<html>
<head>
<style>
body {
font-family: Verdana, sans-serif;
font-size: 0.8em;
color:#484848;
}
h1, h2, h3 { font-family: "Trebuchet MS", Verdana, sans-serif; margin: 0px; }
h1 { font-size: 1.2em; }
h2, h3 { font-size: 1.1em; }
a, a:link, a:visited { color: #2A5685;}
a:hover, a:active { color: #c61a1a; }
a.wiki-anchor { display: none; }
fieldset.attachments {border-width: 1px 0 0 0;}
hr {
width: 100%;
height: 1px;
background: #ccc;
border: 0;
}
span.footer {
font-size: 0.8em;
font-style: italic;
}
</style>
</head>
<body>
Issue #3155 has been updated by Vincent Davis.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15355?detail_id=1642">diff</a>)</li>
<li><strong>Assignee</strong> changed from <i>Biopython Dev Mailing List</i> to <i>Vincent Davis</i></li>
</ul>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/3155#change-15355">Bug #3155: Some Phylip tools seem to fail on Jython</a></h1>
<ul><li>Author: Tiago Antao</li>
<li>Status: New</li>
<li>Priority: Normal</li>
<li>Assignee: Vincent Davis</li>
<li>Category: Main Distribution</li>
<li>Target version: Not Applicable</li>
<li>URL: </li></ul>
<p>According to the integration tests, some Phylip tools seem to fail on Jython.</p>
<p>Please see below or <a class="external" href="http://events.open-bio.org:8010/builders/jython/builds/18">http://events.open-bio.org:8010/builders/jython/builds/18</a></p>
<p>======================================================================<br />ERROR: pseudosample a phylip DNA alignment written with AlignIO<br />----------------------------------------------------------------------<br />Traceback (most recent call last):<br /> File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py", line 270, in test_bootstrap_AlignIO_DNA<br /> self.check_bootstrap("Phylip/opuntia.phy", "phylip")<br /> File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py", line 251, in check_bootstrap<br /> raise ValueError("Return code %s from:\n%s" \<br />ValueError: Return code 1 from:<br />fseqboot -auto -filter -outfile=test_file -sequence=Phylip/opuntia.phy -seqtype=d -reps=2</p>
<p>======================================================================<br />ERROR: pseudosample a phylip protein alignment written with AlignIO<br />----------------------------------------------------------------------<br />Traceback (most recent call last):<br /> File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py", line 279, in test_bootstrap_AlignIO_protein<br /> self.check_bootstrap("Phylip/hedgehog.phy", "phylip", "p")<br /> File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py", line 251, in check_bootstrap<br /> raise ValueError("Return code %s from:\n%s" \<br />ValueError: Return code 1 from:<br />fseqboot -auto -filter -outfile=test_file -sequence=Phylip/hedgehog.phy -seqtype=p -reps=2</p>
<p>======================================================================<br />ERROR: Calculate distance matrix from an AlignIO written protein alignment<br />----------------------------------------------------------------------<br />Traceback (most recent call last):<br /> File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py", line 157, in test_distances_from_protein_AlignIO<br /> self.distances_from_alignment("Phylip/hedgehog.phy", DNA=False)<br /> File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py", line 117, in distances_from_alignment<br /> raise ValueError("Return code %s from:\n%s" \<br />ValueError: Return code 1 from:<br />fprotdist -auto -outfile=test_file -sequence=Phylip/hedgehog.phy -method=j</p>
<p>======================================================================<br />ERROR: Make a parsimony tree from an alignment written with AlignIO<br />----------------------------------------------------------------------<br />Traceback (most recent call last):<br /> File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py", line 210, in test_parsimony_tree_from_AlignIO_DNA<br /> self.parsimony_tree("Phylip/opuntia.phy", "phylip")<br /> File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py", line 194, in parsimony_tree<br /> raise ValueError("Return code %s from:\n%s" \<br />ValueError: Return code 1 from:<br />fdnapars -auto -stdout -sequence=Phylip/opuntia.phy -outtreefile=test_file</p>
<p>======================================================================</p>
<hr />
<span class="footer"><p>You have received this notification because you have either subscribed to it, or are involved in it.<br />To change your notification preferences, please click here and login: <a class="external" href="http://redmine.open-bio.org">http://redmine.open-bio.org</a></p></span>
</body>
</html>