[Biopython] Biopython 1.78 plans - please help with testing

Fri Sep 4 16:16:34 UTC 2020

Hi John,

Mainly, we reorganized a lot of the tests, breaking a large file into
smaller ones. There were also some bug fixes, perhaps the most important
ones about copying and handling disordered atoms.

Thank you Chris and Peter for handling the release, great job!

Cheers,

João

A sexta, 4/09/2020, 05:51, John Berrisford <jmb at ebi.ac.uk> escreveu:

> Dear Joao
>
>
>
> It would be interesting if you summarise the changes you have made to
> Bio.PDB.
>
>
>
> Thanks
>
>
>
> John
>
>
>
> *From:* Biopython <biopython-bounces+jmb=ebi.ac.uk at mailman.open-bio.org> *On
> Behalf Of *João Rodrigues
> *Sent:* 01 September 2020 19:13
> *To:* Peter Cock <p.j.a.cock at googlemail.com>
> *Cc:* Biopython Mailing List <biopython at mailman.open-bio.org>
> *Subject:* Re: [Biopython] Biopython 1.78 plans - please help with testing
>
>
>
> Hi Peter,
>
>
>
> I don't think there's much to add about our changes to Bio.PDB. A lot of
> internal development, nothing worth noting for users I think!
>
>
>
> I'll happily run tests when you build the release here on windows
> machines.
>
>
>
> Cheers,
>
>
>
> João
>
>
>
> A terça, 1/09/2020, 06:31, Peter Cock <p.j.a.cock at googlemail.com>
> escreveu:
>
> Thank you Stéphane,
>
>
>
> We ought really to silence those warnings from Biopython within the test
> suite, that would be neater. The FTP error is probably also harmless under
> the circumstance.
>
>
>
> Regarding "OSError: dnal returned 127", do you have the dnal command line
> tool installed? There may be something not quite right in how
> Tests/test_Wise.py is detecting the tool.
>
>
>
> Kind regards,
>
>
>
> Peter
>
>
>
>
>
> On Tue, Sep 1, 2020 at 2:19 PM Téletchéa Stéphane <
> stephane.teletchea at univ-nantes.fr> wrote:
>
> Le 01/09/2020 à 00:14, Peter Cock a écrit :
>
> If anyone has tested the current master as requested, I have not
>
> seen any replies or new reports about the alphabet removal.
>
> Dear all,
>
> Just for the record, I did the tests on my machine (Ubuntu 18.04 LTS 64
> bits up to date),
> and nothing went wrong, except some warnings (between ~~~ lines):
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> test_MarkovModel ...
> /data/teletchea-s/projets/externes/biopython/Tests/test_MarkovModel.py:408:
> VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences
> (which is a list-or-tuple of lists-or-tuples-or ndarrays with different
> lengths or shapes) is deprecated. If you meant to do this, you must specify
> 'dtype=object' when creating the ndarray
>   [0, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3],
> /data/teletchea-s/projets/externes/biopython/Tests/test_MarkovModel.py:416:
> VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences
> (which is a list-or-t
>
>
> test_SeqIO_Insdc ...
> /data/teletchea-s/projets/externes/biopython/build/lib.linux-x86_64-3.6/Bio/GenBank/Scanner.py:305:
> BiopythonParserWarning: Non-standard feature line wrapping (didn't break on
> comma)?
>   BiopythonParserWarning,
> ok
>
> test_SubsMat ...
> /data/teletchea-s/projets/externes/biopython/build/lib.linux-x86_64-3.6/Bio/SubsMat/__init__.py:131:
> BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend
> to remove it in a future release of Biopython. As an alternative, please
> consider using Bio.Align.substitution_matrices as a replacement, and
> contact the Biopython developers if you still need the Bio.SubsMat module.
>   BiopythonDeprecationWarning,
> ok
>
> test_codonalign ...
> /data/teletchea-s/projets/externes/biopython/build/lib.linux-x86_64-3.6/Bio/codonalign/codonalignment.py:115:
> BiopythonWarning: Please make sure the two CodonAlignment objects are
> sharing the same codon table. This is not checked by Biopython.
>   BiopythonWarning,
> /data/teletchea-s/projets/externes/biopython/build/lib.linux-x86_64-3.6/Bio/Seq.py:2319:
> BiopythonWarning: This table contains 6 codon(s) which code(s) for both
> STOP and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be
> translated as amino acid.
>   BiopythonWarning,
> ok
>
> test_samtools_tool ... skipping. Install samtools and correctly set the
> file path to the program
>         if you want to use it from Biopython
> test_seq ...
> /data/teletchea-s/projets/externes/biopython/build/lib.linux-x86_64-3.6/Bio/Seq.py:2344:
> BiopythonWarning: Partial codon, len(sequence) not a multiple of three.
> Explicitly trim the sequence or add trailing N before translation. This may
> become an error in future.
>   BiopythonWarning,
> ok
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> I do get errors while the ftp lib is called, probably because I'm behind a
> proxy:
>
>   File "/usr/lib/python3.6/ftplib.py", line 210, in getline
>     raise EOFError
> urllib.error.URLError: <urlopen error ftp error: EOFError()>
>
> I'm not sure if this is related to biopython or python (ftp) or my
> environment (the upstream files download fine from a browser).
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> There is one error that may come from the Alphabet drop or the internal
> cmdline management:
>
> ERROR: test_align (test_Wise.TestWise)
> Call dnal with optional arguments, and do a trivial check on the output.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/data/teletchea-s/projets/externes/biopython/Tests/test_Wise.py",
> line 55, in test_align
>     quiet=True,
>   File
> "/data/teletchea-s/projets/externes/biopython/build/lib.linux-x86_64-3.6/Bio/Wise/__init__.py",
> line 114, in align
>     return align(cmdline, pair, 0, force_type, dry_run, quiet, debug)
>   File
> "/data/teletchea-s/projets/externes/biopython/build/lib.linux-x86_64-3.6/Bio/Wise/__init__.py",
> line 116, in align
>     raise OSError("%s returned %s" % (" ".join(cmdline), status))
> OSError: dnal returned 127
>
> I'm not sure how to interpret this :-/
>
> I'm not sure it helps, but at leat you know someone tried :-)
>
> Best,
>
> Stéphane
>
>
> --
>
> Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico
>
> UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France
>
> Tél : +33 251 125 636 / Fax : +33 251 125 632
>
> http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
>
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