Re: [Biopython] Biopython 1.78 plans - please help with testing

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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