[Biopython-dev] [Bug 3042] test_Mafft_tool fails
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bugzilla-daemon at portal.open-bio.org
Fri May 7 06:46:35 UTC 2010
http://bugzilla.open-bio.org/show_bug.cgi?id=3042
------- Comment #3 from mdehoon at ims.u-tokyo.ac.jp 2010-05-07 02:46 EST -------
(In reply to comment #2)
> (In reply to comment #0)
> > This is the error message I get:
> >
> > ======================================================================
> > FAIL: Simple round-trip through app with infile.
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "test_Mafft_tool.py", line 56, in test_Mafft_simple
> > self.assert_("STEP 2 / 2 d" in stderr_string)
> > AssertionError
>
> I have changed that to look for "Progressive alignment ..." instead
> which is present in both this MAFFT 5.x output and in MAFFT 6.x output.
This error has disappeared -- thanks!
> > > ======================================================================
> > FAIL: Round-trip with complex command line.
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "test_Mafft_tool.py", line 126, in test_Mafft_with_complex_command_line
> > self.assertEqual(return_code, 0)
> > AssertionError: 1 != 0
>
> I've changed this to give the command line used to help debug when MAFFT
> returns an error code. Could you retest and report what MAFFT does for
> this particular command?
This is the output I am now getting:
======================================================================
FAIL: Round-trip with complex command line.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_Mafft_tool.py", line 144, in test_Mafft_with_complex_command_line
% (return_code, cmdline))
AssertionError: Got error code 1 back from:
mafft --localpair --weighti 4.2 --retree 5 --maxiterate 200 --nofft --op 2.04
--
ep 0.51 --lop 0.233 --lep 0.2 --reorder --treeout --nuc Fasta/f002
If I just run this mafft command directly, I get:
$ mafft --localpair --weighti 4.2 --retree 5 --maxiterate 200 --nofft --op 2.04
--ep 0.51 --lop 0.233 --lep 0.2 --reorder --treeout --nuc Fasta/f002
/usr/local/bin/mafft: line 184: [: --treeout: integer expression expected
Unknown option: --treeout
MAFFT version 5.732 (2005/09/14)
References:
Katoh et al., 2002, NAR 30: 3059-3066
Katoh et al., 2005, NAR 33: 511-518
http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft
Options:
--localpair : All pairwise local alignment information is included
to the objective function. default: off
--globalpair : All pairwise global alignment information is included
to the objective function. default: off
--op # : Gap opening penalty (>0). default: 1.53
--ep # : Offset (>0, works like gap extension penalty).
default: 0.123
--bl #, --jtt # : Scoring matrix. default: BLOSUM62
Alternatives are BLOSUM (--bl) 30, 45, 62, 80,
or JTT (--jtt) # PAM.
--nuc or --amino : Sequence type. default: auto
--retree # : The number of tree building in progressive method
(see the paper for detail). default: 2
--maxiterate # : Maximum number of iterative refinement. default: 0
--fft or --nofft: FFT is enabled or disabled. default: enabled
--memsave: Memory saving mode (beta). default: off
--clustalout: Output: clustal format (not tested). default: fasta
--reorder: Outorder: aligned (not tested). default: input order
--quiet : Do not report progress.
Input format: fasta format
Typical usages:
% mafft --maxiterate 1000 --localpair input > output
L-INS-i (most accurate in many cases;
assumes there is only one alignable domain)
% mafft --maxiterate 1000 --genafpair input > output
E-INS-i (works even if there are many unalignable residues
between alignable domains)
% mafft --maxiterate 1000 --globalpair input > output
G-INS-i (suitable for globally alignable sequences)
% mafft --maxiterate 1000 input > output
FFT-NS-i (accurate and slow, iterative refinement method)
% mafft --retree 2 input > output (DEFAULT; same as mafft input > output)
FFT-NS-2 (rough and fast; progressive method)
% mafft --retree 1 input > output
FFT-NS-1 (very rough and very fast, applicable to >5,000 sequences;
progressive method with a rough guide tree)
> Also what is the output of "mafft --help" from MAFFT 5.732? That would be
> useful if we do have to make running the test conditional on the version of
> MAFFT.
>
This is the output of "mafft --help":
$ mafft --help
Cannot open --help.
MAFFT version 5.732 (2005/09/14)
References:
Katoh et al., 2002, NAR 30: 3059-3066
Katoh et al., 2005, NAR 33: 511-518
http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft
Options:
--localpair : All pairwise local alignment information is included
to the objective function. default: off
--globalpair : All pairwise global alignment information is included
to the objective function. default: off
--op # : Gap opening penalty (>0). default: 1.53
--ep # : Offset (>0, works like gap extension penalty).
default: 0.123
--bl #, --jtt # : Scoring matrix. default: BLOSUM62
Alternatives are BLOSUM (--bl) 30, 45, 62, 80,
or JTT (--jtt) # PAM.
--nuc or --amino : Sequence type. default: auto
--retree # : The number of tree building in progressive method
(see the paper for detail). default: 2
--maxiterate # : Maximum number of iterative refinement. default: 0
--fft or --nofft: FFT is enabled or disabled. default: enabled
--memsave: Memory saving mode (beta). default: off
--clustalout: Output: clustal format (not tested). default: fasta
--reorder: Outorder: aligned (not tested). default: input order
--quiet : Do not report progress.
Input format: fasta format
Typical usages:
% mafft --maxiterate 1000 --localpair input > output
L-INS-i (most accurate in many cases;
assumes there is only one alignable domain)
% mafft --maxiterate 1000 --genafpair input > output
E-INS-i (works even if there are many unalignable residues
between alignable domains)
% mafft --maxiterate 1000 --globalpair input > output
G-INS-i (suitable for globally alignable sequences)
% mafft --maxiterate 1000 input > output
FFT-NS-i (accurate and slow, iterative refinement method)
% mafft --retree 2 input > output (DEFAULT; same as mafft input > output)
FFT-NS-2 (rough and fast; progressive method)
% mafft --retree 1 input > output
FFT-NS-1 (very rough and very fast, applicable to >5,000 sequences;
progressive method with a rough guide tree)
Thanks,
--Michiel.
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