[Biopython] Biopython 1.78 plans - please help with testing

Fri Sep 4 12:51:15 UTC 2020

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 <mailto: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 <mailto: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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