[Biopython] Biopython 1.78 plans - please help with testing

Tue Sep 1 18:13:28 UTC 2020

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 632http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
>>
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