<div dir="ltr">Thank you Stéphane,<div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>Kind regards,</div><div><br></div><div>Peter</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Sep 1, 2020 at 2:19 PM Téletchéa Stéphane <<a href="mailto:stephane.teletchea@univ-nantes.fr">stephane.teletchea@univ-nantes.fr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div>Le 01/09/2020 à 00:14, Peter Cock a
écrit :<br>
</div>
<blockquote type="cite">
<div>If anyone has tested the current master as requested, I have
not</div>
<div>seen any replies or new reports about the alphabet removal.</div>
</blockquote>
Dear all,<br>
<br>
Just for the record, I did the tests on my machine (Ubuntu 18.04 LTS
64 bits up to date),<br>
and nothing went wrong, except some warnings (between ~~~ lines):<br>
<br>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>
<br>
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<br>
[0, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3],<br>
/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<br>
<br>
<br>
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)?<br>
BiopythonParserWarning,<br>
ok<br>
<br>
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.<br>
BiopythonDeprecationWarning,<br>
ok<br>
<br>
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.<br>
BiopythonWarning,<br>
/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.<br>
BiopythonWarning,<br>
ok<br>
<br>
test_samtools_tool ... skipping. Install samtools and correctly set
the file path to the program<br>
if you want to use it from Biopython<br>
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.<br>
BiopythonWarning,<br>
ok<br>
<br>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>
<br>
I do get errors while the ftp lib is called, probably because I'm
behind a proxy:<br>
<br>
File "/usr/lib/python3.6/ftplib.py", line 210, in getline<br>
raise EOFError<br>
urllib.error.URLError: <urlopen error ftp error: EOFError()><br>
<br>
I'm not sure if this is related to biopython or python (ftp) or my
environment (the upstream files download fine from a browser).<br>
<br>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>
<br>
There is one error that may come from the Alphabet drop or the
internal cmdline management:<br>
<br>
ERROR: test_align (test_Wise.TestWise)<br>
Call dnal with optional arguments, and do a trivial check on the
output.<br>
----------------------------------------------------------------------<br>
Traceback (most recent call last):<br>
File
"/data/teletchea-s/projets/externes/biopython/Tests/test_Wise.py",
line 55, in test_align<br>
quiet=True,<br>
File
"/data/teletchea-s/projets/externes/biopython/build/lib.linux-x86_64-3.6/Bio/Wise/__init__.py",
line 114, in align<br>
return align(cmdline, pair, 0, force_type, dry_run, quiet,
debug)<br>
File
"/data/teletchea-s/projets/externes/biopython/build/lib.linux-x86_64-3.6/Bio/Wise/__init__.py",
line 116, in align<br>
raise OSError("%s returned %s" % (" ".join(cmdline), status))<br>
OSError: dnal returned 127<br>
<br>
I'm not sure how to interpret this :-/<br>
<br>
I'm not sure it helps, but at leat you know someone tried :-)<br>
<br>
Best,<br>
<br>
Stéphane<br>
<br>
<pre cols="72">--
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
<a href="http://www.ufip.univ-nantes.fr/" target="_blank">http://www.ufip.univ-nantes.fr/</a> - <a href="http://www.steletch.org" target="_blank">http://www.steletch.org</a></pre>
</div>
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