
>
> --
> (biopython)
> gasta at gasta-VirtualBox:~/Documents/GitHub/biopython(master)$ python
> setup.py install running install running build
> running build_py
> running build_ext
> running install_lib
> copying build/lib.linux-x86_64-2.7/Bio/GenBank/__init__.py
> -> /home/gasta/venv/biopython/lib/python2.7/site-packages/Bio/GenBank
> byte-compiling /home/gasta/venv/biopython/lib/python2.7/site-packages/Bio/GenBank/__init__.py
> to __init__.pyc running install_egg_info running egg_info
> writing requirements to biopython.egg-info/requires.txt
> writing biopython.egg-info/PKG-INFO
> writing top-level names to biopython.egg-info/top_level.txt
> writing dependency_links to biopython.egg-info/dependency_links.txt
> reading manifest file 'biopython.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> warning: no previously-included files matching '*.pyo' found anywhere
> in distribution warning: no previously-included files matching
> '*.py{}' found anywhere in distribution warning: no
> previously-included files matching '*.py-e' found anywhere in
> distribution writing manifest file 'biopython.egg-info/SOURCES.txt'
> removing
> '/home/gasta/venv/biopython/lib/python2.7/site-packages/biopython-1.72-py2.7.egg-info' (and
> everything under it) Copying biopython.egg-info
> to /home/gasta/venv/biopython/lib/python2.7/site-packages/biopython-1.72-py2.7.egg-info
> running install_scripts -- 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 Michiel
> comment):
>
> --
> (biopython)
> gasta at gasta-VirtualBox:~/Documents/GitHub/biopython(master)$ python
> Python 2.7.15rc1 (default, Apr 15 2018, 21:51:34) [GCC 7.3.0] on
> linux2 Type "help", "copyright", "credits" or "license" for more
> information.
> >>> from Bio import Seq
> >>> from Bio.Alphabet.IUPAC import unambiguous_dna
> >>> new_seq = Seq('GATCAGAAG', unambiguous_dna)
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> TypeError: 'module' object is not callable
> >>> import numpy
> >>> numpy.array([[1, 2], [3, 4]])
> array([[1, 2],
> [3, 4]])
> --
>
> Same happen when I run the exact same test elsewhere but still inside
> the virtual environment
>
> --
> (biopython) gasta at gasta-VirtualBox:~$ python
> Python 2.7.15rc1 (default, Apr 15 2018, 21:51:34)
> [GCC 7.3.0] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import numpy
> >>> numpy.array([[1, 2], [3, 4]])
> array([[1, 2],
> [3, 4]])
> >>> from Bio import Seq
> >>> from Bio.Alphabet.IUPAC import unambiguous_dna
> >>> new_seq = Seq('GATCAGAAG', unambiguous_dna)
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> TypeError: 'module' object is not callable
> --
>
> Francesco
>
>
> ________________________________
> From: Michiel de Hoon <mjldehoon at yahoo.com>
> Sent: 27 June 2018 04:11:05
> To: Francesco Gastaldello (Staff); p.j.a.cock at googlemail.com; Fulton,
> Ben Cc: biopython at mailman.open-bio.org
> Subject: Re: [Biopython] problem with Bio.Align _aligns.c
>
> Francesco, in which directory are you running Python?
> 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. Importing
> Bio.Cluster will also fail for the same reason. Numpy has the same
> problem; there they show an informative error message if somebody
> tries to import numpy from the source tree:
>
> >>> from numpy import *
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "numpy/__init__.py", line 131, in <module>
> raise ImportError(msg)
> ImportError: Error importing numpy: you should not try to import
> numpy from its source directory; please exit the numpy source tree,
> and relaunch your python interpreter from there.
>
>
> -Michiel
>
> On Wednesday, June 27, 2018, 6:38:02 AM GMT+9, Fulton, Ben
> <befulton at iu.edu> wrote:
>
>
>
> Wouldn’t you have to run “python setup.py install” to get the
> libraries into the correct locations?
>
>
>
> --
>
> Ben Fulton
>
> Research Technologies
>
> Scientific Applications and Performance Tuning
>
> Indiana University
>
> E-Mail: befulton at iu.edu<mailto:befulton at iu.edu>
>
>
>
> From: Biopython
> <biopython-bounces+befulton=iu.edu at mailman.open-bio.org> On Behalf Of
> Francesco Gastaldello (Staff) Sent: Tuesday, June 26, 2018 10:36 AM
> To: p.j.a.cock at googlemail.com Cc: biopython at mailman.open-bio.org
> Subject: Re: [Biopython] problem with Bio.Align _aligns.c
>
>
>
> I'm running the test via Pycharm and it is connected to my origin and
> upstream branches on GitHub.
>
>
>
> I've done a quick test of the other modules that use C and I can
> confirm that the same problem is visible.
>
> I've run some tests even on the master branch, which I consider to be
> stable environment.
>
>
>
> Francesco
>
> ________________________________
>
> From: Peter Cock
> <p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>> Sent:
> 26 June 2018 15:29:39 To: Francesco Gastaldello (Staff)
> Cc:
> biopython at mailman.open-bio.org<mailto:biopython at mailman.open-bio.org>
> Subject: Re: [Biopython] problem with Bio.Align _aligns.c
>
>
>
> You must be running from Git, perhaps even the
> provisional tag for Biopython 1.72?
>
> The error is worryingly similar to what I am getting
> with the automated wheels for Linux and macOS
> under TravisCI - they seem to build fine, but when
> running the tests, the compiled code can't be found.
>
> This is holding up the Biopython 1.72 release, see also:
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmailman.open-bio.org%2Fpipermail%2Fbiopython%2F2018-June%2F016474.html&data=02%7C01%7Crobert.campbell%40queensu.ca%7Cdfc1f2c6b5fd43bbdc9008d5dc2589e1%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636656976160367879&sdata=3YjjVImqsGJyEt1Ug721%2Ff0hIazur64ykby0bm9vVjo%3D&reserved=0
>
> Do you see this with other C code as well, e.g.
> Bio.Cluster, or cpairwise2, or KDTree?
>
> Perhaps this is a problem with the current code in
> GitHub, not just something strange with the multi-
> wheel setup as I had been assuming?
>
> Peter
>
> On Tue, Jun 26, 2018 at 12:26 PM, Francesco Gastaldello (Staff)
> <f.gastaldello at dundee.ac.uk<mailto:f.gastaldello at dundee.ac.uk>> wrote:
> > Hi all,
> >
> >
> > I have a virtual environment with python 2.7.15rc1 and I get this
> > error when I run some commands:
> >
> >
> > ////
> >
> > Python 2.7.15rc1 (default, Apr 15 2018, 21:51:34)
> > [GCC 7.3.0] on linux2
> > Type "help", "copyright", "credits" or "license" for more
> > information.
> >>>> from Bio import SeqIO
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in <module>
> > File "Bio/SeqIO/__init__.py", line 375, in <module>
> > from Bio.Align import MultipleSeqAlignment
> > File "Bio/Align/__init__.py", line 22, in <module>
> > from Bio.Align import _aligners
> > ImportError: cannot import name _aligners
> >
> > ////
> >
> >
> > I've made sure to run "python setup.py build" before trying
> > anything but that did not solve the problem.
> >
> > I'm on Ububtu 18.04 on a virtual machine.
> >
> >
> > Thanks,
> >
> > Francesco
> >
> >
> > The University of Dundee is a registered Scottish Charity, No:
> > SC015096
> >
> > _______________________________________________
> > Biopython mailing list -
> > Biopython at mailman.open-bio.org<mailto:Biopython at mailman.open-bio.org>
> > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmailman.open-bio.org%2Fmailman%2Flistinfo%2Fbiopython&data=02%7C01%7Crobert.campbell%40queensu.ca%7Cdfc1f2c6b5fd43bbdc9008d5dc2589e1%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636656976160367879&sdata=M7fyLDpiCDOZ6pRbs1F%2FOFDxzmjo%2Bb225P4olnrnazg%3D&reserved=0
>
> The University of Dundee is a registered Scottish Charity, No:
> SC015096
>
> _______________________________________________
> Biopython mailing list -
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>
> The University of Dundee is a registered Scottish Charity, No:
> SC015096
--
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821
<robert.campbell at queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
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