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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='mso-fareast-language:EN-US'>Dear Joao<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'>It would be interesting if you summarise the changes you have made to Bio.PDB.<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'>Thanks<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'>John<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><b><span lang=EN-US>From:</span></b><span lang=EN-US> Biopython <biopython-bounces+jmb=ebi.ac.uk@mailman.open-bio.org> <b>On Behalf Of </b>João Rodrigues<br><b>Sent:</b> 01 September 2020 19:13<br><b>To:</b> Peter Cock <p.j.a.cock@googlemail.com><br><b>Cc:</b> Biopython Mailing List <biopython@mailman.open-bio.org><br><b>Subject:</b> Re: [Biopython] Biopython 1.78 plans - please help with testing<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi Peter,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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!<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I'll happily run tests when you build the release here on windows machines. <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Cheers, <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>João <o:p></o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>A terça, 1/09/2020, 06:31, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> escreveu:<o:p></o:p></p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><p class=MsoNormal>Thank you Stéphane,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Kind regards,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Peter<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Tue, Sep 1, 2020 at 2:19 PM Téletchéa Stéphane <<a href="mailto:stephane.teletchea@univ-nantes.fr" target="_blank">stephane.teletchea@univ-nantes.fr</a>> wrote:<o:p></o:p></p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><div><p class=MsoNormal>Le 01/09/2020 à 00:14, Peter Cock a écrit :<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>If anyone has tested the current master as requested, I have not<o:p></o:p></p></div><div><p class=MsoNormal>seen any replies or new reports about the alphabet removal.<o:p></o:p></p></div></blockquote><p class=MsoNormal>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><br><o:p></o:p></p><pre>-- <o:p></o:p></pre><pre>Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico<o:p></o:p></pre><pre>UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France<o:p></o:p></pre><pre>Tél : +33 251 125 636 / Fax : +33 251 125 632<o:p></o:p></pre><pre><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><o:p></o:p></pre></div><p class=MsoNormal>_______________________________________________<br>Biopython mailing list - <a href="mailto:Biopython@mailman.open-bio.org" target="_blank">Biopython@mailman.open-bio.org</a><br><a href="https://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">https://mailman.open-bio.org/mailman/listinfo/biopython</a><o:p></o:p></p></blockquote></div><p class=MsoNormal>_______________________________________________<br>Biopython mailing list - <a href="mailto:Biopython@mailman.open-bio.org" target="_blank">Biopython@mailman.open-bio.org</a><br><a href="https://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">https://mailman.open-bio.org/mailman/listinfo/biopython</a><o:p></o:p></p></blockquote></div></div></body></html>