[Biopython] Biopython 1.78 plans - please help with testing

[Peter Cock]

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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