[Biopython-dev] PAML yn00 under Windows

Peter Cock p.j.a.cock at googlemail.com
Wed Aug 17 11:28:16 EDT 2011


Hi Brandon,

It looks like the stats line parsing in yn00 needs a little adjustment
for this platform,

======================================================================
ERROR: Test that the yn00 binary runs and generates correct output.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "c:\repositories\BuildBot\win26\build\Tests\test_PAML_tools.py",
line 139, in testYn00Binary
    results = self.yn.run()
  File "c:\repositories\BuildBot\win26\build\build\lib.win32-2.6\Bio\Phylo\PAML\yn00.py",
line 106, in run
    results = read(self.out_file)
  File "c:\repositories\BuildBot\win26\build\build\lib.win32-2.6\Bio\Phylo\PAML\yn00.py",
line 131, in read
    sequences)
  File "c:\repositories\BuildBot\win26\build\build\lib.win32-2.6\Bio\Phylo\PAML\_parse_yn00.py",
line 110, in parse_others
    value = stats_split[i+2].strip("()")
IndexError: list index out of range

----------------------------------------------------------------------
Ran 157 tests in 282.385 seconds


I added this commit for a more helpful error message:
https://github.com/biopython/biopython/commit/420430164d258aae27714d907705cd729626f3c6

C:\repositories\biopython\Tests>c:\python26\python test_PAML_tools.py
Test that the baseml binary runs and generates correct output ... ok
Test that the codeml binary runs and generates correct output ... ok
Test that the yn00 binary runs and generates correct output. ... ERROR

======================================================================
ERROR: Test that the yn00 binary runs and generates correct output.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_PAML_tools.py", line 139, in testYn00Binary
    results = self.yn.run()
  File "c:\python26\Lib\site-packages\Bio\Phylo\PAML\yn00.py", line 106, in run
    results = read(self.out_file)
  File "c:\python26\Lib\site-packages\Bio\Phylo\PAML\yn00.py", line 131, in read
    sequences)
  File "c:\python26\Lib\site-packages\Bio\Phylo\PAML\_parse_yn00.py",
line 113, in parse_others
    raise ValueError("Problem with stats line: %r" % line)
ValueError: Problem with stats line: 'LWL85m: dS = -1.#IND dN =
-1.#IND w =-1.#IND S =   -1.$ N =   -1.$ (rho = -1.#IO)\n'

----------------------------------------------------------------------
Ran 3 tests in 1.312s

FAILED (errors=1)


It looks like you're not expecting a bracket pattern quite like that
(and/or this is a cross platform C float representation issue).

Hopefully that string is enough to work out how to fix the parser,
even if you can't reproduce this on your own machine. I can try
and find the output file if you like... might have to disable the
tool's clean up code temporarily to leave it behind.

Regards,

Peter


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