[Biopython-dev] [Bug 3155] New: Some Phylip tools seem to fail on Jython

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3155

           Summary: Some Phylip tools seem to fail on Jython
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: tiagoantao at gmail.com


According to the integration tests, some Phylip tools seem to fail on Jython.

Please see below or http://events.open-bio.org:8010/builders/jython/builds/18

======================================================================
ERROR: pseudosample a phylip DNA alignment written with AlignIO
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py",
line 270, in test_bootstrap_AlignIO_DNA
    self.check_bootstrap("Phylip/opuntia.phy", "phylip")
  File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py",
line 251, in check_bootstrap
    raise ValueError("Return code %s from:\n%s" \
ValueError: Return code 1 from:
fseqboot -auto -filter -outfile=test_file -sequence=Phylip/opuntia.phy
-seqtype=d -reps=2

======================================================================
ERROR: pseudosample a phylip protein alignment written with AlignIO
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py",
line 279, in test_bootstrap_AlignIO_protein
    self.check_bootstrap("Phylip/hedgehog.phy", "phylip", "p")
  File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py",
line 251, in check_bootstrap
    raise ValueError("Return code %s from:\n%s" \
ValueError: Return code 1 from:
fseqboot -auto -filter -outfile=test_file -sequence=Phylip/hedgehog.phy
-seqtype=p -reps=2

======================================================================
ERROR: Calculate distance matrix from an AlignIO written protein alignment
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py",
line 157, in test_distances_from_protein_AlignIO
    self.distances_from_alignment("Phylip/hedgehog.phy", DNA=False)
  File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py",
line 117, in distances_from_alignment
    raise ValueError("Return code %s from:\n%s" \
ValueError: Return code 1 from:
fprotdist -auto -outfile=test_file -sequence=Phylip/hedgehog.phy -method=j

======================================================================
ERROR: Make a parsimony tree from an alignment written with AlignIO
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py",
line 210, in test_parsimony_tree_from_AlignIO_DNA
    self.parsimony_tree("Phylip/opuntia.phy", "phylip")
  File "/home/tantao/test/slave/jython/build/Tests/test_EmbossPhylipNew.py",
line 194, in parsimony_tree
    raise ValueError("Return code %s from:\n%s" \
ValueError: Return code 1 from:
fdnapars -auto -stdout -sequence=Phylip/opuntia.phy -outtreefile=test_file

======================================================================


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