[Biopython-dev] [Biopython (old issues only) - Bug #3155] Some Phylip tools seem to fail on Jython

[redmine at redmine.open-bio.org]

Issue #3155 has been updated by Vincent Davis.

Description updated
Assignee changed from Biopython Dev Mailing List to Vincent Davis

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Bug #3155: Some Phylip tools seem to fail on Jython
https://redmine.open-bio.org/issues/3155#change-15355

* Author: Tiago Antao
* Status: New
* Priority: Normal
* Assignee: Vincent Davis
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
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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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